Structure of PDB 2vk1 Chain D Binding Site BS03

Receptor Information

>2vk1 Chain D (length=562) Species: 4932 (Saccharomyces cerevisiae)

SEITLGKYLFERLKQVNVNTVFGLPGAFNLSLLDKIYEVEGMRWAGNANE
LNAAYAADGYARIKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGV
PSISAQAKQLLLHHTLGNGDFTVFHRMSANISETTAMITDIATAPAEIDR
CIRTTYVTQRPVYLGLPANLVDLNVPAKLLQTPIDMSLKPNDAESEKEVI
DTILVLDKDAKNPVILADACCSRHDVKAETKKLIDLTQFPAFVTPMGKGS
IDEQHPRYGGVYVGTLSKPEVKEAVESADLILSVGALLSDFNTGSFSYSY
KTKNIVEFHSDHMKIRNATFPGVQMKFVLQKLLTAIADAAKGYKPVAVPA
RTPANAAVPASTPLKQEWMWNQLGNFLQEGDVVIAETGTSAFGINQTTFP
NNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTV
QEISTMIRWGLKPYLFVLNNDGYTIEKLIHGPKAQYNEIQGWDHLSLLPT
FGAKDYETHRVATTGEWDKLTQDKSFNDNSKIRMIEVMLPVFDAPQNLVE
QAKLTAATNAKQ

Ligand information

• Ligand ID: TPP
• InChI: InChI=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
• InChIKey: AYEKOFBPNLCAJY-UHFFFAOYSA-O
• SMILES:
  CACTVS 3.341: Cc1ncc(C[n+]2csc(CCO[P@@](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
  OpenEye OEToolkits 1.5.0: Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCO[P@](=O)(O)OP(=O)(O)O
  OpenEye OEToolkits 1.5.0: Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(O)OP(=O)(O)O
  CACTVS 3.341: Cc1ncc(C[n+]2csc(CCO[P](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCCc1sc[n+](c1C)Cc2c(nc(nc2)C)N
• Formula: C12 H19 N4 O7 P2 S
• Name: THIAMINE DIPHOSPHATE
• ChEMBL: CHEMBL1236376
• ZINC: ZINC000008215517
• PDB chain: 2vk1 Chain D Residue 600

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2vk1 Covalently Bound Substrate at the Regulatory Site of Yeast Pyruvate Decarboxylases Triggers Allosteric Enzyme Activation.
• Resolution: 1.71 Å
• Binding residue (original residue number in PDB): G389 T390 I415 G443 G445 S446 N471 G473 Y474 T475 I476 E477
• Binding residue (residue number reindexed from 1): G388 T389 I414 G442 G444 S445 N470 G472 Y473 T474 I475 E476
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): L25 G27 A28 F29 N30 E51 T73 H114 H115 L117 G118 A169 T266 N293 T388 G413 I415 D444 N471 G473 Y474 I476 E477 I480 V542
• Catalytic site (residue number reindexed from 1): L24 G26 A27 F28 N29 E50 T72 H113 H114 L116 G117 A168 T265 N292 T387 G412 I414 D443 N470 G472 Y473 I475 E476 I479 V541
• 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

External links

• PDB: RCSB:2vk1, PDBe:2vk1, PDBj:2vk1
• PDBsum: 2vk1
• PubMed: 19246454
• UniProt: P06169|PDC1_YEAST Pyruvate decarboxylase isozyme 1 (Gene Name=PDC1)