Structure of PDB 4qij Chain D Binding Site BS02

Receptor Information
>4qij Chain D (length=297) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRNAFRPHTVD
ELYRVLDHARMSPDVGVVLLTGNGPSPKDGGWAFCSGGDQRIRGRSGYQY
ASGDTADTVDVARAGRLHILEVQRLIRFMPKVVICLVNGWAAGGGHSLHV
VCDLTLASREYARFKQTDADVGSFDGGYGSAYLARQVGQKFAREIFFLGR
TYTAEQMHQMGAVNAVAEHAELETVGLQWAAEINAKSPQAQRMLKFAFNL
LDDGLVGQQLFAGEATRLAYMTDEAVEGRDAFLQKRPPDWSPFPRYF
Ligand information
Ligand ID1HA
InChIInChI=1S/C32H42N7O18P3S/c1-32(2,26(43)29(44)35-10-9-21(40)34-11-12-61-31(45)19-8-7-17-5-3-4-6-18(17)23(19)41)14-54-60(51,52)57-59(49,50)53-13-20-25(56-58(46,47)48)24(42)30(55-20)39-16-38-22-27(33)36-15-37-28(22)39/h3-8,15-16,20,24-26,30,41-43H,9-14H2,1-2H3,(H,34,40)(H,35,44)(H,49,50)(H,51,52)(H2,33,36,37)(H2,46,47,48)/t20-,24-,25-,26+,30-/m1/s1
InChIKeyZHSLHXZSNOSMQG-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)NCCSC(=O)c4ccc5ccccc5c4O
OpenEye OEToolkits 1.7.6CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCSC(=O)c4ccc5ccccc5c4O)O
OpenEye OEToolkits 1.7.6CC(C)(COP(=O)(O)OP(=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)NCCSC(=O)c4ccc5ccccc5c4O)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)NCCSC(=O)c4ccc5ccccc5c4O
ACDLabs 12.01O=C(SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O)c5ccc4ccccc4c5O
FormulaC32 H42 N7 O18 P3 S
Name1-hydroxy-2-naphthoyl-CoA
ChEMBL
DrugBank
ZINCZINC000206504123
PDB chain4qij Chain D Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4qij Ligand-dependent active-site closure revealed in the crystal structure of Mycobacterium tuberculosis MenB complexed with product analogues
Resolution2.2 Å
Binding residue
(original residue number in PDB)		V57 R58 K95 S103 G104 G105 D106 Q107 Y115 I136 W157 G161 T184 D185 S190 F191 D192
Binding residue
(residue number reindexed from 1)		V40 R41 K78 S86 G87 G88 D89 Q90 Y98 I119 W140 G144 T167 D168 S173 F174 D175
Annotation score3
Binding affinityMOAD: Kd=2.9uM
Enzymatic activity
Catalytic site (original residue number in PDB) G105 R110 Y115 R130 H135 G161 S164 D185 S190 D192 G193 A279 Y287
Catalytic site (residue number reindexed from 1) G88 R93 Y98 R113 H118 G144 S147 D168 S173 D175 G176 A262 Y270
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:4qij, PDBe:4qij, PDBj:4qij
PDBsum4qij
PubMed25372686
UniProtP9WNP5|MENB_MYCTU 1,4-dihydroxy-2-naphthoyl-CoA synthase (Gene Name=menB)

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