Structure of PDB 5vrn Chain C Binding Site BS01

Receptor Information
>5vrn Chain C (length=261) Species: 83331 (Mycobacterium tuberculosis CDC1551) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLLDGKRILVSGIITDSSIAFHIARVAQEQGAQLVLTGFDRLRLIQRITD
RLPAKAPLLELDVQNEEHLASLAGRVTEAIGAGNKLDGVVHSIGFMPQPF
FDAPYADVSKGIHISAYSYASMAKALLPIMNPGGSIVGMDFDPSRAMPAY
NWMTVAKSALESVNRFVAREAGKYGVRSNLVAAGPIRTLAMSAIVGGALG
EEAGAQIQLLEEGWDQRAPIGWNMKDATPVAKTVCALLSDWLPATTGDII
YADGGAHTQLL
Ligand information
Ligand ID9JM
InChIInChI=1S/C36H37BN9O18P2/c38-10-18-3-6-24(20(8-18)11-44-52)60-22-4-5-23-21(9-22)13-57-37(23,51)63-31-29(48)26(62-36(31)45-7-1-2-19(12-45)33(40)50)15-59-66(55,56)64-65(53,54)58-14-25-28(47)30(49)35(61-25)46-17-43-27-32(39)41-16-42-34(27)46/h1-9,11-12,16-17,25-26,28-31,35-36,47-49,51H,13-15H2,(H6-,39,40,41,42,50,52,53,54,55,56)/p+1/b44-11+/t25-,26-,28-,29-,30-,31-,35-,36-/m1/s1
InChIKeyFIJWIPIHKAAZRO-KPRSXZNCSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6B1(c2ccc(cc2CO1)Oc3ccc(cc3C=NO)C#N)(O)OC4C(C(OC4[n+]5cccc(c5)C(=O)N)COP(=O)(O)OP(=O)(O)OCC6C(C(C(O6)n7cnc8c7ncnc8N)O)O)O
OpenEye OEToolkits 2.0.6B1(c2ccc(cc2CO1)Oc3ccc(cc3/C=N/O)C#N)(O)O[C@@H]4[C@@H]([C@H](O[C@H]4[n+]5cccc(c5)C(=O)N)COP(=O)(O)OP(=O)(O)OC[C@@H]6[C@H]([C@H]([C@@H](O6)n7cnc8c7ncnc8N)O)O)O
CACTVS 3.385NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O[B]6(O)OCc7cc(Oc8ccc(cc8/C=N/O)C#N)ccc67
CACTVS 3.385NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O[B]6(O)OCc7cc(Oc8ccc(cc8C=NO)C#N)ccc67
FormulaC36 H38 B N9 O18 P2
Name[[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonylpyridin-1-ium-1-yl)-4-[[5-[4-cyano-2-[(~{E})-hydroxyiminomethyl]phenoxy]-1-oxidanyl-3~{H}-2,1$l^{4}-benzoxaborol-1-yl]oxy]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain5vrn Chain C Residue 300 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5vrn Discovery of a cofactor-independent inhibitor ofMycobacterium tuberculosisInhA.
Resolution2.55 Å
Binding residue
(original residue number in PDB)
G14 I16 S20 I21 F41 D64 V65 S94 I95 G96 I122 M147 D148 F149 Y158 M161 K165 P193 I194 T196 M199 L218
Binding residue
(residue number reindexed from 1)
G12 I14 S18 I19 F39 D62 V63 S92 I93 G94 I114 M139 D140 F141 Y150 M153 K157 P185 I186 T188 M191 L210
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) Y158 K165
Catalytic site (residue number reindexed from 1) Y150 K157
Enzyme Commision number 1.3.1.9: enoyl-[acyl-carrier-protein] reductase (NADH).
Gene Ontology
Molecular Function
GO:0004318 enoyl-[acyl-carrier-protein] reductase (NADH) activity
GO:0005504 fatty acid binding
GO:0016491 oxidoreductase activity
GO:0050343 trans-2-enoyl-CoA reductase (NADH) activity
GO:0070403 NAD+ binding
Biological Process
GO:0006633 fatty acid biosynthetic process
GO:0030497 fatty acid elongation
GO:0046677 response to antibiotic
GO:0071768 mycolic acid biosynthetic process
Cellular Component
GO:0005886 plasma membrane
GO:0009274 peptidoglycan-based cell wall

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:5vrn, PDBe:5vrn, PDBj:5vrn
PDBsum5vrn
PubMed30456352
UniProtP9WGR1|INHA_MYCTU Enoyl-[acyl-carrier-protein] reductase [NADH] (Gene Name=inhA)

[Back to BioLiP]