Structure of PDB 6r2c Chain B Binding Site BS03

Receptor Information
>6r2c Chain B (length=815) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DKNARVIELIAAYRNRGHLMADIDPLRLDNTRFWDLDREFKQRKKLRDIL
SVLRDAYCRHVGVEYTHILEPEQQRWIQERVETKHDKPTVAEQKYILSKL
NAAEAFETFLQTKYVGQKRFSLEGAETVIPMMDAVIDQCAEHGLDEVVIA
MPHRGRLNVLANIVGKPYSQIFSEFDVKYHLGATGTYIQMFGDNDIEVSL
TANPSHLEAVDPVLEGLVRAKQDLLDTGEEGSDNRFSVVPLMLHGDAAFA
GQGVVAETLNLALLRGYRTGGTIHIVVNNQIGFTTAPTDSRSSEYCTDVA
KMIGAPIFHVNGDDPEACAWVARLAVDFRQAFKKDVVIDMLCYRRRGHNE
GDDPSMTQPYMYDVIDTKRGSRKAYTEALIGRGDISMKEAEDALRDYQGQ
LERVFNEVRELEKHEIEPLATAVDKAMLQRIGDAHLALPEGFTVHPRVRP
VLEKRREMAYEGRIDWAFAELLALGSLIAEGKLVRLSGQDTQRGTFTQRH
AVIVDRKTGEEFTPLQLLATNPDGTPTGGKFLVYNSALSEFAAVGFEYGY
SVGNPDAMVLWEAQFGDFVNGAQSIIDEFISSGEAKWGQLSDVVLLLPHG
HEGQGPDHTSGRIERFLQLWAEGSMTIAMPSTPANYFHLLRRHGKDGIQR
PLIVFTPKSMLRNKAAVSDIRDFTESKFRSVLEEPMYTDGEGDRNKVTRL
LLTSGKIYYELAARKAKENREDVAIVRIEQLAPLPRRRLAETLDRYPNVK
EKFWVQEEPANQGAWPSFGLTLPEILPDHFTGLKRISRRAMSAPSSGSSK
VHAVEQQEILDTAFG
Ligand information
Ligand IDTPP
InChIInChI=1S/C12H18N4O7P2S/c1-8-11(3-4-22-25(20,21)23-24(17,18)19)26-7-16(8)6-10-5-14-9(2)15-12(10)13/h5,7H,3-4,6H2,1-2H3,(H4-,13,14,15,17,18,19,20,21)/p+1
InChIKeyAYEKOFBPNLCAJY-UHFFFAOYSA-O
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(C[n+]2csc(CCO[P@@](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
OpenEye OEToolkits 1.5.0Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCO[P@](=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(O)OP(=O)(O)O
CACTVS 3.341Cc1ncc(C[n+]2csc(CCO[P](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCCc1sc[n+](c1C)Cc2c(nc(nc2)C)N
FormulaC12 H19 N4 O7 P2 S
NameTHIAMINE DIPHOSPHATE
ChEMBLCHEMBL1236376
DrugBank
ZINCZINC000008215517
PDB chain6r2c 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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PDB6r2c 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.
Resolution2.09 Å
Binding residue
(original residue number in PDB)		R540 S604 L606 G644 D645 A646 A647 N678 I680 H747
Binding residue
(residue number reindexed from 1)		R154 S205 L207 G245 D246 A247 A248 N279 I281 H348
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:6r2c, PDBe:6r2c, PDBj:6r2c
PDBsum6r2c
PubMed31476368
UniProtA0R2B1|KGD_MYCS2 Multifunctional 2-oxoglutarate metabolism enzyme (Gene Name=kgd)

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