Structure of PDB 2yic Chain C Binding Site BS01

Receptor Information
>2yic Chain C (length=806) Species: 1772 (Mycolicibacterium smegmatis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NARVIELIAAYRNRGHLMADIDPLRLDNTRFTLWDLDREFKKLRDILSVL
RDAYCRHVGVEYTHILEPEQQRWIQERVETKHDKPTVAEQKYILSKLNAA
EAFETFLQTKYVGQKRFSLEGAETVIPMMDAVIDQCAEHGLDEVVIAMPH
RGRLNVLANIVGKPYSQIFSEGDVKYHLGATGTYIQMFGDNDIEVSLTAN
PSHLEAVDPVLEGLVRAKQDLLDTGEEGRFSVVPLMLHGDAAFAGQGVVA
ETLNLALLRGYRTGGTIHIVVNNQIGFTTAPTDSRSSEYCTDVAKMIGAP
IFHVNGDDPEACAWVARLAVDFRQAFKKDVVIDMLCYRRRGHNEGDDPSM
TQPYMYDVIDTKRGSRKAYTEALIGRGDISMKEAEDALRDYQGQLERVFN
EVRELEKHELATAVDKAMLQRIGDAHLALPEGFTVHPRVRPVLEKRREMA
YEGRIDWAFAELLALGSLIAEGKLVRLSGQDTQRGTFTQRHAVIVDRKTG
EEFTPLQLLATNPDGTPTGGKFLVYNSALSEFAAVGFEYGYSVGNPDAMV
LWEAQFGDFVNGAQSIIDEFISSGEAKWGQLSDVVLLLPHGHEGQGPDHT
SGRIERFLQLWAEGSMTIAMPSTPANYFHLLRRHGKDGIQRPLIVFTPKS
MLRNKAAVSDIRDFTESKFRSVLEEPMYTDGEGDRNKVTRLLLTSGKIYY
ELAARKAKENREDVAIVRIEQLAPLPRRRLAETLDRYPNVKEKFWVQEEP
ANQGAWPSFGLTLPEILPDHFTGLKRISRRAMSAPSSGSSKVHAVEQQEI
LDTAFG
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 chain2yic Chain C Residue 2001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2yic Functional Plasticity and Allosteric Regulation of Alpha-Ketoglutarate Decarboxylase in Central Mycobacterial Metabolism.
Resolution1.96 Å
Binding residue
(original residue number in PDB)		R540 S604 L606 G644 D645 A646 A647 N678 I680 G681 H747
Binding residue
(residue number reindexed from 1)		R151 S202 L204 G239 D240 A241 A242 N273 I275 G276 H342
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:2yic, PDBe:2yic, PDBj:2yic
PDBsum2yic
PubMed21867916
UniProtA0R2B1|KGD_MYCS2 Multifunctional 2-oxoglutarate metabolism enzyme (Gene Name=kgd)

[Back to BioLiP]