NP-MRD: Showing NP-Card for 2-{[(2s)-2-({[(4s)-2-(6-chloro-4-hydroxy-1-methylindol-3-yl)-4-methyl-5h-1,3-oxazol-4-yl](hydroxy)methylidene}amino)-1-hydroxy-2-[(2r)-pyrrolidin-2-yl]ethylidene]amino}-3-hydroxy-2-methylpropanoic acid (NP0308773)

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Record Information

Version

1.0

Created at

2022-09-11 02:48:57 UTC

Updated at

2022-09-11 02:48:57 UTC

NP-MRD ID

NP0308773

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-{[(2s)-2-({[(4s)-2-(6-chloro-4-hydroxy-1-methylindol-3-yl)-4-methyl-5h-1,3-oxazol-4-yl](hydroxy)methylidene}amino)-1-hydroxy-2-[(2r)-pyrrolidin-2-yl]ethylidene]amino}-3-hydroxy-2-methylpropanoic acid

Description

JBIR-126, also known as tambromycin, belongs to the class of organic compounds known as peptides. Peptides are compounds containing an amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another. Based on a literature review very few articles have been published on JBIR-126.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309112204482D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309112204482D          

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 31 33  1  0  0  0  0
 33 34  2  0  0  0  0
 34 35  1  0  0  0  0
 34 36  1  0  0  0  0
 36 37  2  0  0  0  0
 30 37  1  0  0  0  0
  2 37  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0308773

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1C=C(C2=N[C@@](C)(CO2)C(O)=N[C@@H]([C@H]2CCCN2)C(O)=NC(C)(CO)C(O)=O)C2=C(O)C=C(Cl)C=C12

> <INCHI_IDENTIFIER>
InChI=1S/C24H30ClN5O7/c1-23(10-31,22(35)36)28-19(33)18(14-5-4-6-26-14)27-21(34)24(2)11-37-20(29-24)13-9-30(3)15-7-12(25)8-16(32)17(13)15/h7-9,14,18,26,31-32H,4-6,10-11H2,1-3H3,(H,27,34)(H,28,33)(H,35,36)/t14-,18+,23?,24+/m1/s1

> <INCHI_KEY>
DNRWOARHBKGXQM-NMKZSIDYSA-N

> <FORMULA>
C24H30ClN5O7

> <MOLECULAR_WEIGHT>
535.98

> <EXACT_MASS>
535.183376

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
53.96758180693557

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-{[(2S)-2-({[(4S)-2-(6-chloro-4-hydroxy-1-methyl-1H-indol-3-yl)-4-methyl-4,5-dihydro-1,3-oxazol-4-yl](hydroxy)methylidene}amino)-1-hydroxy-2-[(2R)-pyrrolidin-2-yl]ethylidene]amino}-3-hydroxy-2-methylpropanoic acid

> <JCHEM_LOGP>
-0.5018205195910128

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
3.1672543331738297

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.332255494108118

> <JCHEM_PKA_STRONGEST_BASIC>
10.783838999979263

> <JCHEM_POLAR_SURFACE_AREA>
181.48999999999998

> <JCHEM_REFRACTIVITY>
133.73129999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
2-{[(2S)-2-({[(4S)-2-(6-chloro-4-hydroxy-1-methylindol-3-yl)-4-methyl-5H-1,3-oxazol-4-yl](hydroxy)methylidene}amino)-1-hydroxy-2-[(2R)-pyrrolidin-2-yl]ethylidene]amino}-3-hydroxy-2-methylpropanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0       1.650  -4.013   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       2.126  -2.549   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.126  -0.057   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.650   1.408   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       0.185   1.884   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       0.185   3.424   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.346   3.263   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.135   4.930   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.600   5.406   0.000  0.00  0.00           O+0
HETATM   11  N   UNK     0       1.009   5.960   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       0.689   7.467   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.834   8.497   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       1.513  10.004   0.000  0.00  0.00           O+0
HETATM   15  N   UNK     0       3.298   8.021   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       4.443   9.052   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.412  10.196   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.473   7.907   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       4.997   6.443   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       5.587  10.082   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       5.267  11.589   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       7.052   9.606   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -0.775   7.943   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -2.021   7.037   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -3.267   7.943   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -2.791   9.407   0.000  0.00  0.00           C+0
HETATM   27  N   UNK     0      -1.251   9.407   0.000  0.00  0.00           N+0
HETATM   28  C   UNK     0       1.650   3.899   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       2.555   2.654   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       4.924   1.777   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   35 Cl   UNK     0       7.591  -2.843   0.000  0.00  0.00          Cl+0
HETATM   36  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   37                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   30                                                  
CONECT    5    4    6   29                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9   28                                             
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13   23                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17   18   20                                             
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18                                                            
CONECT   20   16   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20                                                            
CONECT   23   12   24   27                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   23                                                       
CONECT   28    7   29                                                       
CONECT   29   28    5                                                       
CONECT   30    4   31   37                                                  
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34                                                       
CONECT   34   33   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   37                                                       
CONECT   37   36   30    2                                                  
MASTER        0    0    0    0    0    0    0    0   37    0   80    0
END

View in JSmol

Synonyms

Value	Source
Tambromycin	MeSH

Chemical Formula

C₂₄H₃₀ClN₅O₇

Average Mass

535.9800 Da

Monoisotopic Mass

535.18338 Da

IUPAC Name

2-{[(2S)-2-({[(4S)-2-(6-chloro-4-hydroxy-1-methyl-1H-indol-3-yl)-4-methyl-4,5-dihydro-1,3-oxazol-4-yl](hydroxy)methylidene}amino)-1-hydroxy-2-[(2R)-pyrrolidin-2-yl]ethylidene]amino}-3-hydroxy-2-methylpropanoic acid

Traditional Name

2-{[(2S)-2-({[(4S)-2-(6-chloro-4-hydroxy-1-methylindol-3-yl)-4-methyl-5H-1,3-oxazol-4-yl](hydroxy)methylidene}amino)-1-hydroxy-2-[(2R)-pyrrolidin-2-yl]ethylidene]amino}-3-hydroxy-2-methylpropanoic acid

CAS Registry Number

Not Available

SMILES

CN1C=C(C2=N[C@@](C)(CO2)C(O)=N[C@@H]([C@H]2CCCN2)C(O)=NC(C)(CO)C(O)=O)C2=C(O)C=C(Cl)C=C12

InChI Identifier

InChI=1S/C24H30ClN5O7/c1-23(10-31,22(35)36)28-19(33)18(14-5-4-6-26-14)27-21(34)24(2)11-37-20(29-24)13-9-30(3)15-7-12(25)8-16(32)17(13)15/h7-9,14,18,26,31-32H,4-6,10-11H2,1-3H3,(H,27,34)(H,28,33)(H,35,36)/t14-,18+,23?,24+/m1/s1

InChI Key

DNRWOARHBKGXQM-NMKZSIDYSA-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as peptides. Peptides are compounds containing an amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Peptides

Alternative Parents

Substituents

Alpha peptide
N-acyl-alpha amino acid or derivatives
N-acyl-alpha-amino acid
N-alkylindole
Hydroxyindole
Alpha-amino acid or derivatives
Indole or derivatives
Indole
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Beta-hydroxy acid
Benzenoid
Substituted pyrrole
N-methylpyrrole
Hydroxy acid
Aryl halide
Aryl chloride
Heteroaromatic compound
Pyrrolidine
Pyrrole
Oxazoline
Amino acid
Amino acid or derivatives
Oxacycle
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Secondary amine
Monocarboxylic acid or derivatives
Secondary aliphatic amine
Carboxylic acid
Carboximidic acid derivative
Carboximidic acid
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organochloride
Organohalogen compound
Carbonyl group
Amine
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic 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	-0.5	ChemAxon
pKa (Strongest Acidic)	2.33	ChemAxon
pKa (Strongest Basic)	10.78	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	181.49 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	133.73 m³·mol⁻¹	ChemAxon
Polarizability	53.97 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

78441935

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139587554

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 2-{[(2s)-2-({[(4s)-2-(6-chloro-4-hydroxy-1-methylindol-3-yl)-4-methyl-5h-1,3-oxazol-4-yl](hydroxy)methylidene}amino)-1-hydroxy-2-[(2r)-pyrrolidin-2-yl]ethylidene]amino}-3-hydroxy-2-methylpropanoic acid (NP0308773)

MOL for NP0308773 (2-{[(2s)-2-({[(4s)-2-(6-chloro-4-hydroxy-1-methylindol-3-yl)-4-methyl-5h-1,3-oxazol-4-yl](hydroxy)methylidene}amino)-1-hydroxy-2-[(2r)-pyrrolidin-2-yl]ethylidene]amino}-3-hydroxy-2-methylpropanoic acid)

3D MOL for NP0308773 (2-{[(2s)-2-({[(4s)-2-(6-chloro-4-hydroxy-1-methylindol-3-yl)-4-methyl-5h-1,3-oxazol-4-yl](hydroxy)methylidene}amino)-1-hydroxy-2-[(2r)-pyrrolidin-2-yl]ethylidene]amino}-3-hydroxy-2-methylpropanoic acid)

3D SDF for NP0308773 (2-{[(2s)-2-({[(4s)-2-(6-chloro-4-hydroxy-1-methylindol-3-yl)-4-methyl-5h-1,3-oxazol-4-yl](hydroxy)methylidene}amino)-1-hydroxy-2-[(2r)-pyrrolidin-2-yl]ethylidene]amino}-3-hydroxy-2-methylpropanoic acid)

3D-SDF for NP0308773 (2-{[(2s)-2-({[(4s)-2-(6-chloro-4-hydroxy-1-methylindol-3-yl)-4-methyl-5h-1,3-oxazol-4-yl](hydroxy)methylidene}amino)-1-hydroxy-2-[(2r)-pyrrolidin-2-yl]ethylidene]amino}-3-hydroxy-2-methylpropanoic acid)

PDB for NP0308773 (2-{[(2s)-2-({[(4s)-2-(6-chloro-4-hydroxy-1-methylindol-3-yl)-4-methyl-5h-1,3-oxazol-4-yl](hydroxy)methylidene}amino)-1-hydroxy-2-[(2r)-pyrrolidin-2-yl]ethylidene]amino}-3-hydroxy-2-methylpropanoic acid)

3D PDB for NP0308773 (2-{[(2s)-2-({[(4s)-2-(6-chloro-4-hydroxy-1-methylindol-3-yl)-4-methyl-5h-1,3-oxazol-4-yl](hydroxy)methylidene}amino)-1-hydroxy-2-[(2r)-pyrrolidin-2-yl]ethylidene]amino}-3-hydroxy-2-methylpropanoic acid)

SMILES for NP0308773 (2-{[(2s)-2-({[(4s)-2-(6-chloro-4-hydroxy-1-methylindol-3-yl)-4-methyl-5h-1,3-oxazol-4-yl](hydroxy)methylidene}amino)-1-hydroxy-2-[(2r)-pyrrolidin-2-yl]ethylidene]amino}-3-hydroxy-2-methylpropanoic acid)

INCHI for NP0308773 (2-{[(2s)-2-({[(4s)-2-(6-chloro-4-hydroxy-1-methylindol-3-yl)-4-methyl-5h-1,3-oxazol-4-yl](hydroxy)methylidene}amino)-1-hydroxy-2-[(2r)-pyrrolidin-2-yl]ethylidene]amino}-3-hydroxy-2-methylpropanoic acid)

Structure for NP0308773 (2-{[(2s)-2-({[(4s)-2-(6-chloro-4-hydroxy-1-methylindol-3-yl)-4-methyl-5h-1,3-oxazol-4-yl](hydroxy)methylidene}amino)-1-hydroxy-2-[(2r)-pyrrolidin-2-yl]ethylidene]amino}-3-hydroxy-2-methylpropanoic acid)

3D Structure for NP0308773 (2-{[(2s)-2-({[(4s)-2-(6-chloro-4-hydroxy-1-methylindol-3-yl)-4-methyl-5h-1,3-oxazol-4-yl](hydroxy)methylidene}amino)-1-hydroxy-2-[(2r)-pyrrolidin-2-yl]ethylidene]amino}-3-hydroxy-2-methylpropanoic acid)