Receptor
PDB id Resolution Class Description Source Keywords
2VK1 1.71 Å EC: 4.1.1.1 CRYSTAL STRUCTURE OF THE SACCHAROMYCES CEREVISIAE PYRUVATE DECARBOXYLASE VARIANT D28A IN COMPLEX WITH ITS SUBSTRATE SACCHAROMYCES CEREVISIAE ASYMMETRIC ACTIVE SITES PHENYLALANINE CATABOLISM TRYPTOPHACATABOLISM THIAMINE PYROPHOSPHATE DIMER OF DIMERS PHOSPHORYLATION ALLOSTERIC ENZYME TDP TPP LYASE NUCLEUPYRUVATE CYTOPLASM BRANCHED-CHAIN AMINO ACID CATABOLISM ACTIVATION THIAMINE DIPHOSPHATE MAGNESIUM ACETYLATION MBINDING DECARBOXYLASE
Ref.: COVALENTLY BOUND SUBSTRATE AT THE REGULATORY SITE O PYRUVATE DECARBOXYLASES TRIGGERS ALLOSTERIC ENZYME ACTIVATION. J.BIOL.CHEM. V. 284 12136 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:601;
B:601;
C:601;
D:601;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
 submit data
24.305 Mg [Mg+2...
PYR A:603;
B:603;
C:603;
D:603;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
88.062 C3 H4 O3 CC(=O...
TPP PYR A:600;
B:600;
C:600;
D:600;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 submit data
509.349 n/a P(=O)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1QPB 2.4 Å EC: 4.1.1.1 PYRUVATE DECARBOYXLASE FROM YEAST (FORM B) COMPLEXED WITH PYRUVAMIDE SACCHAROMYCES PASTORIANUS THIAMINE PYRUVATE PYRUVAMIDE LYASE
Ref.: THE STRUCTURAL BASIS OF SUBSTRATE ACTIVATION IN YEAST PYRUVATE DECARBOXYLASE A CRYSTALLOGRAPHIC AND KINETIC STUDY EUR.J.BIOCHEM. V. 267 861 2000
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2VK8 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
2 1PYD - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
3 1QPB Kd = 44 mM PYM C3 H5 N O2 CC(=O)C(=O....
4 2VK1 - TPP PYR n/a n/a
5 1PVD - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2VK8 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
2 1PYD - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
3 1QPB Kd = 44 mM PYM C3 H5 N O2 CC(=O)C(=O....
4 2VK1 - TPP PYR n/a n/a
5 1PVD - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
6 6EFG - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
7 2VK4 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
8 2VJY - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
50% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2VK8 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
2 1PYD - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
3 1QPB Kd = 44 mM PYM C3 H5 N O2 CC(=O)C(=O....
4 2VK1 - TPP PYR n/a n/a
5 1PVD - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
6 2VBG - R1T C15 H23 N3 O8 P2 S Cc1c(sc(c1....
7 2VBF - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
8 2WVG - TPU C11 H18 N6 O7 P2 Cc1c(nnn1C....
9 3OE1 - TDL C15 H23 N4 O10 P2 S Cc1c(sc([n....
10 2WVA - PYR C3 H4 O3 CC(=O)C(=O....
11 1ZPD - DPX C11 H20 N4 O8 P2 S Cc1ncc(c(n....
12 6EFG - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
13 2VK4 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
14 2VJY - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: TPP PYR; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 TPP PYR 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: TPP PYR; Similar ligands found: 16
No: Ligand Similarity coefficient
1 TDL 0.9845
2 AUJ 0.9548
3 R1T 0.9309
4 TDK 0.9174
5 1TP 0.9030
6 8N9 0.8975
7 HTL 0.8944
8 TDM 0.8906
9 5SR 0.8826
10 THD 0.8807
11 O2T 0.8796
12 TDN 0.8783
13 S1T 0.8775
14 TD6 0.8671
15 1U0 0.8636
16 HE3 0.8601
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1QPB; Ligand: TPP; Similar sites found with APoc: 10
This union binding pocket(no: 1) in the query (biounit: 1qpb.bio2) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 5WKC TP9 36.7673
2 5WKC TP9 36.7673
3 1T9D 1MM 36.7673
4 1T9D P25 36.7673
5 1T9D FAD 36.7673
6 1T9D PYD 36.7673
7 1T9D 1MM 36.7673
8 1T9D P25 36.7673
9 1T9D FAD 36.7673
10 1T9D PYD 36.7673
Pocket No.: 2; Query (leader) PDB : 1QPB; Ligand: TPP; Similar sites found with APoc: 2
This union binding pocket(no: 2) in the query (biounit: 1qpb.bio2) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 2NXW TPP 42.0959
2 2NXW TPP 42.0959
Pocket No.: 3; Query (leader) PDB : 1QPB; Ligand: PYM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 1qpb.bio2) has 8 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1QPB; Ligand: PYM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 1qpb.bio2) has 27 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 1QPB; Ligand: TPP; Similar sites found with APoc: 8
This union binding pocket(no: 5) in the query (biounit: 1qpb.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 1T9D FAD 36.7673
2 1T9D 1MM 36.7673
3 1T9D PYD 36.7673
4 1T9D P25 36.7673
5 1T9D FAD 36.7673
6 1T9D PYD 36.7673
7 1T9D P25 36.7673
8 1T9D 1MM 36.7673
Pocket No.: 6; Query (leader) PDB : 1QPB; Ligand: TPP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 1qpb.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 1QPB; Ligand: TPP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 1qpb.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 1QPB; Ligand: TPP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 1qpb.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 1QPB; Ligand: PYM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 9) in the query (biounit: 1qpb.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 10; Query (leader) PDB : 1QPB; Ligand: PYM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 10) in the query (biounit: 1qpb.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 11; Query (leader) PDB : 1QPB; Ligand: PYM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 11) in the query (biounit: 1qpb.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 12; Query (leader) PDB : 1QPB; Ligand: PYM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 12) in the query (biounit: 1qpb.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
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