Np mrd loader

Showing NP-Card for Amycolamicin (NP0011234)

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Record Information
Version2.0
Created at2021-01-05 20:59:52 UTC
Updated at2021-07-15 17:08:20 UTC
NP-MRD IDNP0011234
Secondary Accession NumbersNone
Natural Product Identification
Common NameAmycolamicin
Provided ByNPAtlasNPAtlas Logo
Description Amycolamicin is found in Amycolatopsis. Amycolamicin was first documented in 2012 (PMID: 23129443). Based on a literature review very few articles have been published on N-[(1S)-1-[(2R,3R,4R,6R)-6-{[(1R,4aS,5S,6S,8aR)-5-{[(5S)-1-[(2R,3R,4R,5R,6S)-4-(acetyloxy)-5-(C-hydroxycarbonimidoyloxy)-3-methoxy-6-methyloxan-2-yl]-2,4-dioxo-5-(propan-2-yl)pyrrolidin-3-ylidene](hydroxy)methyl}-6-methyl-4-methylidene-1,2,3,4,4a,5,6,8a-octahydronaphthalen-1-yl]oxy}-3,4-dihydroxy-2-methyloxan-4-yl]ethyl]-3,4-dichloro-5-methyl-1H-pyrrole-2-carboximidic acid.
Structure
Thumb
MOL3D MOLSDF3D SDFPDBSMILESInChI

MOL for NP0011234 (Amycolamicin)


  Mrv1652307012121373D          

124129  0  0  0  0            999 V2000
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M  END
Download

3D MOL for NP0011234 (Amycolamicin)

     RDKit          3D

124129  0  0  0  0  0  0  0  0999 V2000
    0.8655   -2.5760   -1.4986 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2402   -1.7246   -0.5833 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3263   -2.1498    0.3714 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5077   -1.1022    1.4512 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8064    0.1998    0.8264 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.1159    0.4455    0.4527 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7355    1.5097    1.0698 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.1083    1.2952    1.5603 C   0  0  0  0  0  0  0  0  0  0  0  0
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    8.2181    2.2489    1.9521 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for NP0011234 (Amycolamicin)


  Mrv1652307012121373D          

124129  0  0  0  0            999 V2000
    0.8655   -2.5760   -1.4986 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2402   -1.7246   -0.5833 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3263   -2.1498    0.3714 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5077   -1.1022    1.4512 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8064    0.1998    0.8264 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.1159    0.4455    0.4527 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7355    1.5097    1.0698 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.1083    1.2952    1.5603 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.1992    2.1142    0.9670 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.2181    2.2489    1.9521 O   0  0  0  0  0  0  0  0  0  0  0  0
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    6.8546    1.2145   -1.3747 C   0  0  0  0  0  0  0  0  0  0  0  0
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    9.2298   -0.5907   -0.7502 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -7.0359    0.8893   -0.2086 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3959    1.1665    1.0989 C   0  0  1  0  0  0  0  0  0  0  0  0
   -7.9484    2.5776    1.2293 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2719    0.1257    1.6745 C   0  0  1  0  0  0  0  0  0  0  0  0
   -9.4494   -0.1377    0.9608 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.7171   -0.0146    1.4921 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.9148   -0.2744    0.8108 N   0  0  0  0  0  0  0  0  0  0  0  0
  -10.7402    0.3627    2.6798 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5169   -1.1715    1.7411 C   0  0  1  0  0  0  0  0  0  0  0  0
   -8.2697   -2.2859    1.3485 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5718   -3.3546    2.1628 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3903   -4.4459    1.5496 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1594   -3.3532    3.3235 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2136   -1.0457    0.9743 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.6825   -2.3157    0.6974 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4501   -2.5461    1.2345 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9731    0.6226   -0.3915 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0422    1.5260    0.4721 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6959   -0.3783   -0.3904 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1310   -2.4561   -2.2441 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3733   -3.5760   -1.5311 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2779   -2.3192   -0.1363 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0302   -3.1144    0.8749 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5619   -1.1060    2.0456 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3590   -1.4897    2.0871 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6223    0.9850    1.6389 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0547    1.8264    1.8929 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0909    1.5415    2.6763 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3991    0.2098    1.5779 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0654    1.6029    2.7063 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.6233    2.0732   -0.7060 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2026    0.3632   -1.1733 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4133    2.1277   -1.7595 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5150    0.8476   -2.2301 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2173   -0.2466    1.0540 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6533   -1.4889    1.8299 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.7131   -4.3231    3.1194 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.2726   -3.4212    3.1288 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.2361   -5.0493    2.3372 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9325    3.7647   -0.4181 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8738    4.6656    2.2961 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1480    3.4761    2.0063 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4831    5.5546    1.4780 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6040    5.6726    0.0872 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8857    5.0406   -0.0978 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4149    0.4513   -1.2425 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6029    2.5936    0.7129 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0959    3.3440   -1.1111 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1959    1.0471   -2.7258 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1562    2.3638   -3.9802 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4264    2.5803   -2.7389 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1881    0.9605   -3.6215 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4655   -0.6605   -2.2050 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9056    2.4298   -0.0504 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1963   -1.5398   -2.4316 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1446    1.2869   -3.0411 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6109    0.4390   -5.4801 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4769   -1.2033   -4.7940 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0827   -0.0044   -4.6907 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4428    1.7112   -2.9555 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9192   -0.0229   -3.2738 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3963    1.0433   -4.5994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9843   -0.9341   -1.0605 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4556    1.1822    1.6827 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9942    2.6355    0.8654 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2664    3.3097    0.7097 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -8.5841    0.4180    2.7014 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.6716    0.4406    0.7802 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.1159   -1.1772    0.3109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2357   -1.3329    2.7998 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2655   -4.5075    0.4534 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.4245   -0.5394    1.5596 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.4118   -2.5189    2.3368 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6583   -1.9403    0.7703 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1707   -0.3868    0.6062 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0011234

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]O\C(=C1/C(=O)N([C@]([H])(C1=O)C([H])(C([H])([H])[H])C([H])([H])[H])[C@]1([H])O[C@@]([H])(C([H])([H])[H])[C@@]([H])(OC(=O)N([H])[H])[C@@]([H])(OC(=O)C([H])([H])[H])[C@@]1([H])OC([H])([H])[H])[C@@]1([H])[C@]([H])(C([H])=C([H])[C@@]2([H])[C@]([H])(O[C@]3([H])O[C@]([H])(C([H])([H])[H])[C@@]([H])(O[H])[C@@](O[H])(C3([H])[H])[C@@]([H])(N([H])C(=O)C3=C(Cl)C(Cl)=C(N3[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])C([H])([H])C(=C([H])[H])[C@]12[H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C44H60Cl2N4O14/c1-16(2)33-35(53)29(41(56)50(33)42-38(59-10)37(62-23(9)51)36(20(6)61-42)64-43(47)57)34(52)28-18(4)11-13-24-25(14-12-17(3)27(24)28)63-26-15-44(58,39(54)21(7)60-26)22(8)49-40(55)32-31(46)30(45)19(5)48-32/h11,13,16,18,20-22,24-28,33,36-39,42,48,52,54,58H,3,12,14-15H2,1-2,4-10H3,(H2,47,57)(H,49,55)/b34-29-/t18-,20-,21+,22-,24-,25+,26-,27-,28-,33-,36+,37+,38+,39+,42+,44+/m0/s1

> <INCHI_KEY>
IKNUYGJLHHAVHT-FHIRBROQSA-N

> <FORMULA>
C44H60Cl2N4O14

> <MOLECULAR_WEIGHT>
939.88

> <EXACT_MASS>
938.348308

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
124

> <JCHEM_AVERAGE_POLARIZABILITY>
97.54727359880799

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4R,5R,6S)-2-[(3Z,5S)-3-{[(1S,2S,4aR,5R,8aS)-5-{[(2R,4R,5R,6R)-4-[(1S)-1-[(3,4-dichloro-5-methyl-1H-pyrrol-2-yl)formamido]ethyl]-4,5-dihydroxy-6-methyloxan-2-yl]oxy}-2-methyl-8-methylidene-1,2,4a,5,6,7,8,8a-octahydronaphthalen-1-yl](hydroxy)methylidene}-2,4-dioxo-5-(propan-2-yl)pyrrolidin-1-yl]-5-(carbamoyloxy)-3-methoxy-6-methyloxan-4-yl acetate

> <ALOGPS_LOGP>
3.12

> <JCHEM_LOGP>
3.66778055

> <ALOGPS_LOGS>
-5.06

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.653816242504938

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.3383182944980465

> <JCHEM_PKA_STRONGEST_BASIC>
-0.01612296254123724

> <JCHEM_POLAR_SURFACE_AREA>
258.5

> <JCHEM_REFRACTIVITY>
231.31310000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.27e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4R,5R,6S)-2-[(3Z,5S)-3-{[(1S,2S,4aR,5R,8aS)-5-{[(2R,4R,5R,6R)-4-[(1S)-1-[(3,4-dichloro-5-methyl-1H-pyrrol-2-yl)formamido]ethyl]-4,5-dihydroxy-6-methyloxan-2-yl]oxy}-2-methyl-8-methylidene-2,4a,5,6,7,8a-hexahydro-1H-naphthalen-1-yl](hydroxy)methylidene}-5-isopropyl-2,4-dioxopyrrolidin-1-yl]-5-(carbamoyloxy)-3-methoxy-6-methyloxan-4-yl acetate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0011234 (Amycolamicin)

     RDKit          3D

124129  0  0  0  0  0  0  0  0999 V2000
    0.8655   -2.5760   -1.4986 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2402   -1.7246   -0.5833 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3263   -2.1498    0.3714 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5077   -1.1022    1.4512 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8064    0.1998    0.8264 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.1159    0.4455    0.4527 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7355    1.5097    1.0698 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.1083    1.2952    1.5603 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1992    2.1142    0.9670 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.2181    2.2489    1.9521 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8187    1.4347   -0.2028 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.8546    1.2145   -1.3747 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4086    0.1626    0.0908 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.2298   -0.5907   -0.7502 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5349   -0.2058   -1.9337 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.7553   -1.8790   -0.2349 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8907   -2.1887    1.0751 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.3431   -3.4305    1.2611 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6262   -4.1428    2.5429 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.5119   -3.9578   -0.0197 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0972   -5.5951   -0.3422 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   10.1461   -2.9927   -0.9405 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1553   -3.1620   -2.6890 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    6.7771    3.5381    0.6561 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.4167    4.4202    1.5014 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2819    3.6848    0.9194 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.8178    5.0429    0.5249 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6920    2.6393    0.2238 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for NP0011234 (Amycolamicin)

HEADER    PROTEIN                                 01-JUL-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   01-JUL-21         0                                  
HETATM    1  C   UNK     0       0.866  -2.576  -1.499  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.240  -1.725  -0.583  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.326  -2.150   0.371  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.508  -1.102   1.451  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.806   0.200   0.826  0.00  0.00           C+0
HETATM    6  O   UNK     0       4.116   0.446   0.453  0.00  0.00           O+0
HETATM    7  C   UNK     0       4.736   1.510   1.070  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.108   1.295   1.560  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.199   2.114   0.967  0.00  0.00           C+0
HETATM   10  O   UNK     0       8.218   2.249   1.952  0.00  0.00           O+0
HETATM   11  C   UNK     0       7.819   1.435  -0.203  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.855   1.214  -1.375  0.00  0.00           C+0
HETATM   13  N   UNK     0       8.409   0.163   0.091  0.00  0.00           N+0
HETATM   14  C   UNK     0       9.230  -0.591  -0.750  0.00  0.00           C+0
HETATM   15  O   UNK     0       9.535  -0.206  -1.934  0.00  0.00           O+0
HETATM   16  C   UNK     0       9.755  -1.879  -0.235  0.00  0.00           C+0
HETATM   17  N   UNK     0       9.891  -2.189   1.075  0.00  0.00           N+0
HETATM   18  C   UNK     0      10.343  -3.430   1.261  0.00  0.00           C+0
HETATM   19  C   UNK     0      10.626  -4.143   2.543  0.00  0.00           C+0
HETATM   20  C   UNK     0      10.512  -3.958  -0.020  0.00  0.00           C+0
HETATM   21 Cl   UNK     0      11.097  -5.595  -0.342  0.00  0.00          Cl+0
HETATM   22  C   UNK     0      10.146  -2.993  -0.941  0.00  0.00           C+0
HETATM   23 Cl   UNK     0      10.155  -3.162  -2.689  0.00  0.00          Cl+0
HETATM   24  C   UNK     0       6.777   3.538   0.656  0.00  0.00           C+0
HETATM   25  O   UNK     0       7.417   4.420   1.501  0.00  0.00           O+0
HETATM   26  C   UNK     0       5.282   3.685   0.919  0.00  0.00           C+0
HETATM   27  C   UNK     0       4.818   5.043   0.525  0.00  0.00           C+0
HETATM   28  O   UNK     0       4.692   2.639   0.224  0.00  0.00           O+0
HETATM   29  C   UNK     0       1.856   0.557  -0.254  0.00  0.00           C+0
HETATM   30  C   UNK     0       1.340   1.949  -0.120  0.00  0.00           C+0
HETATM   31  C   UNK     0       0.534   2.347  -1.098  0.00  0.00           C+0
HETATM   32  C   UNK     0       0.290   1.330  -2.158  0.00  0.00           C+0
HETATM   33  C   UNK     0      -0.716   1.844  -3.169  0.00  0.00           C+0
HETATM   34  C   UNK     0      -0.278   0.092  -1.447  0.00  0.00           C+0
HETATM   35  C   UNK     0      -1.530   0.569  -0.801  0.00  0.00           C+0
HETATM   36  O   UNK     0      -1.357   1.601   0.152  0.00  0.00           O+0
HETATM   37  C   UNK     0      -2.739   0.123  -1.038  0.00  0.00           C+0
HETATM   38  C   UNK     0      -3.182  -0.911  -1.953  0.00  0.00           C+0
HETATM   39  O   UNK     0      -2.495  -1.873  -2.443  0.00  0.00           O+0
HETATM   40  C   UNK     0      -4.614  -0.621  -2.210  0.00  0.00           C+0
HETATM   41  C   UNK     0      -4.759   0.388  -3.328  0.00  0.00           C+0
HETATM   42  C   UNK     0      -4.179  -0.131  -4.608  0.00  0.00           C+0
HETATM   43  C   UNK     0      -6.201   0.764  -3.525  0.00  0.00           C+0
HETATM   44  N   UNK     0      -5.076  -0.116  -0.931  0.00  0.00           N+0
HETATM   45  C   UNK     0      -6.386  -0.319  -0.322  0.00  0.00           C+0
HETATM   46  O   UNK     0      -7.036   0.889  -0.209  0.00  0.00           O+0
HETATM   47  C   UNK     0      -7.396   1.167   1.099  0.00  0.00           C+0
HETATM   48  C   UNK     0      -7.948   2.578   1.229  0.00  0.00           C+0
HETATM   49  C   UNK     0      -8.272   0.126   1.675  0.00  0.00           C+0
HETATM   50  O   UNK     0      -9.449  -0.138   0.961  0.00  0.00           O+0
HETATM   51  C   UNK     0     -10.717  -0.015   1.492  0.00  0.00           C+0
HETATM   52  N   UNK     0     -11.915  -0.274   0.811  0.00  0.00           N+0
HETATM   53  O   UNK     0     -10.740   0.363   2.680  0.00  0.00           O+0
HETATM   54  C   UNK     0      -7.517  -1.172   1.741  0.00  0.00           C+0
HETATM   55  O   UNK     0      -8.270  -2.286   1.349  0.00  0.00           O+0
HETATM   56  C   UNK     0      -8.572  -3.355   2.163  0.00  0.00           C+0
HETATM   57  C   UNK     0      -9.390  -4.446   1.550  0.00  0.00           C+0
HETATM   58  O   UNK     0      -8.159  -3.353   3.324  0.00  0.00           O+0
HETATM   59  C   UNK     0      -6.214  -1.046   0.974  0.00  0.00           C+0
HETATM   60  O   UNK     0      -5.683  -2.316   0.697  0.00  0.00           O+0
HETATM   61  C   UNK     0      -4.450  -2.546   1.234  0.00  0.00           C+0
HETATM   62  C   UNK     0      -3.973   0.623  -0.392  0.00  0.00           C+0
HETATM   63  O   UNK     0      -4.042   1.526   0.472  0.00  0.00           O+0
HETATM   64  C   UNK     0       0.696  -0.378  -0.390  0.00  0.00           C+0
HETATM   65  H   UNK     0       0.131  -2.456  -2.244  0.00  0.00           H+0
HETATM   66  H   UNK     0       1.373  -3.576  -1.531  0.00  0.00           H+0
HETATM   67  H   UNK     0       3.278  -2.319  -0.136  0.00  0.00           H+0
HETATM   68  H   UNK     0       2.030  -3.114   0.875  0.00  0.00           H+0
HETATM   69  H   UNK     0       1.562  -1.106   2.046  0.00  0.00           H+0
HETATM   70  H   UNK     0       3.359  -1.490   2.087  0.00  0.00           H+0
HETATM   71  H   UNK     0       2.622   0.985   1.639  0.00  0.00           H+0
HETATM   72  H   UNK     0       4.055   1.826   1.893  0.00  0.00           H+0
HETATM   73  H   UNK     0       6.091   1.542   2.676  0.00  0.00           H+0
HETATM   74  H   UNK     0       6.399   0.210   1.578  0.00  0.00           H+0
HETATM   75  H   UNK     0       8.065   1.603   2.706  0.00  0.00           H+0
HETATM   76  H   UNK     0       8.623   2.073  -0.706  0.00  0.00           H+0
HETATM   77  H   UNK     0       6.203   0.363  -1.173  0.00  0.00           H+0
HETATM   78  H   UNK     0       6.413   2.128  -1.760  0.00  0.00           H+0
HETATM   79  H   UNK     0       7.515   0.848  -2.230  0.00  0.00           H+0
HETATM   80  H   UNK     0       8.217  -0.247   1.054  0.00  0.00           H+0
HETATM   81  H   UNK     0       9.653  -1.489   1.830  0.00  0.00           H+0
HETATM   82  H   UNK     0       9.713  -4.323   3.119  0.00  0.00           H+0
HETATM   83  H   UNK     0      11.273  -3.421   3.129  0.00  0.00           H+0
HETATM   84  H   UNK     0      11.236  -5.049   2.337  0.00  0.00           H+0
HETATM   85  H   UNK     0       6.933   3.765  -0.418  0.00  0.00           H+0
HETATM   86  H   UNK     0       6.874   4.666   2.296  0.00  0.00           H+0
HETATM   87  H   UNK     0       5.148   3.476   2.006  0.00  0.00           H+0
HETATM   88  H   UNK     0       4.483   5.555   1.478  0.00  0.00           H+0
HETATM   89  H   UNK     0       5.604   5.673   0.087  0.00  0.00           H+0
HETATM   90  H   UNK     0       3.886   5.041  -0.098  0.00  0.00           H+0
HETATM   91  H   UNK     0       2.415   0.451  -1.242  0.00  0.00           H+0
HETATM   92  H   UNK     0       1.603   2.594   0.713  0.00  0.00           H+0
HETATM   93  H   UNK     0       0.096   3.344  -1.111  0.00  0.00           H+0
HETATM   94  H   UNK     0       1.196   1.047  -2.726  0.00  0.00           H+0
HETATM   95  H   UNK     0      -0.156   2.364  -3.980  0.00  0.00           H+0
HETATM   96  H   UNK     0      -1.426   2.580  -2.739  0.00  0.00           H+0
HETATM   97  H   UNK     0      -1.188   0.961  -3.622  0.00  0.00           H+0
HETATM   98  H   UNK     0      -0.466  -0.661  -2.205  0.00  0.00           H+0
HETATM   99  H   UNK     0      -1.906   2.430  -0.050  0.00  0.00           H+0
HETATM  100  H   UNK     0      -5.196  -1.540  -2.432  0.00  0.00           H+0
HETATM  101  H   UNK     0      -4.145   1.287  -3.041  0.00  0.00           H+0
HETATM  102  H   UNK     0      -4.611   0.439  -5.480  0.00  0.00           H+0
HETATM  103  H   UNK     0      -4.477  -1.203  -4.794  0.00  0.00           H+0
HETATM  104  H   UNK     0      -3.083  -0.004  -4.691  0.00  0.00           H+0
HETATM  105  H   UNK     0      -6.443   1.711  -2.955  0.00  0.00           H+0
HETATM  106  H   UNK     0      -6.919  -0.023  -3.274  0.00  0.00           H+0
HETATM  107  H   UNK     0      -6.396   1.043  -4.599  0.00  0.00           H+0
HETATM  108  H   UNK     0      -6.984  -0.934  -1.061  0.00  0.00           H+0
HETATM  109  H   UNK     0      -6.456   1.182   1.683  0.00  0.00           H+0
HETATM  110  H   UNK     0      -8.994   2.636   0.865  0.00  0.00           H+0
HETATM  111  H   UNK     0      -7.266   3.310   0.710  0.00  0.00           H+0
HETATM  112  H   UNK     0      -7.975   2.925   2.283  0.00  0.00           H+0
HETATM  113  H   UNK     0      -8.584   0.418   2.701  0.00  0.00           H+0
HETATM  114  H   UNK     0     -12.672   0.441   0.780  0.00  0.00           H+0
HETATM  115  H   UNK     0     -12.116  -1.177   0.311  0.00  0.00           H+0
HETATM  116  H   UNK     0      -7.236  -1.333   2.800  0.00  0.00           H+0
HETATM  117  H   UNK     0      -9.265  -4.508   0.453  0.00  0.00           H+0
HETATM  118  H   UNK     0      -9.074  -5.427   2.010  0.00  0.00           H+0
HETATM  119  H   UNK     0     -10.453  -4.311   1.836  0.00  0.00           H+0
HETATM  120  H   UNK     0      -5.425  -0.539   1.560  0.00  0.00           H+0
HETATM  121  H   UNK     0      -4.180  -3.610   0.925  0.00  0.00           H+0
HETATM  122  H   UNK     0      -4.412  -2.519   2.337  0.00  0.00           H+0
HETATM  123  H   UNK     0      -3.658  -1.940   0.770  0.00  0.00           H+0
HETATM  124  H   UNK     0       0.171  -0.387   0.606  0.00  0.00           H+0
CONECT    1    2   65   66                                                  
CONECT    2    1    3   64                                                  
CONECT    3    2    4   67   68                                             
CONECT    4    3    5   69   70                                             
CONECT    5    4    6   29   71                                             
CONECT    6    5    7                                                       
CONECT    7    6    8   28   72                                             
CONECT    8    7    9   73   74                                             
CONECT    9    8   10   11   24                                             
CONECT   10    9   75                                                       
CONECT   11    9   12   13   76                                             
CONECT   12   11   77   78   79                                             
CONECT   13   11   14   80                                                  
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   22                                                  
CONECT   17   16   18   81                                                  
CONECT   18   17   19   20                                                  
CONECT   19   18   82   83   84                                             
CONECT   20   18   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   16                                                  
CONECT   23   22                                                            
CONECT   24    9   25   26   85                                             
CONECT   25   24   86                                                       
CONECT   26   24   27   28   87                                             
CONECT   27   26   88   89   90                                             
CONECT   28   26    7                                                       
CONECT   29    5   30   64   91                                             
CONECT   30   29   31   92                                                  
CONECT   31   30   32   93                                                  
CONECT   32   31   33   34   94                                             
CONECT   33   32   95   96   97                                             
CONECT   34   32   35   64   98                                             
CONECT   35   34   36   37                                                  
CONECT   36   35   99                                                       
CONECT   37   35   38   62                                                  
CONECT   38   37   39   40                                                  
CONECT   39   38                                                            
CONECT   40   38   41   44  100                                             
CONECT   41   40   42   43  101                                             
CONECT   42   41  102  103  104                                             
CONECT   43   41  105  106  107                                             
CONECT   44   40   45   62                                                  
CONECT   45   44   46   59  108                                             
CONECT   46   45   47                                                       
CONECT   47   46   48   49  109                                             
CONECT   48   47  110  111  112                                             
CONECT   49   47   50   54  113                                             
CONECT   50   49   51                                                       
CONECT   51   50   52   53                                                  
CONECT   52   51  114  115                                                  
CONECT   53   51                                                            
CONECT   54   49   55   59  116                                             
CONECT   55   54   56                                                       
CONECT   56   55   57   58                                                  
CONECT   57   56  117  118  119                                             
CONECT   58   56                                                            
CONECT   59   54   60   45  120                                             
CONECT   60   59   61                                                       
CONECT   61   60  121  122  123                                             
CONECT   62   44   63   37                                                  
CONECT   63   62                                                            
CONECT   64   34    2   29  124                                             
CONECT   65    1                                                            
CONECT   66    1                                                            
CONECT   67    3                                                            
CONECT   68    3                                                            
CONECT   69    4                                                            
CONECT   70    4                                                            
CONECT   71    5                                                            
CONECT   72    7                                                            
CONECT   73    8                                                            
CONECT   74    8                                                            
CONECT   75   10                                                            
CONECT   76   11                                                            
CONECT   77   12                                                            
CONECT   78   12                                                            
CONECT   79   12                                                            
CONECT   80   13                                                            
CONECT   81   17                                                            
CONECT   82   19                                                            
CONECT   83   19                                                            
CONECT   84   19                                                            
CONECT   85   24                                                            
CONECT   86   25                                                            
CONECT   87   26                                                            
CONECT   88   27                                                            
CONECT   89   27                                                            
CONECT   90   27                                                            
CONECT   91   29                                                            
CONECT   92   30                                                            
CONECT   93   31                                                            
CONECT   94   32                                                            
CONECT   95   33                                                            
CONECT   96   33                                                            
CONECT   97   33                                                            
CONECT   98   34                                                            
CONECT   99   36                                                            
CONECT  100   40                                                            
CONECT  101   41                                                            
CONECT  102   42                                                            
CONECT  103   42                                                            
CONECT  104   42                                                            
CONECT  105   43                                                            
CONECT  106   43                                                            
CONECT  107   43                                                            
CONECT  108   45                                                            
CONECT  109   47                                                            
CONECT  110   48                                                            
CONECT  111   48                                                            
CONECT  112   48                                                            
CONECT  113   49                                                            
CONECT  114   52                                                            
CONECT  115   52                                                            
CONECT  116   54                                                            
CONECT  117   57                                                            
CONECT  118   57                                                            
CONECT  119   57                                                            
CONECT  120   59                                                            
CONECT  121   61                                                            
CONECT  122   61                                                            
CONECT  123   61                                                            
CONECT  124   64                                                            
MASTER        0    0    0    0    0    0    0    0  124    0  258    0
END
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3D PDB for NP0011234 (Amycolamicin)

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SMILES for NP0011234 (Amycolamicin)
[H]O\C(=C1/C(=O)N([C@]([H])(C1=O)C([H])(C([H])([H])[H])C([H])([H])[H])[C@]1([H])O[C@@]([H])(C([H])([H])[H])[C@@]([H])(OC(=O)N([H])[H])[C@@]([H])(OC(=O)C([H])([H])[H])[C@@]1([H])OC([H])([H])[H])[C@@]1([H])[C@]([H])(C([H])=C([H])[C@@]2([H])[C@]([H])(O[C@]3([H])O[C@]([H])(C([H])([H])[H])[C@@]([H])(O[H])[C@@](O[H])(C3([H])[H])[C@@]([H])(N([H])C(=O)C3=C(Cl)C(Cl)=C(N3[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])C([H])([H])C(=C([H])[H])[C@]12[H])C([H])([H])[H]
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INCHI for NP0011234 (Amycolamicin)
InChI=1S/C44H60Cl2N4O14/c1-16(2)33-35(53)29(41(56)50(33)42-38(59-10)37(62-23(9)51)36(20(6)61-42)64-43(47)57)34(52)28-18(4)11-13-24-25(14-12-17(3)27(24)28)63-26-15-44(58,39(54)21(7)60-26)22(8)49-40(55)32-31(46)30(45)19(5)48-32/h11,13,16,18,20-22,24-28,33,36-39,42,48,52,54,58H,3,12,14-15H2,1-2,4-10H3,(H2,47,57)(H,49,55)/b34-29-/t18-,20-,21+,22-,24-,25+,26-,27-,28-,33-,36+,37+,38+,39+,42+,44+/m0/s1
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View in JSmolView NMR Assignments
Synonyms
ValueSource
N-[(1S)-1-[(2R,3R,4R,6R)-6-{[(1R,4as,5S,6S,8ar)-5-{[(5S)-1-[(2R,3R,4R,5R,6S)-4-(acetyloxy)-5-(C-hydroxycarbonimidoyloxy)-3-methoxy-6-methyloxan-2-yl]-2,4-dioxo-5-(propan-2-yl)pyrrolidin-3-ylidene](hydroxy)methyl}-6-methyl-4-methylidene-1,2,3,4,4a,5,6,8a-octahydronaphthalen-1-yl]oxy}-3,4-dihydroxy-2-methyloxan-4-yl]ethyl]-3,4-dichloro-5-methyl-1H-pyrrole-2-carboximidateGenerator
Chemical FormulaC44H60Cl2N4O14
Average Mass939.8800 Da
Monoisotopic Mass938.34831 Da
IUPAC Name(2R,3R,4R,5R,6S)-2-[(3Z,5S)-3-{[(1S,2S,4aR,5R,8aS)-5-{[(2R,4R,5R,6R)-4-[(1S)-1-[(3,4-dichloro-5-methyl-1H-pyrrol-2-yl)formamido]ethyl]-4,5-dihydroxy-6-methyloxan-2-yl]oxy}-2-methyl-8-methylidene-1,2,4a,5,6,7,8,8a-octahydronaphthalen-1-yl](hydroxy)methylidene}-2,4-dioxo-5-(propan-2-yl)pyrrolidin-1-yl]-5-(carbamoyloxy)-3-methoxy-6-methyloxan-4-yl acetate
Traditional Name(2R,3R,4R,5R,6S)-2-[(3Z,5S)-3-{[(1S,2S,4aR,5R,8aS)-5-{[(2R,4R,5R,6R)-4-[(1S)-1-[(3,4-dichloro-5-methyl-1H-pyrrol-2-yl)formamido]ethyl]-4,5-dihydroxy-6-methyloxan-2-yl]oxy}-2-methyl-8-methylidene-2,4a,5,6,7,8a-hexahydro-1H-naphthalen-1-yl](hydroxy)methylidene}-5-isopropyl-2,4-dioxopyrrolidin-1-yl]-5-(carbamoyloxy)-3-methoxy-6-methyloxan-4-yl acetate
CAS Registry NumberNot Available
SMILES
CO[C@@H]1[C@H](OC(C)=O)[C@H](OC(N)=O)[C@H](C)O[C@H]1N1[C@@H](C(C)C)C(=O)C(=C(O)[C@H]2[C@@H](C)C=C[C@H]3[C@@H](CCC(=C)[C@H]23)O[C@H]2C[C@@](O)([C@H](C)NC(=O)C3=C(Cl)C(Cl)=C(C)N3)[C@H](O)[C@@H](C)O2)C1=O
InChI Identifier
InChI=1S/C44H60Cl2N4O14/c1-16(2)33-35(53)29(41(56)50(33)42-38(59-10)37(62-23(9)51)36(20(6)61-42)64-43(47)57)34(52)28-18(4)11-13-24-25(14-12-17(3)27(24)28)63-26-15-44(58,39(54)21(7)60-26)22(8)49-40(55)32-31(46)30(45)19(5)48-32/h11,13,16,18,20-22,24-28,33,36-39,42,48,52,54,58H,3,12,14-15H2,1-2,4-10H3,(H2,47,57)(H,49,55)/t18-,20-,21+,22-,24-,25+,26-,27-,28-,33-,36+,37+,38+,39+,42+,44+/m0/s1
InChI KeyIKNUYGJLHHAVHT-FHIRBROQSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
AmycolatopsisNPAtlas
Chemical Taxonomy
ClassificationNot classified
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP3.12ALOGPS
logP3.67ChemAxon
logS-5.1ALOGPS
pKa (Strongest Acidic)4.34ChemAxon
pKa (Strongest Basic)-0.016ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area258.5 ŲChemAxon
Rotatable Bond Count13ChemAxon
Refractivity231.31 m³·mol⁻¹ChemAxon
Polarizability97.55 ųChemAxon
Number of Rings6ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
NPAtlas IDNPA016731  
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID78438275  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound139587757  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Sawa R, Takahashi Y, Hashizume H, Sasaki K, Ishizaki Y, Umekita M, Hatano M, Abe H, Watanabe T, Kinoshita N, Homma Y, Hayashi C, Inoue K, Ohba S, Masuda T, Arakawa M, Kobayashi Y, Hamada M, Igarashi M, Adachi H, Nishimura Y, Akamatsu Y: Amycolamicin: a novel broad-spectrum antibiotic inhibiting bacterial topoisomerase. Chemistry. 2012 Dec 3;18(49):15772-81. doi: 10.1002/chem.201202645. Epub 2012 Nov 5. [PubMed:23129443  ]