Structure of PDB 6r2a Chain A Binding Site BS04

Receptor Information
>6r2a Chain A (length=846) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KNARVIELIAAYRNRGHLMADIDPLRLDLTLWDLDREFKVDGFAGVQRKK
LRDILSVLRDAYCRHVGVEYTHILEPEQQRWIQERVETKHDKPTVAEQKY
ILSKLNAAEAFETFLQTKYVGQKRFSLEGAETVIPMMDAVIDQCAEHGLD
EVVIAMPHRGRLNVLANIVGKPYSQIFSEFEGNLNPSQAHGSGDVKYHLG
ATGTYIQMFGDNDIEVSLTANPSHLEAVDPVLEGLVRAKQDLLDTGEEGS
DNRFSVVPLMLHGDAAFAGQGVVAETLNLALLRGYRTGGTIHIVVNNQIG
FTTAPTDSRSSEYCTDVAKMIGAPIFHVNGDDPEACAWVARLAVDFRQAF
KKDVVIDMLCYRRRGHNEGDDPSMTQPYMYDVIDTKRGSRKAYTEALIGR
GDISMKEAEDALRDYQGQLERVFNEVRELEKHEIEPSESVEADQQIPSKL
ATAVDKAMLQRIGDAHLALPEGFTVHPRVRPVLEKRREMAYEGRIDWAFA
ELLALGSLIAEGKLVRLSGQDTQRGTFTQRHAVIVDRKTGEEFTPLQLLA
TNPDGTPTGGKFLVYNSALSEFAAVGFEYGYSVGNPDAMVLWEAQFGDFV
NGAQSIIDEFISSGEAKWGQLSDVVLLLPHGHEGQGPDHTSGRIERFLQL
WAEGSMTIAMPSTPANYFHLLRRHGKDGIQRPLIVFTPKSMLRNKAAVSD
IRDFTESKFRSVLEEPMYTDGEGDRNKVTRLLLTSGKIYYELAARKAKEN
REDVAIVRIEQLAPLPRRRLAETLDRYPNVKEKFWVQEEPANQGAWPSFG
LTLPEILPDHFTGLKRISRRAMSAPSSGSSKVHAVEQQEILDTAFG
Ligand information
Ligand IDZP1
InChIInChI=1S/C18H31N4O13P3S/c1-4-33-36(26,27)18(25,7-5-15(23)24)17-22(10-13-9-20-12(3)21-16(13)19)11(2)14(39-17)6-8-34-38(31,32)35-37(28,29)30/h9,17,25H,4-8,10H2,1-3H3,(H,23,24)(H,26,27)(H,31,32)(H2,19,20,21)(H2,28,29,30)/t17-,18+/m1/s1
InChIKeyXUQXUYTXDQCESE-MSOLQXFVSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCO[P](O)(=O)[C](O)(CCC(O)=O)[CH]1SC(=C(C)N1Cc2cnc(C)nc2N)CCO[P](O)(=O)O[P](O)(O)=O
OpenEye OEToolkits 2.0.7CCOP(=O)(C(CCC(=O)O)(C1N(C(=C(S1)CCOP(=O)(O)OP(=O)(O)O)C)Cc2cnc(nc2N)C)O)O
CACTVS 3.385CCO[P](O)(=O)[C@@](O)(CCC(O)=O)[C@H]1SC(=C(C)N1Cc2cnc(C)nc2N)CCO[P](O)(=O)O[P](O)(O)=O
OpenEye OEToolkits 2.0.7CCOP(=O)([C@@](CCC(=O)O)([C@@H]1N(C(=C(S1)CCOP(=O)(O)OP(=O)(O)O)C)Cc2cnc(nc2N)C)O)O
FormulaC18 H31 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-[ethoxy(oxidanyl)phosphoryl]-4-oxidanyl-butanoic acid
ChEMBL
DrugBank
ZINC
PDB chain6r2a 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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PDB6r2a 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.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		Q901 L950 E952 Q976 F977 F980 H1020
Binding residue
(residue number reindexed from 1)		Q520 L569 E571 Q595 F596 F599 H639
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:6r2a, PDBe:6r2a, PDBj:6r2a
PDBsum6r2a
PubMed31476368
UniProtA0R2B1|KGD_MYCS2 Multifunctional 2-oxoglutarate metabolism enzyme (Gene Name=kgd)

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