Structure of PDB 2yid Chain A Binding Site BS01

Receptor Information
>2yid Chain A (length=844) Species: 1772 (Mycolicibacterium smegmatis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DSIEDKNARVIELIAAYRNRGHLMADIDPLRLDNTRLTLWDLDREFKVDV
QRKKLRDILSVLRDAYCRHVGVEYTHILEPEQQRWIQERVETKHDKPTVA
EQKYILSKLNAAEAFETFLQTKYVGQKRFSLEGAETVIPMMDAVIDQCAE
HGLDEVVIAMPHRGRLNVLANIVGKPYSQIFSEFEGNLNPSQAHGSGDVK
YHLGATGTYIQMFGDNDIEVSLTANPSHLEAVDPVLEGLVRAKQDLLDTG
EEGSDNRFSVVPLMLHGDAAFAGQGVVAETLNLALLRGYRTGGTIHIVVN
NQIGFTTAPTDSRSSEYCTDVAKMIGAPIFHVNGDDPEACAWVARLAVDF
RQAFKKDVVIDMLCYRRRGHNEGDDPSMTQPYMYDVIDTKRGSRKAYTEA
LIGRGDISMKEAEDALRDYQGQLERVFNEVRELEIEPSESVEADQQILAT
AVDKAMLQRIGDAHLALPEGFTVHPRVRPVLEKRREMAYEGRIDWAFAEL
LALGSLIAEGKLVRLSGQDTQRGTFTQRHAVIVDRKTGEEFTPLQLLATN
PDGTPTGGKFLVYNSALSEFAAVGFEYGYSVGNPDAMVLWEAQFGDFVNG
AQSIIDEFISSGEAKWGQLSDVVLLLPHGHEGQGPDHTSGRIERFLQLWA
EGSMTIAMPSTPANYFHLLRRHGKDGIQRPLIVFTPKSMLRNKAAVSDIR
DFTESKFRSVLEEPMYTDGEGDRNKVTRLLLTSGKIYYELAARKAKENRE
DVAIVRIEQLAPLPRRRLAETLDRYPNVKEKFWVQEEPANQGAWPSFGLT
LPEILPDHFTGLKRISRRAMSAPSSGSSKVHAVEQQEILDTAFG
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 A 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]
PDB2yid Functional Plasticity and Allosteric Regulation of Alpha-Ketoglutarate Decarboxylase in Central Mycobacterial Metabolism.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		F506 H539 R540 Y578 H579 S604 L606 G644 D645 A646 A647 Q651 N678 I680 H747
Binding residue
(residue number reindexed from 1)		F129 H162 R163 Y201 H202 S227 L229 G267 D268 A269 A270 Q274 N301 I303 H370
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)

[Back to BioLiP]