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Structure of PDB 6r2c Chain B Binding Site BS06

Receptor Information
>6r2c Chain B (length=815) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DKNARVIELIAAYRNRGHLMADIDPLRLDNTRFWDLDREFKQRKKLRDIL
SVLRDAYCRHVGVEYTHILEPEQQRWIQERVETKHDKPTVAEQKYILSKL
NAAEAFETFLQTKYVGQKRFSLEGAETVIPMMDAVIDQCAEHGLDEVVIA
MPHRGRLNVLANIVGKPYSQIFSEFDVKYHLGATGTYIQMFGDNDIEVSL
TANPSHLEAVDPVLEGLVRAKQDLLDTGEEGSDNRFSVVPLMLHGDAAFA
GQGVVAETLNLALLRGYRTGGTIHIVVNNQIGFTTAPTDSRSSEYCTDVA
KMIGAPIFHVNGDDPEACAWVARLAVDFRQAFKKDVVIDMLCYRRRGHNE
GDDPSMTQPYMYDVIDTKRGSRKAYTEALIGRGDISMKEAEDALRDYQGQ
LERVFNEVRELEKHEIEPLATAVDKAMLQRIGDAHLALPEGFTVHPRVRP
VLEKRREMAYEGRIDWAFAELLALGSLIAEGKLVRLSGQDTQRGTFTQRH
AVIVDRKTGEEFTPLQLLATNPDGTPTGGKFLVYNSALSEFAAVGFEYGY
SVGNPDAMVLWEAQFGDFVNGAQSIIDEFISSGEAKWGQLSDVVLLLPHG
HEGQGPDHTSGRIERFLQLWAEGSMTIAMPSTPANYFHLLRRHGKDGIQR
PLIVFTPKSMLRNKAAVSDIRDFTESKFRSVLEEPMYTDGEGDRNKVTRL
LLTSGKIYYELAARKAKENREDVAIVRIEQLAPLPRRRLAETLDRYPNVK
EKFWVQEEPANQGAWPSFGLTLPEILPDHFTGLKRISRRAMSAPSSGSSK
VHAVEQQEILDTAFG
Ligand information
Ligand IDJQ5
InChIInChI=1S/C6H11O6P/c1-2-12-13(10,11)6(9)4-3-5(7)8/h2-4H2,1H3,(H,7,8)(H,10,11)
InChIKeyYEJCRQSMXRSGOQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCO[P](O)(=O)C(=O)CCC(O)=O
OpenEye OEToolkits 2.0.7CCOP(=O)(C(=O)CCC(=O)O)O
FormulaC6 H11 O6 P
Name4-[ethoxy(oxidanyl)phosphoryl]-4-oxidanylidene-butanoic acid
ChEMBL
DrugBank
ZINC
PDB chain6r2c Chain B Residue 2004 [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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PDB6r2c Conformational transitions in the active site of mycobacterial 2-oxoglutarate dehydrogenase upon binding phosphonate analogues of 2-oxoglutarate: From a Michaelis-like complex to ThDP adducts.
Resolution2.09 Å
Binding residue
(original residue number in PDB)		H539 S604 F682
Binding residue
(residue number reindexed from 1)		H153 S205 F283
Annotation score1
Binding affinityMOAD: Ki=0.88mM
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:6r2c, PDBe:6r2c, PDBj:6r2c
PDBsum6r2c
PubMed31476368
UniProtA0R2B1|KGD_MYCS2 Multifunctional 2-oxoglutarate metabolism enzyme (Gene Name=kgd)

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