Receptor
PDB id Resolution Class Description Source Keywords
3DVA 2.35 Å EC: 1.2.4.1 SNAPSHOTS OF CATALYSIS IN THE E1 SUBUNIT OF THE PYRUVATE DEHYDROGENASE MULTI-ENZYME COMPLEX BACILLUS STEAROTHERMOPHILUS OXIDOREDUCTASE PYRUVATE DEHYDROGENASE DIHYDROLIPOYL ACETYL TRANSFERASE MULTIENZYME COMPLEX TRANSFERASE GLYCOLYSIS PHOSPHOPROTEIN THIAMINE PYROPHOSPHATE ACYLTRANSFERASE OXIDOREDUCTASE/TRANSFERASE COMPLEX
Ref.: SNAPSHOTS OF CATALYSIS IN THE E1 SUBUNIT OF THE PYRUVATE DEHYDROGENASE MULTIENZYME COMPLEX STRUCTURE V. 16 1860 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
K B:1325;
D:1325;
Part of Protein;
Part of Protein;
none;
none;
submit data
39.098 K [K+]
MG A:1326;
A:1368;
C:1368;
E:369;
E:370;
G:369;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
TPW A:1370;
C:1370;
E:1370;
G:1370;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
423.318 C13 H19 N3 O7 P2 S Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3DVA 2.35 Å EC: 1.2.4.1 SNAPSHOTS OF CATALYSIS IN THE E1 SUBUNIT OF THE PYRUVATE DEHYDROGENASE MULTI-ENZYME COMPLEX BACILLUS STEAROTHERMOPHILUS OXIDOREDUCTASE PYRUVATE DEHYDROGENASE DIHYDROLIPOYL ACETYL TRANSFERASE MULTIENZYME COMPLEX TRANSFERASE GLYCOLYSIS PHOSPHOPROTEIN THIAMINE PYROPHOSPHATE ACYLTRANSFERASE OXIDOREDUCTASE/TRANSFERASE COMPLEX
Ref.: SNAPSHOTS OF CATALYSIS IN THE E1 SUBUNIT OF THE PYRUVATE DEHYDROGENASE MULTIENZYME COMPLEX STRUCTURE V. 16 1860 2008
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3DUF - R1T C15 H23 N3 O8 P2 S Cc1c(sc(c1....
2 3DVA - TPW C13 H19 N3 O7 P2 S Cc1c(csc1C....
3 3DV0 - PYR C3 H4 O3 CC(=O)C(=O....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3DUF - R1T C15 H23 N3 O8 P2 S Cc1c(sc(c1....
2 3DVA - TPW C13 H19 N3 O7 P2 S Cc1c(csc1C....
3 3DV0 - PYR C3 H4 O3 CC(=O)C(=O....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3DUF - R1T C15 H23 N3 O8 P2 S Cc1c(sc(c1....
2 3DVA - TPW C13 H19 N3 O7 P2 S Cc1c(csc1C....
3 3DV0 - PYR C3 H4 O3 CC(=O)C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TPW; Similar ligands found: 35
No: Ligand ECFP6 Tc MDL keys Tc
1 TPW 1 1
2 S1T 0.574713 0.984375
3 R1T 0.574713 0.984375
4 1U0 0.555556 0.926471
5 TPP 0.546512 0.9
6 HTL 0.516484 0.863014
7 TDW 0.516484 0.875
8 WWF 0.510638 0.84
9 V4E 0.48913 0.9
10 THV 0.484211 0.863014
11 TPU 0.482759 0.821918
12 TD6 0.48 0.828947
13 TOG 0.474747 0.828947
14 THY 0.474227 0.851351
15 TD9 0.470588 0.828947
16 TD8 0.470588 0.828947
17 THW 0.47 0.863014
18 TDL 0.469388 0.807692
19 TZD 0.466667 0.815789
20 TDK 0.464646 0.828947
21 PYI 0.461538 0.84058
22 TDM 0.457447 0.826667
23 TDP 0.451613 0.885714
24 D7K 0.435185 0.818182
25 T6F 0.435185 0.807692
26 5SR 0.43299 0.849315
27 8PA 0.432432 0.851351
28 TDN 0.428571 0.805195
29 MP5 0.424658 0.723077
30 THD 0.424242 0.775
31 T5X 0.422018 0.807692
32 2TP 0.421053 0.837838
33 TD7 0.417476 0.78481
34 TPS 0.41573 0.857143
35 TMV 0.40625 0.861111
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3DVA; Ligand: TPW; Similar sites found: 43
This union binding pocket(no: 1) in the query (biounit: 3dva.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2R5N R5P 0.0000006642 0.56602 4.06504
2 2R5N RP5 0.0000007542 0.56559 4.06504
3 2R5N TPP 0.0000008875 0.56088 4.06504
4 1OZH HE3 0.0006924 0.46486 4.20561
5 3AI7 TPP 0.00000005925 0.59289 4.60705
6 3AHC TPP 0.0002148 0.45904 4.87805
7 5EXE 5SR 0.001135 0.42991 5.06329
8 2NXW TPP 0.0001033 0.47503 5.14019
9 4REP FAD 0.007276 0.40753 5.14019
10 5ESO TDP 0.001235 0.43382 5.69106
11 5ESO ISC 0.001235 0.43382 5.69106
12 3IAE D7K 0.00008837 0.47621 6.15385
13 2UZ1 TPP 0.00005622 0.47529 6.15385
14 1ZPD DPX 0.001316 0.42586 6.15385
15 2VK4 TPP 0.0004248 0.4406 6.30841
16 2IHT TPP 0.0005378 0.43655 6.45724
17 1UPA TPP 0.0005394 0.4365 6.45724
18 4AQ0 DMJ 0.02971 0.40584 6.46154
19 2PHW MAN MAN MAN BMA MAN MAN MAN 0.02237 0.40424 6.74603
20 2PHT MAN MAN MAN BMA MAN 0.02407 0.40264 6.74603
21 1Q8S MAN MMA 0.02856 0.40106 6.74603
22 1T9D P22 0.008794 0.43368 7.00935
23 1T9D PYD 0.006759 0.4259 7.00935
24 1QPB TPP 0.0007514 0.43247 7.58808
25 1QPB PYM 0.0007514 0.43247 7.58808
26 3Q3H UDP 0.02362 0.41111 7.69231
27 2X7J TPP 0.0003645 0.44322 9.23077
28 4K79 GAL A2G 0.03565 0.40164 10
29 1TKB N1T 0.0000005527 0.57112 10.2981
30 2C42 PYR 0.002438 0.41651 10.4615
31 2C42 TPP 0.002438 0.41651 10.4615
32 2VBF TPP 0.000307 0.45122 12.3077
33 3EYA TDP 0.0002279 0.45128 13.2791
34 2C31 ADP 0.0035 0.44303 15.6923
35 2C31 TZD 0.00391 0.44148 15.6923
36 4KXV TDP DX5 0.00006369 0.4094 16
37 4RJK TPP 0.0001127 0.45292 16.8022
38 4RJK TDL 0.00009058 0.44668 16.8022
39 1R9J TPP 0.0000004134 0.5713 17.0732
40 5ND5 TPP 0.0000002086 0.55968 20
41 2YIC TPP 0.0000000002276 0.66364 22.7642
42 1ITZ TPP 0.0000001733 0.58678 25.2308
43 2O1S TDP 0.00001306 0.45817 32.6154
Pocket No.: 2; Query (leader) PDB : 3DVA; Ligand: TPW; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3dva.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3DVA; Ligand: TPW; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3dva.bio2) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3DVA; Ligand: TPW; Similar sites found: 3
This union binding pocket(no: 4) in the query (biounit: 3dva.bio2) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4XWM CBK 0.03138 0.40407 5.37383
2 1Q8Q MAN MMA 0.02346 0.40602 6.74603
3 2Q28 TPP 0.003572 0.40693 10.1538
Feedback