Structure of PDB 3t8a Chain C Binding Site BS01

Receptor Information
>3t8a Chain C (length=249) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DNPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRNAFRPHTV
DELYRVLDHARMSPDVGVVLLTGNGPSPKDGGWAFCSGGDQRLHILEVQR
LIRFMPKVVICLVNGWAAGGGHSLHVVCDLTLASREYARFKQTDADVGSF
DGGYGSAYLARQVGQKFAREIFFLGRTYTAEQMHQMGAVNAVAEHAELET
VGLQWAAEINAKSPQAQRMLKFAFNLLDDGLVGQQLFAGEATRLAYMTD
Ligand information
Ligand IDS0N
InChIInChI=1S/C32H45N8O20P3/c1-32(2,26(45)29(46)36-10-9-22(43)35-12-11-34-21(42)8-7-19(41)17-5-3-4-6-18(17)31(47)48)14-57-63(54,55)60-62(52,53)56-13-20-25(59-61(49,50)51)24(44)30(58-20)40-16-39-23-27(33)37-15-38-28(23)40/h3-6,15-16,20,24-26,30,44-45H,7-14H2,1-2H3,(H,34,42)(H,35,43)(H,36,46)(H,47,48)(H,52,53)(H,54,55)(H2,33,37,38)(H2,49,50,51)/t20-,24-,25-,26+,30-/m1/s1
InChIKeyQCTNXUGGWNSKFY-HSJNEKGZSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCNC(=O)CCC(=O)c4ccccc4C(O)=O
OpenEye OEToolkits 1.7.2CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCNC(=O)CCC(=O)c4ccccc4C(=O)O)O
OpenEye OEToolkits 1.7.2CC(C)(CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCNC(=O)CCC(=O)c4ccccc4C(=O)O)O
CACTVS 3.370CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCNC(=O)CCC(=O)c4ccccc4C(O)=O
ACDLabs 12.01O=C(O)c1ccccc1C(=O)CCC(=O)NCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC4OC(n3cnc2c(ncnc23)N)C(O)C4OP(=O)(O)O
FormulaC32 H45 N8 O20 P3
Nameo-succinylbenzoyl-N-coenzyme A
ChEMBL
DrugBank
ZINCZINC000198511424
PDB chain3t8a Chain C Residue 600 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3t8a Mechanism of the Intramolecular Claisen Condensation Reaction Catalyzed by MenB, a Crotonase Superfamily Member.
Resolution2.245 Å
Binding residue
(original residue number in PDB)		V57 R58 S103 G105 D106 Q107 W157
Binding residue
(residue number reindexed from 1)		V41 R42 S87 G89 D90 Q91 W116
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) G105 H135 G161 S164 D185 S190 D192 G193 A279 Y287
Catalytic site (residue number reindexed from 1) G89 H94 G120 S123 D144 S149 D151 G152 A238 Y246
Enzyme Commision number 4.1.3.36: 1,4-dihydroxy-2-naphthoyl-CoA synthase.
Gene Ontology
Molecular Function
GO:0008935 1,4-dihydroxy-2-naphthoyl-CoA synthase activity
GO:0016829 lyase activity
Biological Process
GO:0009234 menaquinone biosynthetic process
GO:0034214 protein hexamerization
Cellular Component
GO:0005886 plasma membrane

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3t8a, PDBe:3t8a, PDBj:3t8a
PDBsum3t8a
PubMed21830810
UniProtP9WNP5|MENB_MYCTU 1,4-dihydroxy-2-naphthoyl-CoA synthase (Gene Name=menB)

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