Structure of PDB 6r2b Chain D Binding Site BS01

Receptor Information
>6r2b Chain D (length=839) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NARVIELIAAYRNRGHLMADIDPLRLDNTRFLTLWDLDREFKRKKLRDIL
SVLRDAYCRHVGVEYTHILEPEQQRWIQERVETKHDKPTVAEQKYILSKL
NAAEAFETFLQTKYVGQKRFSLEGAETVIPMMDAVIDQCAEHGLDEVVIA
MPHRGRLNVLANIVGKPYSQIFSEFEGNLNPSQAHGSGDVKYHLGATGTY
IQMFGDNDIEVSLTANPSHLEAVDPVLEGLVRAKQDLLDTGEEGSDNRFS
VVPLMLHGDAAFAGQGVVAETLNLALLRGYRTGGTIHIVVNNQIGFTTAP
TDSRSSEYCTDVAKMIGAPIFHVNGDDPEACAWVARLAVDFRQAFKKDVV
IDMLCYRRRGHNEGDDPSMTQPYMYDVIDTKRGSRKAYTEALIGRGDISM
KEAEDALRDYQGQLERVFNEVRELEKHEIEPSESVEADQQIKLATAVDKA
MLQRIGDAHLALPEGFTVHPRVRPVLEKRREMAYEGRIDWAFAELLALGS
LIAEGKLVRLSGQDTQRGTFTQRHAVIVDRKTGEEFTPLQLLATNPDGTP
TGGKFLVYNSALSEFAAVGFEYGYSVGNPDAMVLWEAQFGDFVNGAQSII
DEFISSGEAKWGQLSDVVLLLPHGHEGQGPDHTSGRIERFLQLWAEGSMT
IAMPSTPANYFHLLRRHGKDGIQRPLIVFTPKSMLRNKAAVSDIRDFTES
KFRSVLEEPMYTDGEGDRNKVTRLLLTSGKIYYELAARKAKENREDVAIV
RIEQLAPLPRRRLAETLDRYPNVKEKFWVQEEPANQGAWPSFGLTLPEIL
PDHFTGLKRISRRAMSAPSSGSSKVHAVEQQEILDTAFG
Ligand information
Ligand IDQSP
InChIInChI=1S/C16H27N4O13P3S/c1-9-12(4-6-32-36(30,31)33-35(27,28)29)37-15(16(23,34(24,25)26)5-3-13(21)22)20(9)8-11-7-18-10(2)19-14(11)17/h7,15,23H,3-6,8H2,1-2H3,(H,21,22)(H,30,31)(H2,17,18,19)(H2,24,25,26)(H2,27,28,29)/t15-,16+/m1/s1
InChIKeyXWZWGSGHSWWOAH-CVEARBPZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cc1ncc(c(n1)N)CN2[C@H](SC(=C2C)CCOP(=O)(O)OP(=O)(O)O)[C@@](CCC(=O)O)(O)P(=O)(O)O
CACTVS 3.385Cc1ncc(CN2[C@H](SC(=C2C)CCO[P](O)(=O)O[P](O)(O)=O)[C@](O)(CCC(O)=O)[P](O)(O)=O)c(N)n1
CACTVS 3.385Cc1ncc(CN2[CH](SC(=C2C)CCO[P](O)(=O)O[P](O)(O)=O)[C](O)(CCC(O)=O)[P](O)(O)=O)c(N)n1
OpenEye OEToolkits 2.0.7Cc1ncc(c(n1)N)CN2C(SC(=C2C)CCOP(=O)(O)OP(=O)(O)O)C(CCC(=O)O)(O)P(=O)(O)O
FormulaC16 H27 N4 O13 P3 S
Name(4~{S})-4-[(2~{R})-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-2~{H}-1,3-thiazol-2-yl]-4-oxidanyl-4-phosphono-butanoic acid
ChEMBL
DrugBank
ZINC
PDB chain6r2b Chain C 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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PDB6r2b 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.
Resolution1.96 Å
Binding residue
(original residue number in PDB)		Q901 L950 E952 Q976 F980 H1020
Binding residue
(residue number reindexed from 1)		Q513 L562 E564 Q588 F592 H632
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:6r2b, PDBe:6r2b, PDBj:6r2b
PDBsum6r2b
PubMed31476368
UniProtA0R2B1|KGD_MYCS2 Multifunctional 2-oxoglutarate metabolism enzyme (Gene Name=kgd)

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