Structure of PDB 2y0p Chain C Binding Site BS01

Receptor Information
>2y0p Chain C (length=856) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EDKNARVIELIAAYRNRGHLMADIDPLRLDNTRFNSHGLTLWDLDREFKV
DGFAGVQRKKLRDILSVLRDAYCRHVGVEYTHILEPEQQRWIQERVETKH
DKPTVAEQKYILSKLNAAEAFETFLQTKYVGQKRFSLEGAETVIPMMDAV
IDQCAEHGLDEVVIAMPHRGRLNVLANIVGKPYSQIFSEFEGNLNPSQAH
GSGDVKYHLGATGTYIQMFGDNDIEVSLTANPSHLEAVDPVLEGLVRAKQ
DLLDTGEEGSDNRFSVVPLMLHGDAAFAGQGVVAETLNLALLRGYRTGGT
IHIVVNNQIGFTTAPTDSRSSEYCTDVAKMIGAPIFHVNGDDPEACAWVA
RLAVDFRQAFKKDVVIDMLCYRRRGHNEGDDPSMTQPYMYDVIDTKRGSR
KAYTEALIGRGDISMKEAEDALRDYQGQLERVFNEVRELEKHEIEPSESV
EADQQIPSKLATAVDKAMLQRIGDAHLALPEGFTVHPRVRPVLEKRREMA
YEGRIDWAFAELLALGSLIAEGKLVRLSGQDTQRGTFTQRHAVIVDRKTG
EEFTPLQLLATNPDGTPTGGKFLVYNSALSEFAAVGFEYGYSVGNPDAMV
LWEAQFGDFVNGAQSIIDEFISSGEAKWGQLSDVVLLLPHGHEGQGPDHT
SGRIERFLQLWAEGSMTIAMPSTPANYFHLLRRHGKDGIQRPLIVFTPKS
MLRNKAAVSDIRDFTESKFRSVLEEPMYTDGEGDRNKVTRLLLTSGKIYY
ELAARKAKENREDVAIVRIEQLAPLPRRRLAETLDRYPNVKEKFWVQEEP
ANQGAWPSFGLTLPEILPDHFTGLKRISRRAMSAPSSGSSKVHAVEQQEI
LDTAFG
Ligand information
Ligand IDTD7
InChIInChI=1S/C16H24N4O10P2S/c1-9-13(5-6-29-32(27,28)30-31(24,25)26)33-16(12(21)3-4-14(22)23)20(9)8-11-7-18-10(2)19-15(11)17/h7,21H,3-6,8H2,1-2H3,(H,22,23)(H,27,28)(H2,17,18,19)(H2,24,25,26)/b16-12+
InChIKeyVGWJMSNWDAXPBE-FOWTUZBSSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCCC=1S\C(=C(\O)CCC(=O)O)N(C=1C)Cc2cnc(nc2N)C
OpenEye OEToolkits 1.6.1Cc1ncc(c(n1)N)CN2C(=C(SC2=C(CCC(=O)O)O)CCOP(=O)(O)OP(=O)(O)O)C
CACTVS 3.352Cc1ncc(CN2C(=C(CCO[P](O)(=O)O[P](O)(O)=O)SC2=C(O)CCC(O)=O)C)c(N)n1
CACTVS 3.352Cc1ncc(CN2C(=C(CCO[P](O)(=O)O[P](O)(O)=O)S\C2=C(\O)CCC(O)=O)C)c(N)n1
OpenEye OEToolkits 1.6.1Cc1ncc(c(n1)N)CN2C(=C(SC2=C(CCC(=O)O)O)CCO[P@](=O)(O)OP(=O)(O)O)C
FormulaC16 H24 N4 O10 P2 S
Name(4E)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-2(3H)-ylidene}-4-hydroxybutanoic acid
ChEMBL
DrugBank
ZINCZINC000103557812
PDB chain2y0p 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

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PDB2y0p Functional Plasticity and Allosteric Regulation of Alpha-Ketoglutarate Decarboxylase in Central Mycobacterial Metabolism.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		F506 H539 R540 Y578 H579 S604 L606 G644 D645 A646 A647 N678 I680 H747
Binding residue
(residue number reindexed from 1)		F135 H168 R169 Y207 H208 S233 L235 G273 D274 A275 A276 N307 I309 H376
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:2y0p, PDBe:2y0p, PDBj:2y0p
PDBsum2y0p
PubMed21867916
UniProtA0R2B1|KGD_MYCS2 Multifunctional 2-oxoglutarate metabolism enzyme (Gene Name=kgd)

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