Structure of PDB 4qii Chain E Binding Site BS02

Receptor Information
>4qii Chain E (length=298) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DNPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRNAFRPHTV
DELYRVLDHARMSPDVGVVLLTGNGPSPKDGGWAFCSGGDQRIRGRSGYQ
YASGDTADTVDVARAGRLHILEVQRLIRFMPKVVICLVNGWAAGGGHSLH
VVCDLTLASREYARFKQTDADVGSFDGGYGSAYLARQVGQKFAREIFFLG
RTYTAEQMHQMGAVNAVAEHAELETVGLQWAAEINAKSPQAQRMLKFAFN
LLDDGLVGQQLFAGEATRLAYMTDEAVEGRDAFLQKRPPDWSPFPRYF
Ligand information
Ligand ID2NE
InChIInChI=1S/C28H40N7O18P3S/c1-28(2,22(39)25(40)31-8-7-18(37)30-9-10-57-27(41)15-5-3-4-6-16(15)36)12-50-56(47,48)53-55(45,46)49-11-17-21(52-54(42,43)44)20(38)26(51-17)35-14-34-19-23(29)32-13-33-24(19)35/h3-6,13-14,17,20-22,26,36,38-39H,7-12H2,1-2H3,(H,30,37)(H,31,40)(H,45,46)(H,47,48)(H2,29,32,33)(H2,42,43,44)/t17-,20-,21-,22+,26-/m1/s1
InChIKeyYTKKDFTVSNSVEE-TYHXJLICSA-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)c4ccccc4O
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)c4ccccc4O
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)c4ccccc4O)O
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)c4ccccc4O)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)c4ccccc4O
FormulaC28 H40 N7 O18 P3 S
NameSalicylyl CoA
ChEMBL
DrugBank
ZINCZINC000096068394
PDB chain4qii Chain E Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4qii Ligand-dependent active-site closure revealed in the crystal structure of Mycobacterium tuberculosis MenB complexed with product analogues
Resolution1.64 Å
Binding residue
(original residue number in PDB)		V57 R58 A60 K95 S103 G104 G105 D106 Q107 Y115 W157 G161 T184 D185 V188 S190
Binding residue
(residue number reindexed from 1)		V41 R42 A44 K79 S87 G88 G89 D90 Q91 Y99 W141 G145 T168 D169 V172 S174
Annotation score3
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) G89 R94 Y99 R114 H119 G145 S148 D169 S174 D176 G177 A263 Y271
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:4qii, PDBe:4qii, PDBj:4qii
PDBsum4qii
PubMed25372686
UniProtP9WNP5|MENB_MYCTU 1,4-dihydroxy-2-naphthoyl-CoA synthase (Gene Name=menB)

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