Structure of PDB 2g28 Chain A Binding Site BS03

Receptor Information
>2g28 Chain A (length=801) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ISNYINTIPVEEQPEYPGNLELERRIRSAIRWNAIMTVLRASKKDLELGG
HMASFQSSATIYDVCFNHFFRARNEQDGGDLVYFQGHISPGVYARAFLEG
RLTQEQLDNFRQEVHGNGLSSYPHPKLMPEFWQFPTVSMGLGPIGAIYQA
KFLKYLEHRGLKDTSKQTVYAFLGDGEMDEPESKGAITIATREKLDNLVF
VINCNLQRLDGPVTGNGKIINELEGIFEGAGWNVIKVMWGSRWDELLRKD
TSGKLIQLMNETVDGDYQTFKSKDGAYVREHFFGKYPETAALVADWTDEQ
IWALNRGGHDPKKIYAAFKKAQETKGKATVILAHTIKGYGMGDAAMDGVR
HIRDRFNVPVSDADIEKLPYITFPEGSEEHTYLHAQRQKLHGYLPSRQPN
FTEKLELPSLQDFGALLEEQSKEISTTIAFVRALNVMLKNKSIKDRLVPI
IADEARTFGMEGLFRQIGIYSPEDEKGQILQEGINELGAGCSWLAAATSY
STNNLPMIPFYIYYSMFGFQRIGDLCWAAGDQQARGFLIGGTSGRTTLNG
EGLQHEDGHSHIQSLTIPNCISYDPAYAYEVAVIMHDGLERMYGEKQENV
YYYITTLNENYHMPAMPEGAEEGIRKGIYKLETIEGSKGKVQLLGSGSIL
RHVREAAEILAKDYGVGSDVYSVTSFTELARDGQDCERWNMLHPLETPRV
PYIAQVMNDAPAVASTDYMKLFAEQVRTYVPADDYRVLGTDGFGRSDSRE
NLRHHFEVDASYVVVAALGELAKRGEIDKKVVADAIAKFNIDADKVNPRL
A
Ligand information
Ligand IDTDK
InChIInChI=1S/C15H25N4O11P3S/c1-9-12(5-6-29-33(26,27)30-32(23,24)25)34-14(15(3,20)31(21,22)28-4)19(9)8-11-7-17-10(2)18-13(11)16/h7,20H,5-6,8H2,1-4H3,(H5-,16,17,18,21,22,23,24,25,26,27)/p+1/t15-/m0/s1
InChIKeyILGXNMPRCMTAOK-HNNXBMFYSA-O
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCCc1sc([n+](c1C)Cc2cnc(nc2N)C)C(O)(P(=O)(OC)O)C
OpenEye OEToolkits 1.7.5Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(C)(O)P(=O)(O)OC)CCOP(=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.7.5Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@](C)(O)[P@@](=O)(O)OC)CCO[P@@](=O)(O)OP(=O)(O)O
CACTVS 3.385CO[P](O)(=O)[C](C)(O)c1sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)[n+]1Cc2cnc(C)nc2N
CACTVS 3.385CO[P](O)(=O)[C@](C)(O)c1sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)[n+]1Cc2cnc(C)nc2N
FormulaC15 H26 N4 O11 P3 S
Name3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(1S)-1-HYDROXY-1-[(R)-HYDROXY(METHOXY)PHOSPHORYL]ETHYL}-5-(2-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM;
2-PHOSPHONOLACTYLTHIAMIN DIPHOSPHATE
ChEMBL
DrugBank
ZINCZINC000016051991
PDB chain2g28 Chain B Residue 887 [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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PDB2g28 A Thiamin-bound, Pre-decarboxylation Reaction Intermediate Analogue in the Pyruvate Dehydrogenase E1 Subunit Induces Large Scale Disorder-to-Order Transformations in the Enzyme and Reveals Novel Structural Features in the Covalently Bound Adduct.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		H106 S109 Q140 H142 V192 M194 G229 G231 E232 N260 Q262 K392
Binding residue
(residue number reindexed from 1)		H51 S54 Q85 H87 V137 M139 G174 G176 E177 N205 Q207 K337
Annotation score1
Enzymatic activity
Enzyme Commision number 1.2.4.1: pyruvate dehydrogenase (acetyl-transferring).
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0004738 pyruvate dehydrogenase activity
GO:0004739 pyruvate dehydrogenase (acetyl-transferring) activity
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0030976 thiamine pyrophosphate binding
GO:0036094 small molecule binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0060090 molecular adaptor activity
Biological Process
GO:0042867 pyruvate catabolic process
Cellular Component
GO:0005829 cytosol
GO:0016020 membrane
GO:0045254 pyruvate dehydrogenase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2g28, PDBe:2g28, PDBj:2g28
PDBsum2g28
PubMed16531404
UniProtP0AFG8|ODP1_ECOLI Pyruvate dehydrogenase E1 component (Gene Name=aceE)

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