Structure of PDB 3zht Chain D Binding Site BS02

Receptor Information
>3zht Chain D (length=807) Species: 1772 (Mycolicibacterium smegmatis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NARVIELIAAYRNRGHLMADIDPLRLDNTRFWDLDREFKKLRDILSVLRD
AYCRHVGVEYTHILEPEQQRWIQERVETKHDKPTVAEQKYILSKLNAAEA
FETFLQTKYVGQKRFSLEGAETVIPMMDAVIDQCAEHGLDEVVIAMPHRG
RLNVLANIVGKPYSQIFSEDVKYHLGATGTYIQMFGDNDIEVSLTANPSH
LEAVDPVLEGLVRAKQDLLDTGEEGSDNRFSVVPLMLHGDAAFAGQGVVA
ETLNLALLRGYRTGGTIHIVVNNQIGFTTAPTDSRSSEYCTDVAKMIGAP
IFHVNGDDPEACAWVARLAVDFRQAFKKDVVIDMLCYRRRGHNEGDDPSM
TQPYMYDVIDTKRGSRKAYTEALIGRGDISMKEAEDALRDYQGQLERVFN
EVRELEKHEILATAVDKAMLQRIGDAHLALPEGFTVHPRVRPVLEKRREM
AYEGRIDWAFAELLALGSLIAEGKLVRLSGQDTQRGTFTQRHAVIVDRKT
GEEFTPLQLLATNPDGTPTGGKFLVYNSALSEFAAVGFEYGYSVGNPDAM
VLWEAQFGDFVNGAQSIIDEFISSGEAKWGQLSDVVLLLPHGHEGQGPDH
TSGRIERFLQLWAEGSMTIAMPSTPANYFHLLRRHGKDGIQRPLIVFTPK
SMLRNKAAVSDIRDFTESKFRSVLEEPMYTDGEGDRNKVTRLLLTSGKIY
YELAARKAKENREDVAIVRIEQLAPLPRRRLAETLDRYPNVKEKFWVQEE
PANQGAWPSFGLTLPEILPDHFTGLKRISRRAMSAPSSGSSKVHAVEQQE
ILDTAFG
Ligand information
Ligand IDTD9
InChIInChI=1S/C17H26N4O10P2S/c1-10-14(6-7-30-33(28,29)31-32(25,26)27)34-17(13(22)4-3-5-15(23)24)21(10)9-12-8-19-11(2)20-16(12)18/h8,13,22H,3-7,9H2,1-2H3,(H5-,18,19,20,23,24,25,26,27,28,29)/p-3/t13-/m0/s1
InChIKeyWMOBQHPEAJZBCW-ZDUSSCGKSA-K
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@H](CCCC(=O)O)O)CCOP(=O)(O)OP(=O)(O)O
CACTVS 3.370Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C@@H](O)CCCC(O)=O)c(N)n1
CACTVS 3.370Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[CH](O)CCCC(O)=O)c(N)n1
OpenEye OEToolkits 1.7.6Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(CCCC(=O)O)O)CCOP(=O)(O)OP(=O)(O)O
ACDLabs 12.01[O-]C(=O)CCCC(O)c1sc(c([n+]1Cc2cnc(nc2N)C)C)CCOP([O-])(=O)OP([O-])([O-])=O
FormulaC17 H27 N4 O10 P2 S
Name(5S)-5-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-4-methyl-5-(2-{[(phosphonatooxy)phosphinato]oxy}ethyl)-1,3-thiazol-3-ium-2-yl}-5-hydroxypentanoate
ChEMBL
DrugBank
ZINC
PDB chain3zht Chain D Residue 2001 [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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PDB3zht A Dual Conformation of the Post-Decarboxylation Intermediate is Associated with Distinct Enzyme States in Mycobacterial Alpha-Ketoglutarate Decarboxylase (Kgd).
Resolution2.15 Å
Binding residue
(original residue number in PDB)		R540 S604 L606 G644 D645 A646 A647 Q651 N678 I680 H747 N748
Binding residue
(residue number reindexed from 1)		R149 S199 L201 G239 D240 A241 A242 Q246 N273 I275 H342 N343
Annotation score1
Enzymatic activity
Enzyme Commision number 1.2.4.2: oxoglutarate dehydrogenase (succinyl-transferring).
2.2.1.5: 2-hydroxy-3-oxoadipate synthase.
2.3.1.61: dihydrolipoyllysine-residue succinyltransferase.
4.1.1.71: 2-oxoglutarate decarboxylase.
Gene Ontology
Molecular Function
GO:0016624 oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
GO:0030976 thiamine pyrophosphate binding

View graph for
Molecular Function
External links
PDB RCSB:3zht, PDBe:3zht, PDBj:3zht
PDBsum3zht
PubMed24171907
UniProtA0R2B1|KGD_MYCS2 Multifunctional 2-oxoglutarate metabolism enzyme (Gene Name=kgd)

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