Structure of PDB 5ess Chain A Binding Site BS03

Receptor Information
>5ess Chain A (length=551) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNPSTTQARVVVDELIRGGVRDVVLCPGSRNAPLAFALQDADRSGRIRLH
VRIDERTAGYLAIGLAIGAGAPVCVAMTSGTAVANLGPAVVEANYARVPL
IVLSANRPYELLGTGANQTMEQLGYFGTQVRASISLGLAEDAPERTSALN
ATWRSATCRVLAAATGARTANAGPVHFDIPLREPLVPDPEPLGAVTPPGR
PAGKPWTYTPPVTFDQPLDIDLSVDTVVISGHGAGVHPNLAALPTVAEPT
APRSGDNPLHPLALPLLRPQQVIMLGRPTLHRPVSVLLADAEVPVFALTT
GPRWPDVSGNSQATGTRAVTTGAPRPAWLDRCAAMNRHAIAAVREQLAAH
PLTTGLHVAAAVSHALRPGDQLVLGASNPVRDVALAGLDTRGIRVRSNRG
VAGIDGTVSTAIGAALAYEGAHERTGSPDSPPRTIALIGDLTFVHDSSGL
LIGPTEPIPRSLTIVVSNDNGGGIFELLGDPRFSDVSSRIFGTPHDVDVG
ALCRAYHVESRQIEVDELGPTLDQPAGMRVLEVKADRSSLRQLHAAIKAA
L
Ligand information
Ligand IDTOG
InChIInChI=1S/C16H24N4O10P2S/c1-9-13(5-6-29-32(27,28)30-31(24,25)26)33-16(12(21)3-4-14(22)23)20(9)8-11-7-18-10(2)19-15(11)17/h7,21H,3-6,8H2,1-2H3,(H,22,23)(H,27,28)(H2,17,18,19)(H2,24,25,26)
InChIKeyVGWJMSNWDAXPBE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C-](O)CCC(O)=O)c(N)n1
OpenEye OEToolkits 2.0.4Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C-](CCC(=O)O)O)CCOP(=O)(O)OP(=O)(O)O
FormulaC16 H24 N4 O10 P2 S
Name4-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3 -ium-2-yl]-4-oxidanyl-butanoic acid;
ThDP and decarboxylated 2-oxoglutarate adduct, covalent intermediate I, carboanion form
ChEMBL
DrugBank
ZINC
PDB chain5ess Chain D Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ess Structural Views along the Mycobacterium tuberculosis MenD Reaction Pathway Illuminate Key Aspects of Thiamin Diphosphate-Dependent Enzyme Mechanisms.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		P27 E55 T78 Q118
Binding residue
(residue number reindexed from 1)		P27 E55 T78 Q118
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C26 E55
Catalytic site (residue number reindexed from 1) C26 E55
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:5ess, PDBe:5ess, PDBj:5ess
PDBsum5ess
PubMed27291649
UniProtP9WK11|MEND_MYCTU 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase (Gene Name=menD)

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