Structure of PDB 6o0j Chain D Binding Site BS03

Receptor Information
>6o0j Chain D (length=532) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PSTTQARVVVDELIRGGVRDVVLCPGSRNAPLAFALQDADRSGRIRLHVR
IDERTAGYLAIGLAIGAGAPVCVAMTSGTAVANLGPAVVEANYARVPLIV
LSANRPYELLGTGANQTMEQLGYFGTQVRASISLGLAERTSALNATWRSA
TCRVLAAATGARTANAGPVHFDIPLRVTPPGRPAGKPWTYTPPVTFDQPL
DIDLSVDTVVISGHGAGVHPNLAALPTVAEPTAPRSGDNPLHPLALPLLR
PQQVIMLGRPTLHRPVSVLLADAEVPVFALTTGPRWPDVSGNSQATGTRA
VTTGAPRPAWLDRCAAMNRHAIAAVREQLAAHPLTTGLHVAAAVSHALRP
GDQLVLGASNPVRDVALAGLDTRGIRVRSNRGVAGIDGTVSTAIGAALAY
EGAHERTGPPRTIALIGDLTFVHDSSGLLIGPTEPIPRSLTIVVSNDNGG
GIFELLEQGDPRFSDVSSRIFGTPHDVDVGALCRAYHVESRQIEVDELGP
TLDQPGAGMRVLEVKADRSSLRQLHAAIKAAL
Ligand information
Ligand IDTPP
InChIInChI=1S/C12H18N4O7P2S/c1-8-11(3-4-22-25(20,21)23-24(17,18)19)26-7-16(8)6-10-5-14-9(2)15-12(10)13/h5,7H,3-4,6H2,1-2H3,(H4-,13,14,15,17,18,19,20,21)/p+1
InChIKeyAYEKOFBPNLCAJY-UHFFFAOYSA-O
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(C[n+]2csc(CCO[P@@](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
OpenEye OEToolkits 1.5.0Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCO[P@](=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(O)OP(=O)(O)O
CACTVS 3.341Cc1ncc(C[n+]2csc(CCO[P](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCCc1sc[n+](c1C)Cc2c(nc(nc2)C)N
FormulaC12 H19 N4 O7 P2 S
NameTHIAMINE DIPHOSPHATE
ChEMBLCHEMBL1236376
DrugBank
ZINCZINC000008215517
PDB chain6o0j Chain D Residue 604 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6o0j Allosteric regulation of menaquinone (vitamin K2) biosynthesis in the human pathogenMycobacterium tuberculosis.
Resolution2.35 Å
Binding residue
(original residue number in PDB)		S377 N378 G403 I404 D405 G439 D440 L441 T442 D469 G471 G472 G473 I474 F475
Binding residue
(residue number reindexed from 1)		S359 N360 G385 I386 D387 G417 D418 L419 T420 D447 G449 G450 G451 I452 F453
Annotation score1
Enzymatic activity
Enzyme Commision number 2.2.1.9: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0016740 transferase activity
GO:0030145 manganese ion binding
GO:0030976 thiamine pyrophosphate binding
GO:0046872 metal ion binding
GO:0070204 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity
Biological Process
GO:0009234 menaquinone biosynthetic process
Cellular Component
GO:0005886 plasma membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6o0j, PDBe:6o0j, PDBj:6o0j
PDBsum6o0j
PubMed32029475
UniProtP9WK11|MEND_MYCTU 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase (Gene Name=menD)

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