Receptor
PDB id Resolution Class Description Source Keywords
4GV8 2.1 Å EC: 3.6.1.23 DUTPASE FROM PHAGE PHI11 OF S.AUREUS: VISUALIZATION OF THE S SPECIFIC INSERT STAPHYLOCOCCUS PHAGE 11 JELLY-ROLL HYDROLASE
Ref.: STRUCTURE AND ENZYMATIC MECHANISM OF A MOONLIGHTING ACTA CRYSTALLOGR.,SECT.D V. 69 2298 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DUP C:201;
E:201;
B:201;
A:201;
F:201;
D:201;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
Kd = 0.32 uM
467.157 C9 H16 N3 O13 P3 C1[C@...
MG B:202;
A:203;
E:202;
A:202;
F:202;
D:203;
C:202;
Invalid;
Part of Protein;
Invalid;
Invalid;
Invalid;
Part of Protein;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4GV8 2.1 Å EC: 3.6.1.23 DUTPASE FROM PHAGE PHI11 OF S.AUREUS: VISUALIZATION OF THE S SPECIFIC INSERT STAPHYLOCOCCUS PHAGE 11 JELLY-ROLL HYDROLASE
Ref.: STRUCTURE AND ENZYMATIC MECHANISM OF A MOONLIGHTING ACTA CRYSTALLOGR.,SECT.D V. 69 2298 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 4GV8 Kd = 0.32 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 217 families.
1 5NYZ - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
2 5CCO - UMP C9 H13 N2 O8 P C1[C@@H]([....
3 5CCT - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
4 4GV8 Kd = 0.32 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
50% Homology Family (26)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 181 families.
1 5NYZ - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
2 5CCO - UMP C9 H13 N2 O8 P C1[C@@H]([....
3 5CCT - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
4 4GV8 Kd = 0.32 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
5 3EHW - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
6 2HQU Kd = 1.6 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
7 3ARA ic50 = 0.32 uM MKH C24 H27 N3 O5 S c1ccc(cc1)....
8 3ARN ic50 = 3.9 uM MSJ C17 H23 N3 O5 S CC(C)(CCCO....
9 3P48 - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
10 1Q5H - DUD C9 H14 N2 O11 P2 C1[C@@H]([....
11 4OOP - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
12 1F7P - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
13 3F4F - UMP C9 H13 N2 O8 P C1[C@@H]([....
14 1DUC - DUD C9 H14 N2 O11 P2 C1[C@@H]([....
15 1SEH - UMP C9 H13 N2 O8 P C1[C@@H]([....
16 1DUD Ki = 15 uM DUD C9 H14 N2 O11 P2 C1[C@@H]([....
17 1SYL - DUT C9 H15 N2 O14 P3 C1[C@@H]([....
18 2HR6 Kd = 12 uM DUD C9 H14 N2 O11 P2 C1[C@@H]([....
19 2HRM Kd = 287.5 uM UC5 C10 H16 N2 O10 P2 C1[C@@H]([....
20 2OL0 - DUD C9 H14 N2 O11 P2 C1[C@@H]([....
21 2OKE - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
22 2OL1 - UMP C9 H13 N2 O8 P C1[C@@H]([....
23 3H6D - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
24 3HZA - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
25 3LOJ - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
26 1SMC - DUT C9 H15 N2 O14 P3 C1[C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DUP; Similar ligands found: 35
No: Ligand ECFP6 Tc MDL keys Tc
1 DUP 1 1
2 DUN 0.816901 1
3 DU 0.742857 0.956522
4 UMP 0.742857 0.956522
5 DUD 0.739726 0.971014
6 DUT 0.701299 0.971014
7 UC5 0.671053 0.957143
8 DUT MG 0.621951 0.876712
9 DUS 0.6 0.820513
10 UMP AF3 PO4 0.595238 0.842105
11 DUR 0.585714 0.842857
12 2KH 0.585366 0.915493
13 UM3 0.506329 0.914286
14 DU DU DU DU BRU DU DU 0.495238 0.831169
15 DDN 0.47561 0.956522
16 DU4 0.472527 0.730769
17 BRU 0.458824 0.891892
18 DDU 0.453333 0.722222
19 DUA 0.450549 0.776316
20 DU3 0.450549 0.773333
21 TYD 0.449438 0.930556
22 UFP 0.447059 0.891892
23 5HU 0.44186 0.930556
24 TMP 0.44186 0.916667
25 5IU 0.436782 0.891892
26 UNP 0.434783 0.915493
27 YYY 0.433333 0.90411
28 UDP 0.431818 0.887324
29 TTP 0.430108 0.930556
30 DC 0.425287 0.890411
31 DCM 0.425287 0.890411
32 UTP 0.417582 0.887324
33 DCP 0.414894 0.90411
34 U5P 0.411765 0.873239
35 BVP 0.408602 0.90411
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4GV8; Ligand: DUP; Similar sites found: 15
This union binding pocket(no: 1) in the query (biounit: 4gv8.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2FXV 5GP 0.009002 0.40919 1.77515
2 2CBZ ATP 0.01205 0.40594 2.36686
3 1UWK NAD 0.02865 0.40822 3.5503
4 1UWK URO 0.02865 0.40822 3.5503
5 1PZM 5GP 0.009736 0.41288 5.91716
6 1XMV ADP 0.004667 0.40155 5.91716
7 1XS1 DUT 0.00001235 0.53588 7.10059
8 5G5G FAD 0.0187 0.41404 7.54717
9 5G5G MCN 0.01623 0.41227 7.54717
10 1T3Q FAD 0.02547 0.40373 7.7381
11 4Z24 FAD 0.02165 0.41179 8.28402
12 1FFU FAD 0.01793 0.41017 8.87574
13 3HRD FAD 0.02016 0.41244 21.3018
14 4XJC TTP 0.000006484 0.54857 26.6272
15 3QF7 ANP 0.01729 0.40424 28
Pocket No.: 2; Query (leader) PDB : 4GV8; Ligand: DUP; 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: 4gv8.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4GV8; Ligand: DUP; 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: 4gv8.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4GV8; Ligand: DUP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 4gv8.bio2) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 4GV8; Ligand: DUP; Similar sites found: 14
This union binding pocket(no: 5) in the query (biounit: 4gv8.bio2) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1GTE IUR 0.02158 0.40418 2.95858
2 1GTE FMN 0.02158 0.40418 2.95858
3 4BGB ADP 0.006997 0.40723 5.91716
4 3MJY FMN 0.01336 0.41195 6.50888
5 3MJY IJZ 0.01336 0.41195 6.50888
6 1TDF NAP 0.04683 0.41127 6.50888
7 2ZJ1 NAD 0.03539 0.40732 7.69231
8 1V97 FAD 0.04628 0.40531 7.69231
9 2ZJ1 ARJ 0.04445 0.40228 7.69231
10 2B4G FMN 0.01271 0.40666 8.87574
11 2JB2 FAD 0.02795 0.40364 8.87574
12 2JB2 PHE 0.02915 0.40364 8.87574
13 3A4V PYR 0.02558 0.40266 12.426
14 3A4V NAD 0.02558 0.40266 12.426
Pocket No.: 6; Query (leader) PDB : 4GV8; Ligand: DUP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 4gv8.bio2) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Feedback