Receptor
PDB id Resolution Class Description Source Keywords
2G25 2.1 Å EC: 1.2.4.1 E. COLI PYRUVATE DEHYDROGENASE PHOSPHONOLACTYLTHIAMIN DIPHOS COMPLEX ESCHERICHIA COLI PLTHDP PHOSPHONOLACTYLTHIAMIN DIPHOSPHATE PYRUVATE DEHYDROCOMPONENT OXIDOREDUCTASE
Ref.: A THIAMIN-BOUND, PRE-DECARBOXYLATION REACTION INTER ANALOGUE IN THE PYRUVATE DEHYDROGENASE E1 SUBUNIT I LARGE SCALE DISORDER-TO-ORDER TRANSFORMATIONS IN TH AND REVEALS NOVEL STRUCTURAL FEATURES IN THE COVALE BOUND ADDUCT. J.BIOL.CHEM.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:888;
B:888;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
24.305 Mg [Mg+2...
PO4 A:889;
A:890;
B:889;
B:890;
B:891;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
94.971 O4 P [O-]P...
TDK A:887;
B:887;
 Valid;
Valid;
 none;
none;
 submit data
563.373 C15 H26 N4 O11 P3 S Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1RP7 2.09 Å EC: 1.2.4.1 E. COLI PYRUVATE DEHYDROGENASE INHIBITOR COMPLEX ESCHERICHIA COLI, ESCHERICHIA COLI O157:H7 THDP THIAMIN-THIAZOLONE DIPHOSPHATE PYRUVATE DEHYDROGENASE OXIDOREDUCTASE
Ref.: STRUCTURAL DETERMINANTS OF ENZYME BINDING AFFINITY: THE E1 COMPONENT OF PYRUVATE DEHYDROGENASE FROM ESCHERICHIA COLI IN COMPLEX WITH THE INHIBITOR THIAMIN THIAZOLONE DIPHOSPHATE. BIOCHEMISTRY V. 43 2405 2004
Members (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3LQ4 Kd = 5.97 uM TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
2 2G25 - TDK C15 H26 N4 O11 P3 S Cc1c(sc([n....
3 2QTA Kd = 1.75 uM TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
4 2IEA - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
5 1L8A - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
6 1RP7 Ki > 0.003 uM TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
7 2G28 - TDK C15 H26 N4 O11 P3 S Cc1c(sc([n....
8 3LQ2 Kd = 5.97 uM TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
9 2QTC - TDK C15 H26 N4 O11 P3 S Cc1c(sc([n....
10 3LPL Kd = 2.39 uM TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
70% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3LQ4 Kd = 5.97 uM TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
2 2G25 - TDK C15 H26 N4 O11 P3 S Cc1c(sc([n....
3 2QTA Kd = 1.75 uM TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
4 2IEA - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
5 1L8A - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
6 1RP7 Ki > 0.003 uM TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
7 2G28 - TDK C15 H26 N4 O11 P3 S Cc1c(sc([n....
8 3LQ2 Kd = 5.97 uM TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
9 2QTC - TDK C15 H26 N4 O11 P3 S Cc1c(sc([n....
10 3LPL Kd = 2.39 uM TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3LQ4 Kd = 5.97 uM TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
2 2G25 - TDK C15 H26 N4 O11 P3 S Cc1c(sc([n....
3 2QTA Kd = 1.75 uM TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
4 2IEA - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
5 1L8A - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
6 1RP7 Ki > 0.003 uM TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
7 2G28 - TDK C15 H26 N4 O11 P3 S Cc1c(sc([n....
8 3LQ2 Kd = 5.97 uM TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
9 2QTC - TDK C15 H26 N4 O11 P3 S Cc1c(sc([n....
10 3LPL Kd = 2.39 uM TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: TDK; Similar ligands found: 38
No: Ligand ECFP6 Tc MDL keys Tc
1 TDK 1 1
2 AUJ 0.744444 0.974026
3 TDL 0.728261 0.949367
4 D7K 0.7 0.987013
5 T6F 0.634615 0.949367
6 T5X 0.634615 0.949367
7 O2T 0.616162 0.961538
8 HTL 0.610526 0.935065
9 TDW 0.610526 0.947368
10 THV 0.608247 0.935065
11 WWF 0.602041 0.911392
12 THY 0.59596 0.923077
13 TD6 0.567308 0.9
14 TOG 0.563107 0.9
15 THW 0.557692 0.935065
16 TD9 0.556604 0.9
17 TD8 0.556604 0.9
18 TPP 0.525773 0.921053
19 5SR 0.524752 0.897436
20 8PA 0.5 0.923077
21 V4E 0.490196 0.921053
22 TDP DX5 0.474138 0.924051
23 PYI 0.465347 0.818182
24 TPW 0.464646 0.828947
25 1Y7 TDP 0.458333 0.924051
26 1U0 0.448598 0.846154
27 S1T 0.447619 0.842105
28 R1T 0.447619 0.842105
29 TDP 0.442308 0.907895
30 8EO 0.432692 0.851852
31 TPU 0.425743 0.802469
32 8FL 0.419048 0.829268
33 NDQ 0.415094 0.888889
34 TPS 0.41 0.881579
35 8EL 0.40566 0.829268
36 2TP 0.401869 0.886076
37 TMV 0.401869 0.884615
38 TZD 0.4 0.819277
Similar Ligands (3D)
Ligand no: 1; Ligand: TDK; Similar ligands found: 6
No: Ligand Similarity coefficient
1 TPP PYR 0.9174
2 TDM 0.8792
3 QSP 0.8725
4 1TP 0.8712
5 THD 0.8625
6 8N9 0.8560
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1RP7; Ligand: TZD; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 1rp7.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1RP7; Ligand: TZD; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 1rp7.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
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