Structure of PDB 5esd Chain D Binding Site BS01

Receptor Information
>5esd Chain D (length=541) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NPSTTQARVVVDELIRGGVRDVVLCPGSRNAPLAFALQDADRSGRIRLHV
RIDERTAGYLAIGLAIGAGAPVCVAMTSGTAVANLGPAVVEANYARVPLI
VLSANRPYELLGTGANQTMEQLGYFGTQVRASISLGLAEDAPERTSALNA
TWRSATCRVLAAATGARTANAGPVHFDIPLREPVTPPGRPAGKPWTYTPP
VTFDQPLDIDLSVDTVVISGHGAGVHPNLAALPTVAEPTAPRSGDNPLHP
LALPLLRPQQVIMLGRPTLHRPVSVLLADAEVPVFALTTGPRWPDVSGNS
QATGTRAVTTGAPRPAWLDRCAAMNRHAIAAVREQLAAHPLTTGLHVAAA
VSHALRPGDQLVLGASNPVRDVALAGLDTRGIRVRSNRGVAGIDGTVSTA
IGAALAYEGAHERTGSSPPRTIALIGDLTFVHDSSGLLIGPTEPIPRSLT
IVVSNDNGGGIFELLEQGDPRFSDVSSRIFGTPHDVDVGALCRAYHVESR
QIEVDELGPTLDQPGAGMRVLEVKADRSSLRQLHAAIKAAL
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 chain5esd Chain D Residue 601 [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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PDB5esd Structural Views along the Mycobacterium tuberculosis MenD Reaction Pathway Illuminate Key Aspects of Thiamin Diphosphate-Dependent Enzyme Mechanisms.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		S377 I404 G439 D440 L441 T442 G471 G472 G473 I474 F475
Binding residue
(residue number reindexed from 1)		S366 I393 G426 D427 L428 T429 G458 G459 G460 I461 F462
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C26 E55
Catalytic site (residue number reindexed from 1) C25 E54
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:5esd, PDBe:5esd, PDBj:5esd
PDBsum5esd
PubMed27291649
UniProtP9WK11|MEND_MYCTU 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase (Gene Name=menD)

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