Receptor
PDB id Resolution Class Description Source Keywords
1W85 2 Å EC: 1.2.4.1 THE CRYSTAL STRUCTURE OF PYRUVATE DEHYDROGENASE E1 BOUND TO THE PERIPHERAL SUBUNIT BINDING DOMAIN OF E2 GEOBACILLUS STEAROTHERMOPHILUS PYRUVATE DEHYDROGENASE DIHYDROLIPOYL ACETYL TRANSFERASE MULTIENZYME COMPLEX OXIDOREDUCTASE TRANSFERASE
Ref.: A MOLECULAR SWITCH AND PROTON WIRE SYNCHRONIZE THE ACTIVE SITES IN THIAMINE ENZYMES SCIENCE V. 306 872 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
K B:1325;
D:1325;
F:1325;
H:1325;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
39.098 K [K+]
MG A:1368;
B:1326;
C:1368;
E:1368;
F:1326;
G:1368;
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...
PEG A:1369;
C:1369;
G:1369;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
106.12 C4 H10 O3 C(COC...
TDP A:1370;
C:1370;
E:1370;
G:1370;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
424.306 C12 H18 N4 O7 P2 S Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1W85 2 Å EC: 1.2.4.1 THE CRYSTAL STRUCTURE OF PYRUVATE DEHYDROGENASE E1 BOUND TO THE PERIPHERAL SUBUNIT BINDING DOMAIN OF E2 GEOBACILLUS STEAROTHERMOPHILUS PYRUVATE DEHYDROGENASE DIHYDROLIPOYL ACETYL TRANSFERASE MULTIENZYME COMPLEX OXIDOREDUCTASE TRANSFERASE
Ref.: A MOLECULAR SWITCH AND PROTON WIRE SYNCHRONIZE THE ACTIVE SITES IN THIAMINE ENZYMES SCIENCE V. 306 872 2004
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1W88 - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
2 1W85 - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1W88 - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
2 1W85 - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1W88 - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
2 1W85 - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TDP; Similar ligands found: 32
No: Ligand ECFP6 Tc MDL keys Tc
1 TDP 1 1
2 TPP 0.84 0.985714
3 V4E 0.797468 0.985714
4 TPS 0.77027 0.942857
5 TMV 0.75 0.944444
6 VNP 0.703704 0.945205
7 N1T 0.674699 1
8 2TP 0.609195 0.918919
9 VIB 0.605263 0.760563
10 5SR 0.582418 0.958333
11 FTP 0.574713 0.847222
12 O2T 0.546392 0.896104
13 PYI 0.483871 0.873239
14 TDW 0.474227 0.958333
15 HTL 0.474227 0.945205
16 THV 0.46 0.945205
17 TD6 0.457143 0.907895
18 WWF 0.455446 0.92
19 TOG 0.451923 0.907895
20 TPW 0.451613 0.885714
21 THY 0.45098 0.932432
22 TD9 0.448598 0.907895
23 TD8 0.448598 0.907895
24 THW 0.447619 0.945205
25 TDL 0.446602 0.884615
26 TDK 0.442308 0.907895
27 D7K 0.415929 0.896104
28 TPU 0.410526 0.828947
29 R1T 0.405941 0.873239
30 S1T 0.405941 0.873239
31 T6F 0.403509 0.884615
32 T5X 0.403509 0.884615
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1W85; Ligand: TDP; Similar sites found: 49
This union binding pocket(no: 1) in the query (biounit: 1w85.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1T9D P22 0.008086 0.42922 4.93827
2 1T9D PYD 0.007356 0.4177 4.93827
3 5AB1 BCD TA5 HP6 MAN 0.02603 0.40467 5.33333
4 2NXW TPP 0.0000558 0.50373 6.12245
5 4FMS BDP 0.02912 0.40353 6.12245
6 1YBH P22 0.005109 0.42969 7.88043
7 3GDN FAD 0.02192 0.40072 8.16327
8 3GDN HBX 0.02973 0.40072 8.16327
9 2X7J TPP 0.0005352 0.42261 9.25926
10 3Q9T FAY 0.01424 0.40468 9.51087
11 3KO0 TFP 0.02942 0.40351 9.90099
12 2Q28 TPP 0.004553 0.41178 10.1852
13 2UZ1 TPP 0.00002929 0.46654 10.2041
14 1ZPD DPX 0.001424 0.43796 10.2041
15 3IAE D7K 0.00004801 0.43066 10.2041
16 1TKB N1T 0.000001458 0.57661 10.5978
17 1R9J TPP 0.0000004421 0.55346 12.2449
18 2G77 AF3 0.01266 0.42057 12.2449
19 2VBF TPP 0.0003009 0.46714 12.3457
20 5EW0 3C7 0.02813 0.40123 13.6752
21 2IHT TPP 0.00034 0.45983 14.2857
22 3EYA TDP 0.0001513 0.44079 14.2857
23 1UPA TPP 0.0002667 0.43385 14.2857
24 2C31 ADP 0.001944 0.46756 15.7407
25 2C31 TZD 0.002042 0.46716 15.7407
26 4KXV TDP DX5 0.00002523 0.40433 16.0494
27 2C42 PYR 0.002303 0.43034 16.3265
28 3Q3H UDP 0.01746 0.41197 18.3673
29 5CAD PCA 0.01825 0.40597 18.3673
30 1Q8Q MAN MMA 0.02013 0.40384 18.3673
31 1Q8S MAN MMA 0.02182 0.40258 18.3673
32 5ND5 TPP 0.000000291 0.56003 20.0617
33 3AI7 TPP 0.00000002706 0.63446 22.449
34 2R5N TPP 0.0000009105 0.58381 22.449
35 2R5N R5P 0.0000009629 0.58274 22.449
36 2R5N RP5 0.000001137 0.58136 22.449
37 2VK4 TPP 0.0003396 0.45985 22.449
38 4RJK TPP 0.00008491 0.44378 22.449
39 4RJK TDL 0.00007879 0.43321 22.449
40 1QPB TPP 0.0007245 0.41451 22.449
41 1QPB PYM 0.0007245 0.41451 22.449
42 2YIC TPP 0.000000004306 0.58567 22.8261
43 3AHC TPP 0.00003583 0.50882 24.4898
44 1V5F FAD 0.01476 0.4217 24.4898
45 5TCI MLI 0.02916 0.40367 24.4898
46 1ITZ TPP 0.0000002378 0.56347 25.3086
47 5EXE 5SR 0.0005038 0.40055 30.6122
48 2O1S TDP 0.00001478 0.48467 32.716
49 1FL2 FAD 0.01378 0.40629 36.7347
Pocket No.: 2; Query (leader) PDB : 1W85; Ligand: TDP; 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: 1w85.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1W85; Ligand: TDP; 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: 1w85.bio2) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1W85; Ligand: TDP; Similar sites found: 3
This union binding pocket(no: 4) in the query (biounit: 1w85.bio2) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2VZ6 FEF 0.01951 0.40119 14.2857
2 5CXX FER 0.02153 0.40304 16.3265
3 2E5V FAD 0.01766 0.4067 46.9388
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