Structure of PDB 3zht Chain B Binding Site BS01

Receptor Information
>3zht Chain B (length=809) Species: 1772 (Mycolicibacterium smegmatis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DKNARVIELIAAYRNRGHLMADIDPLRLDNTRFWDLDREFKRKKLRDILS
VLRDAYCRHVGVEYTHILEPEQQRWIQERVETKHDKPTVAEQKYILSKLN
AAEAFETFLQTKYVGQKRFSLEGAETVIPMMDAVIDQCAEHGLDEVVIAM
PHRGRLNVLANIVGKPYSQIFSEDVKYHLGATGTYIQMFGDNDIEVSLTA
NPSHLEAVDPVLEGLVRAKQDLLDTGEEGSDNRFSVVPLMLHGDAAFAGQ
GVVAETLNLALLRGYRTGGTIHIVVNNQIGFTTAPTDSRSSEYCTDVAKM
IGAPIFHVNGDDPEACAWVARLAVDFRQAFKKDVVIDMLCYRRRGHNEGD
DPSMTQPYMYDVIDTKRGSRKAYTEALIGRGDISMKEAEDALRDYQGQLE
RVFNEVRELEKHLATAVDKAMLQRIGDAHLALPEGFTVHPRVRPVLEKRR
EMAYEGRIDWAFAELLALGSLIAEGKLVRLSGQDTQRGTFTQRHAVIVDR
KTGEEFTPLQLLATNPDGTPTGGKFLVYNSALSEFAAVGFEYGYSVGNPD
AMVLWEAQFGDFVNGAQSIIDEFISSGEAKWGQLSDVVLLLPHGHEGQGP
DHTSGRIERFLQLWAEGSMTIAMPSTPANYFHLLRRHGKDGIQRPLIVFT
PKSMLRNKAAVSDIRDFTESKFRSVLEEPMYTDGEGDRNKVTRLLLTSGK
IYYELAARKAKENREDVAIVRIEQLAPLPRRRLAETLDRYPNVKEKFWVQ
EEPANQGAWPSFGLTLPEILPDHFTGLKRISRRAMSAPSSGSSKVHAVEQ
QEILDTAFG
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 A 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)		Q901 L950 E952 Q976 F977 F980 H1020
Binding residue
(residue number reindexed from 1)		Q483 L532 E534 Q558 F559 F562 H602
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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