Structure of PDB 2yic Chain D Binding Site BS02

Receptor Information
>2yic Chain D (length=809) Species: 1772 (Mycolicibacterium smegmatis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NARVIELIAAYRNRGHLMADIDPLRLDNTRFWDLDREFKKLRDILSVLRD
AYCRHVGVEYTHILEPEQQRWIQERVETKHDKPTVAEQKYILSKLNAAEA
FETFLQTKYVGQKRFSLEGAETVIPMMDAVIDQCAEHGLDEVVIAMPHRG
RLNVLANIVGKPYSQIFSEFGDVKYHLGATGTYIQMFGDNDIEVSLTANP
SHLEAVDPVLEGLVRAKQDLLDTGEEGSDNRFSVVPLMLHGDAAFAGQGV
VAETLNLALLRGYRTGGTIHIVVNNQIGFTTAPTDSRSSEYCTDVAKMIG
APIFHVNGDDPEACAWVARLAVDFRQAFKKDVVIDMLCYRRRGHNEGDDP
SMTQPYMYDVIDTKRGSRKAYTEALIGRGDISMKEAEDALRDYQGQLERV
FNEVRELEKHEILATAVDKAMLQRIGDAHLALPEGFTVHPRVRPVLEKRR
EMAYEGRIDWAFAELLALGSLIAEGKLVRLSGQDTQRGTFTQRHAVIVDR
KTGEEFTPLQLLATNPDGTPTGGKFLVYNSALSEFAAVGFEYGYSVGNPD
AMVLWEAQFGDFVNGAQSIIDEFISSGEAKWGQLSDVVLLLPHGHEGQGP
DHTSGRIERFLQLWAEGSMTIAMPSTPANYFHLLRRHGKDGIQRPLIVFT
PKSMLRNKAAVSDIRDFTESKFRSVLEEPMYTDGEGDRNKVTRLLLTSGK
IYYELAARKAKENREDVAIVRIEQLAPLPRRRLAETLDRYPNVKEKFWVQ
EEPANQGAWPSFGLTLPEILPDHFTGLKRISRRAMSAPSSGSSKVHAVEQ
QEILDTAFG
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 D 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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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)		R149 S201 L203 G241 D242 A243 A244 N275 I277 G278 H344
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)

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