NP-MRD: Showing NP-Card for (1s,2r,3r,4s)-2,3-bis({[(4-bromo-1h-pyrrol-2-yl)formamido]methyl})-4-(2-imino-1,3-dihydroimidazol-4-yl)cyclobutane-1-carboxylic acid (NP0325054)

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Record Information

Version

2.0

Created at

2022-09-12 05:31:15 UTC

Updated at

2022-09-12 05:31:15 UTC

NP-MRD ID

NP0325054

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s,2r,3r,4s)-2,3-bis({[(4-bromo-1h-pyrrol-2-yl)formamido]methyl})-4-(2-imino-1,3-dihydroimidazol-4-yl)cyclobutane-1-carboxylic acid

Description

Nakamuric acid, also known as nakamate, belongs to the class of organic compounds known as gamma amino acids and derivatives. These are amino acids having a (-NH2) group attached to the gamma carbon atom. (1s,2r,3r,4s)-2,3-bis({[(4-bromo-1h-pyrrol-2-yl)formamido]methyl})-4-(2-imino-1,3-dihydroimidazol-4-yl)cyclobutane-1-carboxylic acid is found in Agelas nakamurai. (1s,2r,3r,4s)-2,3-bis({[(4-bromo-1h-pyrrol-2-yl)formamido]methyl})-4-(2-imino-1,3-dihydroimidazol-4-yl)cyclobutane-1-carboxylic acid was first documented in 2007 (PMID: 17375928). Based on a literature review a small amount of articles have been published on nakamuric acid (PMID: 32585891) (PMID: 26328059) (PMID: 25983349).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309122207312D          

 33 36  0  0  1  0            999 V2000
    2.5816    1.0568    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0666    0.3894    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8916    0.3894    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1465   -0.3952    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4791   -0.8802    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4791   -1.7052    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.0624   -2.2885    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.8874   -2.2885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2999   -3.0030    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2999   -1.5741    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4791   -2.8719    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4791   -3.6969    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1935   -4.1094    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1935   -4.9344    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4791   -5.3469    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9080   -5.3469    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6617   -5.0113    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2137   -5.6244    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0342   -5.5382    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
    5.8012   -6.3389    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9942   -6.1674    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8957   -2.2885    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0707   -2.2885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6582   -1.5741    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8332   -1.5741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4207   -2.2885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4207   -0.8596    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3998   -0.7733    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5713    0.0336    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3250    0.3692    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
    0.1432    0.4461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7563   -0.1059    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8116   -0.3952    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  6  5  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  1  1  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  7 11  1  0  0  0  0
 11 12  1  6  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  2  0  0  0  0
 20 21  1  0  0  0  0
 16 21  1  0  0  0  0
 11 22  1  0  0  0  0
  6 22  1  0  0  0  0
 22 23  1  1  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 25 27  1  0  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 29 31  2  0  0  0  0
 31 32  1  0  0  0  0
 27 32  1  0  0  0  0
  5 33  1  0  0  0  0
  2 33  1  0  0  0  0
M  END

     RDKit          3D

 54 57  0  0  0  0  0  0  0  0999 V2000
   -2.5920    6.7754   -0.9318 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3365    5.7869   -1.0989 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7029    5.0732   -0.2262 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3202    5.5530    0.9757 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6908    4.5301    1.6103 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6954    3.4276    0.7833 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1071    2.1274    1.1215 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7683    1.5297    0.0377 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2193    1.6977    0.2570 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9909    1.9056   -0.7315 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7548    1.6318    1.5313 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2337    0.1694    0.5115 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0585   -0.8316   -0.5910 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3406   -1.0550   -1.2206 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4271   -1.5607   -0.4652 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2993   -1.8238    0.7550 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7399   -1.7965   -1.0747 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8589   -2.2804   -0.4464 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8568   -2.3475   -1.3650 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6284   -2.9505   -1.0319 Br  0  0  0  0  0  0  0  0  0  0  0  0
    5.3441   -1.9062   -2.5442 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0675   -1.5771   -2.3563 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0417    0.9354    0.8714 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7231    0.4291    2.1092 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0851   -0.9508    1.9002 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9683   -1.2960    0.8419 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4371   -0.3808    0.0814 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3715   -2.6690    0.5785 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2192   -3.0676   -0.4250 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3652   -4.4471   -0.3608 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4478   -5.4953   -1.5450 Br  0  0  0  0  0  0  0  0  0  0  0  0
   -3.5992   -4.8652    0.6866 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0145   -3.7861    1.2334 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3255    3.7871   -0.3439 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4615    6.5152    1.3759 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2791    4.6361    2.5996 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3668    2.0392    2.1043 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4725    1.7813   -0.9892 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7317    1.8321    1.6963 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8206   -0.1526    1.3811 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7270   -0.5753   -1.3017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2740   -1.7852   -0.0836 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5054   -0.8561   -2.2295 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9598   -2.5661    0.5925 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9131   -1.8422   -3.4828 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4024   -1.1982   -3.1002 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6443    1.1049   -0.0229 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9402    0.4714    2.9250 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5720    1.0542    2.4197 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7197   -1.7109    2.5020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7244   -2.4547   -1.1768 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4945   -5.9118    1.0087 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3797   -3.8434    2.0492 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5013    3.1904   -1.1750 H   0  0  0  0  0  0  0  0  0  0  0  0
 11  9  1  0
  9 10  2  0
  9  8  1  0
  8 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  1  0
 19 21  2  0
 21 22  1  0
 12 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  1  0
 26 27  2  0
 26 28  1  0
 28 29  2  0
 29 30  1  0
 30 31  1  0
 30 32  2  0
 32 33  1  0
 23  7  1  0
  7  6  1  0
  6  5  2  0
  5  4  1  0
  4  3  1  0
  3  2  2  0
  3 34  1  0
  7  8  1  0
 34  6  1  0
 22 17  1  0
 33 28  1  0
 11 39  1  0
  8 38  1  6
 12 40  1  1
 13 41  1  0
 13 42  1  0
 14 43  1  0
 18 44  1  0
 21 45  1  0
 22 46  1  0
 23 47  1  6
 24 48  1  0
 24 49  1  0
 25 50  1  0
 29 51  1  0
 32 52  1  0
 33 53  1  0
  7 37  1  1
  5 36  1  0
  4 35  1  0
  2  1  1  0
 34 54  1  0
M  END


  Mrv1652309122207312D          

 33 36  0  0  1  0            999 V2000
    2.5816    1.0568    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0666    0.3894    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8916    0.3894    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1465   -0.3952    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4791   -0.8802    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4791   -1.7052    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.0624   -2.2885    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.8874   -2.2885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2999   -3.0030    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2999   -1.5741    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4791   -2.8719    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4791   -3.6969    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1935   -4.1094    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1935   -4.9344    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4791   -5.3469    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9080   -5.3469    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6617   -5.0113    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2137   -5.6244    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0342   -5.5382    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
    5.8012   -6.3389    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9942   -6.1674    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8957   -2.2885    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0707   -2.2885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6582   -1.5741    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8332   -1.5741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4207   -2.2885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4207   -0.8596    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3998   -0.7733    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5713    0.0336    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3250    0.3692    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
    0.1432    0.4461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7563   -0.1059    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8116   -0.3952    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  6  5  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  1  1  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  7 11  1  0  0  0  0
 11 12  1  6  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  2  0  0  0  0
 20 21  1  0  0  0  0
 16 21  1  0  0  0  0
 11 22  1  0  0  0  0
  6 22  1  0  0  0  0
 22 23  1  1  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 25 27  1  0  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 29 31  2  0  0  0  0
 31 32  1  0  0  0  0
 27 32  1  0  0  0  0
  5 33  1  0  0  0  0
  2 33  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0325054

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)[C@H]1[C@H](CNC(=O)C2=CC(Br)=CN2)[C@@H](CNC(=O)C2=CC(Br)=CN2)[C@@H]1C1=CNC(=N)N1

> <INCHI_IDENTIFIER>
InChI=1S/C20H21Br2N7O4/c21-8-1-12(24-3-8)17(30)26-5-10-11(6-27-18(31)13-2-9(22)4-25-13)16(19(32)33)15(10)14-7-28-20(23)29-14/h1-4,7,10-11,15-16,24-25H,5-6H2,(H,26,30)(H,27,31)(H,32,33)(H3,23,28,29)/t10-,11-,15-,16+/m1/s1

> <INCHI_KEY>
SJXLCFWCEINREE-WVATUKLVSA-N

> <FORMULA>
C20H21Br2N7O4

> <MOLECULAR_WEIGHT>
583.241

> <EXACT_MASS>
581.002178

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
54

> <JCHEM_AVERAGE_POLARIZABILITY>
51.10651484200237

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2R,3R,4S)-2,3-bis({[(4-bromo-1H-pyrrol-2-yl)formamido]methyl})-4-(2-imino-2,3-dihydro-1H-imidazol-4-yl)cyclobutane-1-carboxylic acid

> <JCHEM_LOGP>
-1.3260726151292328

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.896849517996042

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.1712094467282705

> <JCHEM_PKA_STRONGEST_BASIC>
7.680369668698081

> <JCHEM_POLAR_SURFACE_AREA>
174.98999999999998

> <JCHEM_REFRACTIVITY>
137.53240000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2R,3R,4S)-2,3-bis({[(4-bromo-1H-pyrrol-2-yl)formamido]methyl})-4-(2-imino-1,3-dihydroimidazol-4-yl)cyclobutane-1-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  N   UNK     0       4.819   1.973   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       5.724   0.727   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       7.264   0.727   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       7.740  -0.738   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.494  -1.643   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.494  -3.183   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.583  -4.272   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.123  -4.272   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       9.893  -5.606   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       9.893  -2.938   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       6.494  -5.361   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.494  -6.901   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       7.828  -7.671   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       7.828  -9.211   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       6.494  -9.981   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       9.162  -9.981   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      10.568  -9.354   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      11.599 -10.499   0.000  0.00  0.00           C+0
HETATM   19 Br   UNK     0      13.130 -10.338   0.000  0.00  0.00          Br+0
HETATM   20  C   UNK     0      10.829 -11.833   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0       9.323 -11.512   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0       5.405  -4.272   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       3.865  -4.272   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0       3.095  -2.938   0.000  0.00  0.00           N+0
HETATM   25  C   UNK     0       1.555  -2.938   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       0.785  -4.272   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       0.785  -1.605   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -0.746  -1.444   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -1.066   0.063   0.000  0.00  0.00           C+0
HETATM   30 Br   UNK     0      -2.473   0.689   0.000  0.00  0.00          Br+0
HETATM   31  C   UNK     0       0.267   0.833   0.000  0.00  0.00           C+0
HETATM   32  N   UNK     0       1.412  -0.198   0.000  0.00  0.00           N+0
HETATM   33  N   UNK     0       5.248  -0.738   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3   33                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   33                                                  
CONECT    6    5    7   22                                                  
CONECT    7    6    8   11                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    7   12   22                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   21                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   16                                                       
CONECT   22   11    6   23                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   32                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32                                                       
CONECT   32   31   27                                                       
CONECT   33    5    2                                                       
MASTER        0    0    0    0    0    0    0    0   33    0   72    0
END

View in JSmol

Synonyms

Value	Source
Nakamate	Generator
Nakamic acid	Generator

Chemical Formula

C₂₀H₂₁Br₂N₇O₄

Average Mass

583.2410 Da

Monoisotopic Mass

581.00218 Da

IUPAC Name

(1S,2R,3R,4S)-2,3-bis({[(4-bromo-1H-pyrrol-2-yl)formamido]methyl})-4-(2-imino-2,3-dihydro-1H-imidazol-4-yl)cyclobutane-1-carboxylic acid

Traditional Name

(1S,2R,3R,4S)-2,3-bis({[(4-bromo-1H-pyrrol-2-yl)formamido]methyl})-4-(2-imino-1,3-dihydroimidazol-4-yl)cyclobutane-1-carboxylic acid

CAS Registry Number

Not Available

SMILES

OC(=O)[C@H]1[C@H](CNC(=O)C2=CC(Br)=CN2)[C@@H](CNC(=O)C2=CC(Br)=CN2)[C@@H]1C1=CNC(=N)N1

InChI Identifier

InChI=1S/C20H21Br2N7O4/c21-8-1-12(24-3-8)17(30)26-5-10-11(6-27-18(31)13-2-9(22)4-25-13)16(19(32)33)15(10)14-7-28-20(23)29-14/h1-4,7,10-11,15-16,24-25H,5-6H2,(H,26,30)(H,27,31)(H,32,33)(H3,23,28,29)/t10-,11-,15-,16+/m1/s1

InChI Key

SJXLCFWCEINREE-WVATUKLVSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Agelas nakamurai	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as gamma amino acids and derivatives. These are amino acids having a (-NH2) group attached to the gamma carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Gamma amino acids and derivatives

Alternative Parents

Substituents

Gamma amino acid or derivatives
2-heteroaryl carboxamide
Pyrrole-2-carboxylic acid or derivatives
Pyrrole-2-carboxamide
Imidazolyl carboxylic acid derivative
Aminoimidazole
Aryl bromide
Aryl halide
Substituted pyrrole
Azole
Heteroaromatic compound
Pyrrole
Imidazole
Amino acid
Carboxamide group
Secondary carboxylic acid amide
Azacycle
Carboxylic acid
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Organooxygen compound
Primary amine
Organic nitrogen compound
Amine
Carbonyl group
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Organohalogen compound
Organobromide
Organonitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-1.3	ChemAxon
pKa (Strongest Acidic)	3.17	ChemAxon
pKa (Strongest Basic)	7.68	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	174.99 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	137.53 m³·mol⁻¹	ChemAxon
Polarizability	51.11 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

8162801

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9987215

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Pech-Puch D, Perez-Povedano M, Martinez-Guitian M, Lasarte-Monterrubio C, Vazquez-Ucha JC, Bou G, Rodriguez J, Beceiro A, Jimenez C: In Vitro and In Vivo Assessment of the Efficacy of Bromoageliferin, an Alkaloid Isolated from the Sponge Agelas dilatata, against Pseudomonas aeruginosa. Mar Drugs. 2020 Jun 23;18(6). pii: md18060326. doi: 10.3390/md18060326. [PubMed:32585891 ]
O'Malley DP, Li K, Maue M, Zografos AL, Baran PS: Total synthesis of dimeric pyrrole-imidazole alkaloids: sceptrin, ageliferin, nagelamide e, oxysceptrin, nakamuric acid, and the axinellamine carbon skeleton. J Am Chem Soc. 2007 Apr 18;129(15):4762-75. doi: 10.1021/ja069035a. Epub 2007 Mar 22. [PubMed:17375928 ]
Wang X, Gao Y, Ma Z, Rodriguez RA, Yu ZX, Chen C: Syntheses of Sceptrins and Nakamuric Acid and Insights into the Biosyntheses of Pyrrole-Imidazole Dimers. Org Chem Front. 2015 Aug 1;2(8):978-984. doi: 10.1039/C5QO00165J. [PubMed:26328059 ]
Wang X, Chen C: An approach for the synthesis of nakamuric acid. Tetrahedron. 2015 Jun 3;71(22):3690-3693. doi: 10.1016/j.tet.2014.10.027. [PubMed:25983349 ]
LOTUS database [Link]

Showing NP-Card for (1s,2r,3r,4s)-2,3-bis({[(4-bromo-1h-pyrrol-2-yl)formamido]methyl})-4-(2-imino-1,3-dihydroimidazol-4-yl)cyclobutane-1-carboxylic acid (NP0325054)

MOL for NP0325054 ((1s,2r,3r,4s)-2,3-bis({[(4-bromo-1h-pyrrol-2-yl)formamido]methyl})-4-(2-imino-1,3-dihydroimidazol-4-yl)cyclobutane-1-carboxylic acid)

3D MOL for NP0325054 ((1s,2r,3r,4s)-2,3-bis({[(4-bromo-1h-pyrrol-2-yl)formamido]methyl})-4-(2-imino-1,3-dihydroimidazol-4-yl)cyclobutane-1-carboxylic acid)

3D SDF for NP0325054 ((1s,2r,3r,4s)-2,3-bis({[(4-bromo-1h-pyrrol-2-yl)formamido]methyl})-4-(2-imino-1,3-dihydroimidazol-4-yl)cyclobutane-1-carboxylic acid)

3D-SDF for NP0325054 ((1s,2r,3r,4s)-2,3-bis({[(4-bromo-1h-pyrrol-2-yl)formamido]methyl})-4-(2-imino-1,3-dihydroimidazol-4-yl)cyclobutane-1-carboxylic acid)

PDB for NP0325054 ((1s,2r,3r,4s)-2,3-bis({[(4-bromo-1h-pyrrol-2-yl)formamido]methyl})-4-(2-imino-1,3-dihydroimidazol-4-yl)cyclobutane-1-carboxylic acid)

3D PDB for NP0325054 ((1s,2r,3r,4s)-2,3-bis({[(4-bromo-1h-pyrrol-2-yl)formamido]methyl})-4-(2-imino-1,3-dihydroimidazol-4-yl)cyclobutane-1-carboxylic acid)

SMILES for NP0325054 ((1s,2r,3r,4s)-2,3-bis({[(4-bromo-1h-pyrrol-2-yl)formamido]methyl})-4-(2-imino-1,3-dihydroimidazol-4-yl)cyclobutane-1-carboxylic acid)

INCHI for NP0325054 ((1s,2r,3r,4s)-2,3-bis({[(4-bromo-1h-pyrrol-2-yl)formamido]methyl})-4-(2-imino-1,3-dihydroimidazol-4-yl)cyclobutane-1-carboxylic acid)

Structure for NP0325054 ((1s,2r,3r,4s)-2,3-bis({[(4-bromo-1h-pyrrol-2-yl)formamido]methyl})-4-(2-imino-1,3-dihydroimidazol-4-yl)cyclobutane-1-carboxylic acid)

3D Structure for NP0325054 ((1s,2r,3r,4s)-2,3-bis({[(4-bromo-1h-pyrrol-2-yl)formamido]methyl})-4-(2-imino-1,3-dihydroimidazol-4-yl)cyclobutane-1-carboxylic acid)