NP-MRD: Showing NP-Card for Antibiotic OA 6129E (NP0062198)

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Record Information

Version

2.0

Created at

2022-04-28 06:51:17 UTC

Updated at

2022-04-28 06:51:17 UTC

NP-MRD ID

NP0062198

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Antibiotic OA 6129E

Description

OA-6129 E belongs to the class of organic compounds known as thienamycins. These are beta-lactam antibiotics that differ from penicillins in having the thiazolidine sulfur atom replaced by carbon, the sulfur then becoming the first atom in the side chain. Antibiotic OA 6129E is found in Apis cerana and Streptomyces sp. OA-6129. It was first documented in 1984 (PMID: 6547129). Based on a literature review a significant number of articles have been published on OA-6129 E (PMID: 35483916) (PMID: 35483915) (PMID: 35483914) (PMID: 35483913).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282208512D          

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M  END

     RDKit          3D

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M  END


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M  END
> <DATABASE_ID>
NP0062198

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)(O)[C@H]1[C@H]2C[C@H](SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO)[C@@H](N2C1=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C21H35N3O8S/c1-20(2,10-25)16(27)17(28)23-6-5-13(26)22-7-8-33-12-9-11-14(21(3,4)32)18(29)24(11)15(12)19(30)31/h11-12,14-16,25,27,32H,5-10H2,1-4H3,(H,22,26)(H,23,28)(H,30,31)/t11-,12+,14+,15-,16+/m1/s1

> <INCHI_KEY>
NSMABMGRXUKVDE-IVCRCZCHSA-N

> <FORMULA>
C21H35N3O8S

> <MOLECULAR_WEIGHT>
489.58

> <EXACT_MASS>
489.214486273

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
51.84176327446879

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S,5R,6R)-3-[(2-{3-[(2R)-2,4-dihydroxy-3,3-dimethylbutanamido]propanamido}ethyl)sulfanyl]-6-(2-hydroxypropan-2-yl)-7-oxo-1-azabicyclo[3.2.0]heptane-2-carboxylic acid

> <ALOGPS_LOGP>
-0.58

> <JCHEM_LOGP>
-2.5906262139999976

> <ALOGPS_LOGS>
-2.33

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.681392605084799

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.723648349156561

> <JCHEM_PKA_STRONGEST_BASIC>
-2.0122964748889753

> <JCHEM_POLAR_SURFACE_AREA>
176.49999999999997

> <JCHEM_REFRACTIVITY>
119.43479999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.28e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S,5R,6R)-3-[(2-{3-[(2R)-2,4-dihydroxy-3,3-dimethylbutanamido]propanamido}ethyl)sulfanyl]-6-(2-hydroxypropan-2-yl)-7-oxo-1-azabicyclo[3.2.0]heptane-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      -2.991   2.513   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.221   1.179   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -2.620  -0.309   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0      -0.888   1.949   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      -1.658   3.283   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.627   4.427   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.780   3.801   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.619   2.269   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.763   1.239   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.443  -0.268   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       3.228   1.715   0.000  0.00  0.00           O+0
HETATM   12  S   UNK     0       2.113   4.571   0.000  0.00  0.00           S+0
HETATM   13  C   UNK     0       3.447   3.801   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.781   4.571   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0       6.114   3.801   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       7.448   4.571   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       7.448   6.111   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       8.782   3.801   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      10.115   4.571   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0      11.449   3.801   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0      12.783   4.571   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      12.783   6.111   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      14.116   3.801   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      14.116   2.261   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      15.450   4.571   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      14.680   5.904   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      16.220   3.237   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      16.784   5.341   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      18.117   4.571   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -4.479   2.911   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -5.967   3.310   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -4.080   4.399   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      -4.878   1.424   0.000  0.00  0.00           C+0
CONECT    1    2    5   30                                                  
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    8                                                  
CONECT    5    4    1    6                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   12                                                  
CONECT    8    7    4    9                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    7   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26   27   28                                             
CONECT   26   25                                                            
CONECT   27   25                                                            
CONECT   28   25   29                                                       
CONECT   29   28                                                            
CONECT   30    1   31   32   33                                             
CONECT   31   30                                                            
CONECT   32   30                                                            
CONECT   33   30                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   68    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₁H₃₅N₃O₈S

Average Mass

489.5800 Da

Monoisotopic Mass

489.21449 Da

IUPAC Name

(2S,3S,5R,6R)-3-[(2-{3-[(2R)-2,4-dihydroxy-3,3-dimethylbutanamido]propanamido}ethyl)sulfanyl]-6-(2-hydroxypropan-2-yl)-7-oxo-1-azabicyclo[3.2.0]heptane-2-carboxylic acid

Traditional Name

(2S,3S,5R,6R)-3-[(2-{3-[(2R)-2,4-dihydroxy-3,3-dimethylbutanamido]propanamido}ethyl)sulfanyl]-6-(2-hydroxypropan-2-yl)-7-oxo-1-azabicyclo[3.2.0]heptane-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

CC(C)(O)[C@H]1[C@H]2C[C@H](SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO)[C@@H](N2C1=O)C(O)=O

InChI Identifier

InChI=1S/C21H35N3O8S/c1-20(2,10-25)16(27)17(28)23-6-5-13(26)22-7-8-33-12-9-11-14(21(3,4)32)18(29)24(11)15(12)19(30)31/h11-12,14-16,25,27,32H,5-10H2,1-4H3,(H,22,26)(H,23,28)(H,30,31)/t11-,12+,14+,15-,16+/m1/s1

InChI Key

NSMABMGRXUKVDE-IVCRCZCHSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Apis cerana	LOTUS Database	35616633
Streptomyces sp. OA-6129	Bacteria	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as thienamycins. These are beta-lactam antibiotics that differ from penicillins in having the thiazolidine sulfur atom replaced by carbon, the sulfur then becoming the first atom in the side chain.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Lactams

Sub Class

Beta lactams

Direct Parent

Thienamycins

Alternative Parents

Substituents

Thienamycin
Beta amino acid or derivatives
Carbapenam
Alpha-amino acid or derivatives
Caprolactam
Pyrrolidine carboxylic acid
Pyrrolidine carboxylic acid or derivatives
Azepane
Monosaccharide
N-acyl-amine
Fatty amide
Fatty acyl
Pyrrolidine
Tertiary alcohol
Tertiary carboxylic acid amide
Secondary alcohol
Azetidine
Carboxamide group
Secondary carboxylic acid amide
Monocarboxylic acid or derivatives
Thioether
Carboxylic acid derivative
Carboxylic acid
Azacycle
Dialkylthioether
Sulfenyl compound
Hydrocarbon derivative
Organonitrogen compound
Organooxygen compound
Organosulfur compound
Primary alcohol
Carbonyl group
Alcohol
Organic oxygen compound
Organic nitrogen compound
Organopnictogen compound
Organic oxide
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

carbapenems (CHEBI:81043 )

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	-0.58	ALOGPS
logP	-2.6	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	3.72	ChemAxon
pKa (Strongest Basic)	-2	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	176.5 Å²	ChemAxon
Rotatable Bond Count	12	ChemAxon
Refractivity	119.43 m³·mol⁻¹	ChemAxon
Polarizability	51.84 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00018575

Chemspider ID

30791676

KEGG Compound ID

C17376

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

46173896

PDB ID

Not Available

ChEBI ID

81043

Good Scents ID

Not Available

References

General References

Uchida Y, Kan H, Sakurai K, Horimoto Y, Hayashi E, Iida A, Okamura N, Oishi K, Matsukawa N: APOE varepsilon4 dose associates with increased brain iron and beta-amyloid via blood-brain barrier dysfunction. J Neurol Neurosurg Psychiatry. 2022 Apr 28. pii: jnnp-2021-328519. doi: 10.1136/jnnp-2021-328519. [PubMed:35483916 ]
Cacciaguerra L, Pagani E, Radaelli M, Mesaros S, Martinelli V, Ivanovic J, Drulovic J, Filippi M, Rocca MA: MR T2-relaxation time as an indirect measure of brain water content and disease activity in NMOSD. J Neurol Neurosurg Psychiatry. 2022 Apr 28. pii: jnnp-2022-328956. doi: 10.1136/jnnp-2022-328956. [PubMed:35483915 ]
Broomfield NM, West R, Barber M, Quinn TJ, Gillespie D, Walters M, House A: TEARS: a longitudinal investigation of the prevalence, psychological associations and trajectory of poststroke emotionalism. J Neurol Neurosurg Psychiatry. 2022 Apr 28. pii: jnnp-2022-329042. doi: 10.1136/jnnp-2022-329042. [PubMed:35483914 ]
Khankari J, Yu Y, Ouyang J, Hussein R, Do HM, Heit JJ, Zaharchuk G: Automated detection of arterial landmarks and vascular occlusions in patients with acute stroke receiving digital subtraction angiography using deep learning. J Neurointerv Surg. 2022 Apr 28. pii: neurintsurg-2021-018638. doi: 10.1136/neurintsurg-2021-018638. [PubMed:35483913 ]
Yoshioka T, Watanabe A, Kojima I, Shimauchi Y, Okabe M, Fukagawa Y, Ishikura T: Structures of OA-6129D and E, new carbapenam antibiotics. J Antibiot (Tokyo). 1984 Mar;37(3):211-7. doi: 10.7164/antibiotics.37.211. [PubMed:6547129 ]

Showing NP-Card for Antibiotic OA 6129E (NP0062198)

MOL for NP0062198 (Antibiotic OA 6129E)

3D MOL for NP0062198 (Antibiotic OA 6129E)

3D SDF for NP0062198 (Antibiotic OA 6129E)

3D-SDF for NP0062198 (Antibiotic OA 6129E)

PDB for NP0062198 (Antibiotic OA 6129E)

3D PDB for NP0062198 (Antibiotic OA 6129E)

SMILES for NP0062198 (Antibiotic OA 6129E)

INCHI for NP0062198 (Antibiotic OA 6129E)

Structure for NP0062198 (Antibiotic OA 6129E)

3D Structure for NP0062198 (Antibiotic OA 6129E)