Structure of PDB 2yid Chain D Binding Site BS01

Receptor Information
>2yid Chain D (length=852) Species: 1772 (Mycolicibacterium smegmatis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DSIEDKNARVIELIAAYRNRGHLMADIDPLRLDNTRFRLTLWDLDREFKV
DGGVQRKKLRDILSVLRDAYCRHVGVEYTHILEPEQQRWIQERVETKHDK
PTVAEQKYILSKLNAAEAFETFLQTKYVGQKRFSLEGAETVIPMMDAVID
QCAEHGLDEVVIAMPHRGRLNVLANIVGKPYSQIFSEFEGNLNPSQAHGS
GDVKYHLGATGTYIQMFGDNDIEVSLTANPSHLEAVDPVLEGLVRAKQDL
LDTGEEGSDNRFSVVPLMLHGDAAFAGQGVVAETLNLALLRGYRTGGTIH
IVVNNQIGFTTAPTDSRSSEYCTDVAKMIGAPIFHVNGDDPEACAWVARL
AVDFRQAFKKDVVIDMLCYRRRGHNEGDDPSMTQPYMYDVIDTKRGSRKA
YTEALIGRGDISMKEAEDALRDYQGQLERVFNEVRELEKHEIEPSESVEA
DQQIPLATAVDKAMLQRIGDAHLALPEGFTVHPRVRPVLEKRREMAYEGR
IDWAFAELLALGSLIAEGKLVRLSGQDTQRGTFTQRHAVIVDRKTGEEFT
PLQLLATNPDGTPTGGKFLVYNSALSEFAAVGFEYGYSVGNPDAMVLWEA
QFGDFVNGAQSIIDEFISSGEAKWGQLSDVVLLLPHGHEGQGPDHTSGRI
ERFLQLWAEGSMTIAMPSTPANYFHLLRRHGKDGIQRPLIVFTPKSMLRN
KAAVSDIRDFTESKFRSVLEEPMYTDGEGDRNKVTRLLLTSGKIYYELAA
RKAKENREDVAIVRIEQLAPLPRRRLAETLDRYPNVKEKFWVQEEPANQG
AWPSFGLTLPEILPDHFTGLKRISRRAMSAPSSGSSKVHAVEQQEILDTA
FG
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 chain2yid 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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PDB2yid Functional Plasticity and Allosteric Regulation of Alpha-Ketoglutarate Decarboxylase in Central Mycobacterial Metabolism.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		Q901 L950 E952 Q976 F980 H1020
Binding residue
(residue number reindexed from 1)		Q526 L575 E577 Q601 F605 H645
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:2yid, PDBe:2yid, PDBj:2yid
PDBsum2yid
PubMed21867916
UniProtA0R2B1|KGD_MYCS2 Multifunctional 2-oxoglutarate metabolism enzyme (Gene Name=kgd)

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