Structure of PDB 6r2b Chain B Binding Site BS02

Receptor Information
>6r2b Chain B (length=840) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DKNARVIELIAAYRNRGHLMADIDPLRLDWDLDREFKVGVQRKKLRDILS
VLRDAYCRHVGVEYTHILEPEQQRWIQERVETKHDKPTVAEQKYILSKLN
AAEAFETFLQTKYVGQKRFSLEGAETVIPMMDAVIDQCAEHGLDEVVIAM
PHRGRLNVLANIVGKPYSQIFSEFEGNLNPSQAHGSGDVKYHLGATGTYI
QMFGDNDIEVSLTANPSHLEAVDPVLEGLVRAKQDLLDTGEEGSDNRFSV
VPLMLHGDAAFAGQGVVAETLNLALLRGYRTGGTIHIVVNNQIGFTTAPT
DSRSSEYCTDVAKMIGAPIFHVNGDDPEACAWVARLAVDFRQAFKKDVVI
DMLCYRRRGHNEGDDPSMTQPYMYDVIDTKRGSRKAYTEALIGRGDISMK
EAEDALRDYQGQLERVFNEVRELEKHEIEPSESVEADQQIPSKLATAVDK
AMLQRIGDAHLALPEGFTVHPRVRPVLEKRREMAYEGRIDWAFAELLALG
SLIAEGKLVRLSGQDTQRGTFTQRHAVIVDRKTGEEFTPLQLLATNPDGT
PTGGKFLVYNSALSEFAAVGFEYGYSVGNPDAMVLWEAQFGDFVNGAQSI
IDEFISSGEAKWGQLSDVVLLLPHGHEGQGPDHTSGRIERFLQLWAEGSM
TIAMPSTPANYFHLLRRHGKDGIQRPLIVFTPKSMLRNKAAVSDIRDFTE
SKFRSVLEEPMYTDGEGDRNKVTRLLLTSGKIYYELAARKAKENREDVAI
VRIEQLAPLPRRRLAETLDRYPNVKEKFWVQEEPANQGAWPSFGLTLPEI
LPDHFTGLKRISRRAMSAPSSGSSKVHAVEQQEILDTAFG
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 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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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)		F506 H539 R540 Y578 H579 S604 L606 G644 D645 A646 A647 Q651 N678 I680 G681 H747
Binding residue
(residue number reindexed from 1)		F119 H152 R153 Y191 H192 S217 L219 G257 D258 A259 A260 Q264 N291 I293 G294 H360
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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