NP-MRD: Showing NP-Card for Antibiotic X 1092 (NP0062021)

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Record Information

Version

1.0

Created at

2022-04-28 06:42:23 UTC

Updated at

2022-04-28 06:42:23 UTC

NP-MRD ID

NP0062021

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Antibiotic X 1092

Description

55051-90-6 Belongs to the class of organic compounds known as valine and derivatives. Valine and derivatives are compounds containing valine or a derivative thereof resulting from reaction of valine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. Antibiotic X 1092 is found in Streptomyces sp. X-1092. It was first documented in 2022 (PMID: 35483916). Based on a literature review a significant number of articles have been published on 55051-90-6 (PMID: 35483915) (PMID: 35483914) (PMID: 35483913) (PMID: 35483912).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 37 37  0  0  0  0  0  0  0  0999 V2000
   -2.8167    0.0129   -1.7575 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0515    0.1243   -0.2739 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8167   -1.1515    0.4478 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3483    1.3204    0.3363 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8449    2.5436   -0.2885 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8947    1.3034    0.1990 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3243    2.1825   -0.5373 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0482    0.3611    0.8391 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3944    0.3716    0.6753 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1078    0.3255    2.0100 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0507   -1.1977    1.9120 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9217   -1.0159    0.3990 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9801   -1.8600   -0.1760 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2757   -1.0819   -0.2443 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3399   -0.4080   -1.5621 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4066    0.8430   -1.6342 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3259   -1.1647   -2.7178 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7245    1.0609   -2.1489 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7276   -0.3871   -2.2457 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9246   -0.6077   -1.9743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1566    0.3662   -0.1620 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9091   -1.7057    0.1565 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7004   -1.8542    0.3392 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7733   -0.9521    1.5439 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6258    1.3709    1.4071 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0541    3.2752    0.4147 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1965    2.8676   -1.0413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4713   -0.3558    1.4512 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7699    1.1671   -0.0016 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1594    0.6736    1.8487 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5893    0.7628    2.8590 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0099   -1.6469    2.2356 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1627   -1.6386    2.3876 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9572   -1.6433   -1.1463 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5367   -2.1645   -0.3412 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0697   -0.6729    0.4439 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3513   -0.7375   -3.6532 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  1  0
  4  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  6
 12 14  1  0
 14 15  1  0
 15 17  1  0
 15 16  2  0
 12  9  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  2 21  1  6
  3 22  1  0
  3 23  1  0
  3 24  1  0
  4 25  1  1
  5 26  1  0
  5 27  1  0
  8 28  1  0
  9 29  1  6
 10 30  1  0
 10 31  1  0
 11 32  1  0
 11 33  1  0
 13 34  1  0
 14 35  1  0
 14 36  1  0
 17 37  1  0
M  END


  Mrv1652304282208422D          

 17 17  0  0  1  0            999 V2000
    0.5628    0.3979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2341    0.6115    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0206    1.4084    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7763    1.1948    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4908    1.6073    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2053    1.1948    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2053    0.3698    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9197    1.6073    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6342    1.1948    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3487    1.6073    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6342    0.3698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9197    2.4323    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7456    1.8020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7672    2.6267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4922    3.0204    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0638    3.0578    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0010    2.2331    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  1  4  1  0  0  0  0
  4  5  1  1  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
  8 12  1  1  0  0  0
  3 13  1  6  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
  3 17  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0062021

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C11H20N2O4/c1-6(2)9(12)10(16)13-7-3-4-11(7,17)5-8(14)15/h6-7,9,17H,3-5,12H2,1-2H3,(H,13,16)(H,14,15)/t7-,9-,11-/m0/s1

> <INCHI_KEY>
CDPFOFWZIQBLQF-ARENWVFISA-N

> <FORMULA>
C11H20N2O4

> <MOLECULAR_WEIGHT>
244.291

> <EXACT_MASS>
244.142307132

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
25.05924756903729

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(1S,2S)-2-[(2S)-2-amino-3-methylbutanamido]-1-hydroxycyclobutyl]acetic acid

> <ALOGPS_LOGP>
-2.34

> <JCHEM_LOGP>
-3.0661239749808837

> <ALOGPS_LOGS>
-0.58

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.819938334442725

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.190790730278618

> <JCHEM_PKA_STRONGEST_BASIC>
8.513911965181407

> <JCHEM_POLAR_SURFACE_AREA>
112.65

> <JCHEM_REFRACTIVITY>
60.0591

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.49e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(1S,2S)-2-[(2S)-2-amino-3-methylbutanamido]-1-hydroxycyclobutyl]acetic 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       1.051   0.743   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.437   1.141   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.038   2.629   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.449   2.230   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       2.783   3.000   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       4.116   2.230   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.116   0.690   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       5.450   3.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.784   2.230   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.118   3.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.784   0.690   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       5.450   4.540   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0      -1.392   3.364   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.432   4.903   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -2.785   5.638   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -0.119   5.708   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.002   4.168   0.000  0.00  0.00           O+0
CONECT    1    2    4                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   13   17                                             
CONECT    4    3    1    5                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   12                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    8                                                            
CONECT   13    3   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17    3                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   34    0
END

View in JSmol

Synonyms

Value	Source
1-(S)-Hydroxy-2-(S,S)-valylamidocyclobutane-1-acetic acid	MeSH

Chemical Formula

C₁₁H₂₀N₂O₄

Average Mass

244.2910 Da

Monoisotopic Mass

244.14231 Da

IUPAC Name

2-[(1S,2S)-2-[(2S)-2-amino-3-methylbutanamido]-1-hydroxycyclobutyl]acetic acid

Traditional Name

[(1S,2S)-2-[(2S)-2-amino-3-methylbutanamido]-1-hydroxycyclobutyl]acetic acid

CAS Registry Number

Not Available

SMILES

CC(C)[C@H](N)C(=O)N[C@H]1CC[C@]1(O)CC(O)=O

InChI Identifier

InChI=1S/C11H20N2O4/c1-6(2)9(12)10(16)13-7-3-4-11(7,17)5-8(14)15/h6-7,9,17H,3-5,12H2,1-2H3,(H,13,16)(H,14,15)/t7-,9-,11-/m0/s1

InChI Key

CDPFOFWZIQBLQF-ARENWVFISA-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. X-1092	Bacteria	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as valine and derivatives. Valine and derivatives are compounds containing valine or a derivative thereof resulting from reaction of valine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Valine and derivatives

Alternative Parents

Substituents

Valine or derivatives
Alpha-amino acid amide
Gamma amino acid or derivatives
Fatty amide
Fatty acyl
N-acyl-amine
Tertiary alcohol
Carboxamide group
Cyclobutanol
Amino acid
Secondary carboxylic acid amide
Carboxylic acid
Monocarboxylic acid or derivatives
Alcohol
Organonitrogen compound
Organooxygen compound
Primary aliphatic amine
Primary amine
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Carbonyl group
Amine
Organic nitrogen compound
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic 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	-2.3	ALOGPS
logP	-3.1	ChemAxon
logS	-0.58	ALOGPS
pKa (Strongest Acidic)	4.19	ChemAxon
pKa (Strongest Basic)	8.51	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	112.65 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	60.06 m³·mol⁻¹	ChemAxon
Polarizability	25.06 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

C00018012

Chemspider ID

166182

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

191356

PDB ID

Not Available

ChEBI ID

Not Available

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 ]
Adeeb N, Dibas M, Diestro JDB, Phan K, Cuellar-Saenz HH, Sweid A, Lay SV, Guenego A, Aslan A, Renieri L, Sundararajan SH, Saliou G, Mohlenbruch M, Regenhardt RW, Vranic JE, Lylyk I, Foreman PM, Vachhani JA, Zupancic V, Hafeez MU, Rutledge C, Waqas M, Tutino VM, Rabinov JD, Ren Y, Schirmer CM, Piano M, Kuhn AL, Michelozzi C, Elens S, Starke RM, Hassan A, Salehani A, Brehm A, MohammedAli M, Jones J, Psychogios M, Spears J, Lubicz B, Panni P, Puri AS, Pero G, Griessenauer CJ, Asadi H, Siddiqui A, Ducruet A, Albuquerque FC, Du R, Kan P, Kalousek V, Lylyk P, Stapleton CJ, Boddu S, Knopman J, Aziz-Sultan MA, Limbucci N, Jabbour P, Cognard C, Patel AB, Dmytriw AA: Comparing treatment outcomes of various intracranial bifurcation aneurysms locations using the Woven EndoBridge (WEB) device. J Neurointerv Surg. 2022 Apr 28. pii: neurintsurg-2022-018694. doi: 10.1136/neurintsurg-2022-018694. [PubMed:35483912 ]

Showing NP-Card for Antibiotic X 1092 (NP0062021)

MOL for NP0062021 (Antibiotic X 1092)

3D MOL for NP0062021 (Antibiotic X 1092)

3D SDF for NP0062021 (Antibiotic X 1092)

3D-SDF for NP0062021 (Antibiotic X 1092)

PDB for NP0062021 (Antibiotic X 1092)

3D PDB for NP0062021 (Antibiotic X 1092)

SMILES for NP0062021 (Antibiotic X 1092)

INCHI for NP0062021 (Antibiotic X 1092)

Structure for NP0062021 (Antibiotic X 1092)

3D Structure for NP0062021 (Antibiotic X 1092)