Structure of PDB 1pyd Chain A Binding Site BS02

Receptor Information
>1pyd Chain A (length=537) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SEITLGKYLFERLKQVNVNTVFGLPGDFNLSLLDKIYEVEGMRWAGNANE
LNAAYAADGYARIKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGV
PSISHHTLGNGDFTVFHRMSANISETTAMITDIATAPAEIDRCIRTTYVT
QRPVYLGLPANLVDLNVPAKLLQTPIDMSLKPNDAESEKEVIDTILALVK
DAKNPVILADACCSRHDVKAETKKLIDLTQFPAFVTPMGKGSISEQHPRY
GGVYVGTLSKPEVKEAVESADLILSVGALLSDKTKNIVEFHSDHMKIRNA
TFPGVQMKFVLQKLLTNIADAAKGYKPVAVPARTPANAAVPASTPLKQEW
MWNQLGNFLQEGDVVIAETGTSAFGINQTTFPNNTYGISQVLWGSIGFTT
GATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEISTMIRWGLKPYLFVL
NNDGYTIEKLIHGPKAQYNEIQGWDHLSLLPTFGAKDYETHRVATTGEWD
KLTQDKSFNDNSKIRMIEIMLPVFDAPQNLVKQAKLT
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 chain1pyd Chain A Residue 557 [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]
PDB1pyd Catalytic centers in the thiamin diphosphate dependent enzyme pyruvate decarboxylase at 2.4-A resolution.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		T390 I415 G443 G445 S446 N471 G473 Y474 T475 I476 E477
Binding residue
(residue number reindexed from 1)		T371 I396 G424 G426 S427 N452 G454 Y455 T456 I457 E458
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) L25 G27 D28 F29 N30 E51 T73 H114 H115 L117 G118 A169 T266 T388 G413 I415 D444 N471 G473 Y474 I476 E477 I480 V542
Catalytic site (residue number reindexed from 1) L24 G26 D27 F28 N29 E50 T72 H105 H106 L108 G109 A160 T257 T369 G394 I396 D425 N452 G454 Y455 I457 E458 I461 V523
Enzyme Commision number 4.1.1.-
4.1.1.43: phenylpyruvate decarboxylase.
4.1.1.72: branched-chain-2-oxoacid decarboxylase.
4.1.1.74: indolepyruvate decarboxylase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0004737 pyruvate decarboxylase activity
GO:0005515 protein binding
GO:0016831 carboxy-lyase activity
GO:0030976 thiamine pyrophosphate binding
GO:0046872 metal ion binding
GO:0047433 branched-chain-2-oxoacid decarboxylase activity
GO:0047434 indolepyruvate decarboxylase activity
GO:0050177 phenylpyruvate decarboxylase activity
Biological Process
GO:0000949 aromatic amino acid family catabolic process to alcohol via Ehrlich pathway
GO:0000955 amino acid catabolic process via Ehrlich pathway
GO:0006090 pyruvate metabolic process
GO:0006559 L-phenylalanine catabolic process
GO:0006569 tryptophan catabolic process
GO:0009083 branched-chain amino acid catabolic process
GO:0019655 glycolytic fermentation to ethanol
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1pyd, PDBe:1pyd, PDBj:1pyd
PDBsum1pyd
PubMed8512926
UniProtP06169|PDC1_YEAST Pyruvate decarboxylase isozyme 1 (Gene Name=PDC1)

[Back to BioLiP]