Structure of PDB 6r2b Chain A Binding Site BS01

Receptor Information
>6r2b Chain A (length=844) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SIEDKNARVIELIAAYRNRGHLMADIDPLRLDNTRTLWDLDREFKVQRKK
LRDILSVLRDAYCRHVGVEYTHILEPEQQRWIQERVETKHDKPTVAEQKY
ILSKLNAAEAFETFLQTKYVGQKRFSLEGAETVIPMMDAVIDQCAEHGLD
EVVIAMPHRGRLNVLANIVGKPYSQIFSEFEGNLNPSQAHGSGDVKYHLG
ATGTYIQMFGDNDIEVSLTANPSHLEAVDPVLEGLVRAKQDLLDTGEEGS
DNRFSVVPLMLHGDAAFAGQGVVAETLNLALLRGYRTGGTIHIVVNNQIG
FTTAPTDSRSSEYCTDVAKMIGAPIFHVNGDDPEACAWVARLAVDFRQAF
KKDVVIDMLCYRRRGHNEGDDPSMTQPYMYDVIDTKRGSRKAYTEALIGR
GDISMKEAEDALRDYQGQLERVFNEVRELEKHEIEPSESVEADQQIKLAT
AVDKAMLQRIGDAHLALPEGFTVHPRVRPVLEKRREMAYEGRIDWAFAEL
LALGSLIAEGKLVRLSGQDTQRGTFTQRHAVIVDRKTGEEFTPLQLLATN
PDGTPTGGKFLVYNSALSEFAAVGFEYGYSVGNPDAMVLWEAQFGDFVNG
AQSIIDEFISSGEAKWGQLSDVVLLLPHGHEGQGPDHTSGRIERFLQLWA
EGSMTIAMPSTPANYFHLLRRHGKDGIQRPLIVFTPKSMLRNKAAVSDIR
DFTESKFRSVLEEPMYTDGEGDRNKVTRLLLTSGKIYYELAARKAKENRE
DVAIVRIEQLAPLPRRRLAETLDRYPNVKEKFWVQEEPANQGAWPSFGLT
LPEILPDHFTGLKRISRRAMSAPSSGSSKVHAVEQQEILDTAFG
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 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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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)		H539 R540 Y578 S604 L606 G644 D645 A646 A647 Q651 N678 I680 G681 H747
Binding residue
(residue number reindexed from 1)		H158 R159 Y197 S223 L225 G263 D264 A265 A266 Q270 N297 I299 G300 H366
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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