Structure of PDB 6r29 Chain B Binding Site BS02

Receptor Information
>6r29 Chain B (length=855) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GDSIEDKNARVIELIAAYRNRGHLMADIDPLRLDLDVNSHGLTLWDLDRE
FKVDVQRKKLRDILSVLRDAYCRHVGVEYTHILEPEQQRWIQERVETKHD
KPTVAEQKYILSKLNAAEAFETFLQTKYVGQKRFSLEGAETVIPMMDAVI
DQCAEHGLDEVVIAMPHRGRLNVLANIVGKPYSQIFSEFEGNLNPSQAHG
SGDVKYHLGATGTYIQMFGDNDIEVSLTANPSHLEAVDPVLEGLVRAKQD
LLDTGEEGSDNRFSVVPLMLHGDAAFAGQGVVAETLNLALLRGYRTGGTI
HIVVNNQIGFTTAPTDSRSSEYCTDVAKMIGAPIFHVNGDDPEACAWVAR
LAVDFRQAFKKDVVIDMLCYRRRGHNEGDDPSMTQPYMYDVIDTKRGSRK
AYTEALIGRGDISMKEAEDALRDYQGQLERVFNEVRELEKHEIEPSESVE
ADQQIPSKLATAVDKAMLQRIGDAHLALPEGFTVHPRVRPVLEKRREMAY
EGRIDWAFAELLALGSLIAEGKLVRLSGQDTQRGTFTQRHAVIVDRKTGE
EFTPLQLLATNPDGTPTGGKFLVYNSALSEFAAVGFEYGYSVGNPDAMVL
WEAQFGDFVNGAQSIIDEFISSGEAKWGQLSDVVLLLPHGHEGQGPDHTS
GRIERFLQLWAEGSMTIAMPSTPANYFHLLRRHGKDGIQRPLIVFTPKSM
LRNKAAVSDIRDFTESKFRSVLEEPMYTDGEGDRNKVTRLLLTSGKIYYE
LAARKAKENREDVAIVRIEQLAPLPRRRLAETLDRYPNVKEKFWVQEEPA
NQGAWPSFGLTLPEILPDHFTGLKRISRRAMSAPSSGSSKVHAVEQQEIL
DTAFG
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 chain6r29 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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PDB6r29 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.
Resolution1.67 Å
Binding residue
(original residue number in PDB)		H539 R540 Y578 H579 S604 L606 G644 D645 A646 A647 Q651 N678 I680 G681 H747
Binding residue
(residue number reindexed from 1)		H167 R168 Y206 H207 S232 L234 G272 D273 A274 A275 Q279 N306 I308 G309 H375
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:6r29, PDBe:6r29, PDBj:6r29
PDBsum6r29
PubMed31476368
UniProtA0R2B1|KGD_MYCS2 Multifunctional 2-oxoglutarate metabolism enzyme (Gene Name=kgd)

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