NP-MRD: Showing NP-Card for Antibiotic X 372A (NP0062025)

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Record Information

Version

2.0

Created at

2022-04-28 06:42:33 UTC

Updated at

2022-04-28 06:42:33 UTC

NP-MRD ID

NP0062025

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Antibiotic X 372A

Description

(2S,4S)-2-{[(2R)-2-amino-1-hydroxypropylidene]amino}-4-chloro-4-[(3S)-3,4-dihydroxy-2,3-dihydroazet-3-yl]butanoic acid belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond. Antibiotic X 372A is found in Streptomyces sp. 372A. Based on a literature review very few articles have been published on (2S,4S)-2-{[(2R)-2-amino-1-hydroxypropylidene]amino}-4-chloro-4-[(3S)-3,4-dihydroxy-2,3-dihydroazet-3-yl]butanoic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 35 35  0  0  0  0  0  0  0  0999 V2000
   -4.0760    2.1654    0.1476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6172    0.7816    0.4307 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.5913   -0.2367    0.4010 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5004    0.4152   -0.5701 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7282    0.7754   -1.7273 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4265   -0.2407   -0.0546 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712   -0.7219   -0.5426 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9236   -0.2398    0.3032 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2245   -0.8561    0.0165 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2727   -2.5653    0.3663 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    3.4683   -0.1579    0.3584 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.5838   -1.0040    0.2030 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4743    0.9387    1.3175 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6309    1.9373    0.2682 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7898    0.9340   -0.7080 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0723    0.7966   -1.9099 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1821   -2.0943   -0.9829 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0575   -2.5199   -2.1565 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3503   -3.1509   -0.0210 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1721    2.8042    0.1302 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6888    2.4924    1.0148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5942    2.2183   -0.8042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1514    0.7949    1.4558 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1659   -1.1381    0.7036 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9661   -0.3642   -0.5776 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5115   -0.5704    1.0237 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0435   -0.1095   -1.5967 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6172   -0.5263    1.3734 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9624    0.8807    0.3188 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2444   -0.8395   -1.1852 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2742   -1.8512   -0.1658 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5338    1.0986    1.9160 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3456    1.0087    1.9896 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6420    2.9810    0.2135 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0655   -3.8363   -0.2652 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  1
 11 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  2  0
  7 17  1  0
 17 19  1  0
 17 18  2  0
 15 11  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  2 23  1  1
  3 24  1  0
  3 25  1  0
  6 26  1  0
  7 27  1  6
  8 28  1  0
  8 29  1  0
  9 30  1  6
 12 31  1  0
 13 32  1  0
 13 33  1  0
 14 34  1  0
 19 35  1  0
M  END


  Mrv1652304282208422D          

 19 19  0  0  1  0            999 V2000
   -3.5901    0.1715    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3151    0.5652    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7990    0.4058    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5647   -0.3852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3558   -0.6195    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8422    1.2297    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0846    0.8183    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0846    1.6433    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -1.3701    0.4058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6556    0.8183    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0588    0.4058    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7733    0.8183    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7733    1.6433    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4878    0.4058    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2023    0.8183    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4878   -0.4192    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6556    1.6433    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0588    2.0558    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3701    2.0558    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  1  5  1  0  0  0  0
  3  6  1  1  0  0  0
  3  7  1  6  0  0  0
  7  8  1  1  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  1  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  6  0  0  0
 14 16  1  0  0  0  0
 10 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0062025

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H](N)C(=O)N[C@@H](C[C@H](Cl)[C@]1(O)CNC1=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H16ClN3O5/c1-4(12)7(15)14-5(8(16)17)2-6(11)10(19)3-13-9(10)18/h4-6,19H,2-3,12H2,1H3,(H,13,18)(H,14,15)(H,16,17)/t4-,5+,6+,10-/m1/s1

> <INCHI_KEY>
FJBMORPRPLWSNA-VGFPCUMBSA-N

> <FORMULA>
C10H16ClN3O5

> <MOLECULAR_WEIGHT>
293.7

> <EXACT_MASS>
293.0778483

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
26.76265225745054

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,4S)-2-[(2R)-2-aminopropanamido]-4-chloro-4-[(3S)-3-hydroxy-2-oxoazetidin-3-yl]butanoic acid

> <ALOGPS_LOGP>
-2.43

> <JCHEM_LOGP>
-4.63117881095878

> <ALOGPS_LOGS>
-1.07

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.195855784269087

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.4438533234108895

> <JCHEM_PKA_STRONGEST_BASIC>
8.38749852501572

> <JCHEM_POLAR_SURFACE_AREA>
141.75

> <JCHEM_REFRACTIVITY>
63.76180000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.48e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,4S)-2-[(2R)-2-aminopropanamido]-4-chloro-4-[(3S)-3-hydroxy-2-oxoazetidin-3-yl]butanoic 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      -6.701   0.320   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -8.055   1.055   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -5.225   0.758   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -4.787  -0.719   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -6.264  -1.156   0.000  0.00  0.00           N+0
HETATM    6  O   UNK     0      -5.305   2.295   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -3.891   1.528   0.000  0.00  0.00           C+0
HETATM    8 Cl   UNK     0      -3.891   3.068   0.000  0.00  0.00          Cl+0
HETATM    9  C   UNK     0      -2.558   0.758   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.224   1.528   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       0.110   0.758   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       1.444   1.528   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       1.444   3.068   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       2.777   0.758   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0       4.111   1.528   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       2.777  -0.782   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.224   3.068   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       0.110   3.838   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -2.558   3.838   0.000  0.00  0.00           O+0
CONECT    1    2    3    5                                                  
CONECT    2    1                                                            
CONECT    3    1    4    6    7                                             
CONECT    4    3    5                                                       
CONECT    5    4    1                                                       
CONECT    6    3                                                            
CONECT    7    3    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11   17                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17   10   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   38    0
END

View in JSmol

Synonyms

Value	Source
(2S,4S)-2-{[(2R)-2-amino-1-hydroxypropylidene]amino}-4-chloro-4-[(3S)-3,4-dihydroxy-2,3-dihydroazet-3-yl]butanoate	Generator

Chemical Formula

C₁₀H₁₆ClN₃O₅

Average Mass

293.7000 Da

Monoisotopic Mass

293.07785 Da

IUPAC Name

(2S,4S)-2-[(2R)-2-aminopropanamido]-4-chloro-4-[(3S)-3-hydroxy-2-oxoazetidin-3-yl]butanoic acid

Traditional Name

(2S,4S)-2-[(2R)-2-aminopropanamido]-4-chloro-4-[(3S)-3-hydroxy-2-oxoazetidin-3-yl]butanoic acid

CAS Registry Number

Not Available

SMILES

C[C@@H](N)C(=O)N[C@@H](C[C@H](Cl)[C@]1(O)CNC1=O)C(O)=O

InChI Identifier

InChI=1S/C10H16ClN3O5/c1-4(12)7(15)14-5(8(16)17)2-6(11)10(19)3-13-9(10)18/h4-6,19H,2-3,12H2,1H3,(H,13,18)(H,14,15)(H,16,17)/t4-,5+,6+,10-/m1/s1

InChI Key

FJBMORPRPLWSNA-VGFPCUMBSA-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
Streptomyces sp. 372A	Bacteria	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Dipeptides

Alternative Parents

Substituents

Alpha-dipeptide
Monobactam
N-acyl-l-alpha-amino acid
N-acyl-alpha-amino acid
N-acyl-alpha amino acid or derivatives
Alpha-amino acid amide
Alanine or derivatives
Alpha-amino acid or derivatives
Halogenated fatty acid
Heterocyclic fatty acid
Hydroxy fatty acid
Fatty acyl
Fatty acid
Tertiary alcohol
Beta-lactam
Amino acid or derivatives
Azetidine
Secondary carboxylic acid amide
Carboxamide group
Chlorohydrin
Halohydrin
Amino acid
Lactam
Azacycle
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Carboxylic acid
Primary amine
Organic oxide
Organic oxygen compound
Organopnictogen compound
Organic nitrogen compound
Amine
Alkyl halide
Carbonyl group
Alkyl chloride
Primary aliphatic amine
Hydrocarbon derivative
Alcohol
Organohalogen compound
Organochloride
Organonitrogen compound
Organooxygen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic 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	-2.4	ALOGPS
logP	-4.6	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	3.44	ChemAxon
pKa (Strongest Basic)	8.39	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	141.75 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	63.76 m³·mol⁻¹	ChemAxon
Polarizability	26.76 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

162991593

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Antibiotic X 372A (NP0062025)

MOL for NP0062025 (Antibiotic X 372A)

3D MOL for NP0062025 (Antibiotic X 372A)

3D SDF for NP0062025 (Antibiotic X 372A)

3D-SDF for NP0062025 (Antibiotic X 372A)

PDB for NP0062025 (Antibiotic X 372A)

3D PDB for NP0062025 (Antibiotic X 372A)

SMILES for NP0062025 (Antibiotic X 372A)

INCHI for NP0062025 (Antibiotic X 372A)

Structure for NP0062025 (Antibiotic X 372A)

3D Structure for NP0062025 (Antibiotic X 372A)