Structure of PDB 3zhv Chain A Binding Site BS04

Receptor Information
>3zhv Chain A (length=820) Species: 1772 (Mycolicibacterium smegmatis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DKNARVIELIAAYRNRGHLMADIDPLRLDNTRFRSHPDLTLWDLDREFKQ
RKKLRDILSVLRDAYCRHVGVEYTHILEPEQQRWIQERVETKHDKPTVAE
QKYILSKLNAAEAFETFLQTKYVGQKRFSLEGAETVIPMMDAVIDQCAEH
GLDEVVIAMPHRGRLNVLANIVGKPYSQIFSEFGDVKYHLGATGTYIQMF
GDNDIEVSLTANPSHLEAVDPVLEGLVRAKQDLLDTGEEGSDNRFSVVPL
MLHGDAAFAGQGVVAETLNLALLRGYRTGGTIHIVVNNQIGFTTAPTDSR
SSEYCTDVAKMIGAPIFHVNGDDPEACAWVARLAVDFRQAFKKDVVIDML
CYRRRGHNEGDDPSMTQPYMYDVIDTKRGSRKAYTEALIGRGDISMKEAE
DALRDYQGQLERVFNEVRELEKHLATAVDKAMLQRIGDAHLALPEGFTVH
PRVRPVLEKRREMAYEGRIDWAFAELLALGSLIAEGKLVRLSGQDTQRGT
FTQRHAVIVDRKTGEEFTPLQLLATNPDGTPTGGKFLVYNSALSEFAAVG
FEYGYSVGNPDAMVLWEAQFGDFVNGAQSIIDEFISSGEAKWGQLSDVVL
LLPHGHEGQGPDHTSGRIERFLQLWAEGSMTIAMPSTPANYFHLLRRHGK
DGIQRPLIVFTPKSMLRNKAAVSDIRDFTESKFRSVLEEPMYTDGEGDRN
KVTRLLLTSGKIYYELAARKAKENREDVAIVRIEQLAPLPRRRLAETLDR
YPNVKEKFWVQEEPANQGAWPSFGLTLPEILPDHFTGLKRISRRAMSAPS
SGSSKVHAVEQQEILDTAFG
Ligand information
Ligand IDTDW
InChIInChI=1S/C14H24N4O8P2S/c1-8-12(4-5-25-28(23,24)26-27(20,21)22)29-14(9(2)19)18(8)7-11-6-16-10(3)17-13(11)15/h6,9,18-19H,4-5,7H2,1-3H3,(H,23,24)(H2,15,16,17)(H2,20,21,22)/t9-/m0/s1
InChIKeyWHPLAPKWYDKPQH-VIFPVBQESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(C)O)CCOP(=O)(O)OP(=O)(O)O
CACTVS 3.370C[C@H](O)c1sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)[n+]1Cc2cnc(C)nc2N
CACTVS 3.370C[CH](O)c1sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)[n+]1Cc2cnc(C)nc2N
OpenEye OEToolkits 1.7.6Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@H](C)O)CCOP(=O)(O)OP(=O)(O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCCc1sc(C(O)C)n(c1C)Cc2cnc(nc2N)C
FormulaC14 H23 N4 O8 P2 S
Name2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2-[(1S)-1-oxidanylethyl]-1,3-thiazol-3-ium-5-yl]ethyl phosphono hydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain3zhv Chain B 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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PDB3zhv A Dual Conformation of the Post-Decarboxylation Intermediate is Associated with Distinct Enzyme States in Mycobacterial Alpha-Ketoglutarate Decarboxylase (Kgd).
Resolution2.3 Å
Binding residue
(original residue number in PDB)		Q901 L950 E952 Q976 F980
Binding residue
(residue number reindexed from 1)		Q494 L543 E545 Q569 F573
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:3zhv, PDBe:3zhv, PDBj:3zhv
PDBsum3zhv
PubMed24171907
UniProtA0R2B1|KGD_MYCS2 Multifunctional 2-oxoglutarate metabolism enzyme (Gene Name=kgd)

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