Receptor
PDB id Resolution Class Description Source Keywords
5HVA 2.1 Å EC: 3.6.1.19 CRYSTAL STRUCTURE OF DR2231 IN COMPLEX WITH DUMPNPP AND MAGN DEINOCOCCUS RADIODURANS ALPHA HELIX HYDROLASE
Ref.: DEINOCOCCUS RADIODURANS DR2231 IS A TWO-METAL-ION M HYDROLASE WITH EXCLUSIVE ACTIVITY ON DUTP. FEBS J. V. 283 4274 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DUP C:201;
D:201;
Valid;
Valid;
Atoms found MORE than expected: % Diff = 2;
Atoms found MORE than expected: % Diff = 2;
Kd = 0.086 uM
467.157 C9 H16 N3 O13 P3 C1[C@...
MG C:202;
D:202;
C:203;
D:203;
B:201;
A:201;
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...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5HVA 2.1 Å EC: 3.6.1.19 CRYSTAL STRUCTURE OF DR2231 IN COMPLEX WITH DUMPNPP AND MAGN DEINOCOCCUS RADIODURANS ALPHA HELIX HYDROLASE
Ref.: DEINOCOCCUS RADIODURANS DR2231 IS A TWO-METAL-ION M HYDROLASE WITH EXCLUSIVE ACTIVITY ON DUTP. FEBS J. V. 283 4274 2016
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2YFD - UMP C9 H13 N2 O8 P C1[C@@H]([....
2 5HZZ - UMP C9 H13 N2 O8 P C1[C@@H]([....
3 5HYL - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
4 5HWU Kd = 5.35 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
5 5I0M - UMP C9 H13 N2 O8 P C1[C@@H]([....
6 2YFC - UMP C9 H13 N2 O8 P C1[C@@H]([....
7 5HVA Kd = 0.086 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
8 5I0J - UMP C9 H13 N2 O8 P C1[C@@H]([....
70% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2YFD - UMP C9 H13 N2 O8 P C1[C@@H]([....
2 5HZZ - UMP C9 H13 N2 O8 P C1[C@@H]([....
3 5HYL - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
4 5HWU Kd = 5.35 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
5 5I0M - UMP C9 H13 N2 O8 P C1[C@@H]([....
6 2YFC - UMP C9 H13 N2 O8 P C1[C@@H]([....
7 5HVA Kd = 0.086 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
8 5I0J - UMP C9 H13 N2 O8 P C1[C@@H]([....
9 5HX1 - UMP C9 H13 N2 O8 P C1[C@@H]([....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2YFD - UMP C9 H13 N2 O8 P C1[C@@H]([....
2 5HZZ - UMP C9 H13 N2 O8 P C1[C@@H]([....
3 5HYL - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
4 5HWU Kd = 5.35 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
5 5I0M - UMP C9 H13 N2 O8 P C1[C@@H]([....
6 2YFC - UMP C9 H13 N2 O8 P C1[C@@H]([....
7 5HVA Kd = 0.086 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
8 5I0J - UMP C9 H13 N2 O8 P C1[C@@H]([....
9 5HX1 - UMP C9 H13 N2 O8 P C1[C@@H]([....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: DUP; Similar ligands found: 39
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 0.62963 0.914286
9 0KX 0.614458 0.931507
10 DUS 0.6 0.820513
11 UMP AF3 PO4 0.595238 0.842105
12 DUR 0.585714 0.842857
13 2KH 0.585366 0.915493
14 UM3 0.506329 0.914286
15 DU DU DU DU BRU DU DU 0.495238 0.831169
16 DDN 0.47561 0.956522
17 DU4 0.472527 0.730769
18 BRU 0.458824 0.891892
19 DDU 0.453333 0.722222
20 DU3 0.450549 0.773333
21 DUA 0.450549 0.776316
22 TYD 0.449438 0.930556
23 UFP 0.447059 0.891892
24 TMP 0.44186 0.916667
25 5HU 0.44186 0.930556
26 5IU 0.436782 0.891892
27 UNP 0.434783 0.915493
28 YYY 0.433333 0.90411
29 UDP 0.431818 0.887324
30 TTP 0.430108 0.930556
31 DCM 0.425287 0.890411
32 DC 0.425287 0.890411
33 UTP 0.417582 0.887324
34 DCP 0.414894 0.90411
35 U5F 0.413043 0.887324
36 U 0.411765 0.873239
37 U5P 0.411765 0.873239
38 BVP 0.408602 0.90411
39 DZ4 0.40404 0.820513
Similar Ligands (3D)
Ligand no: 1; Ligand: DUP; Similar ligands found: 14
No: Ligand Similarity coefficient
1 MG TTP 0.9430
2 ANP 0.9039
3 7D4 0.8940
4 FZQ 0.8841
5 2TM 0.8798
6 CTP 0.8797
7 ATP 0.8755
8 FZK 0.8750
9 3AT 0.8719
10 HF4 0.8636
11 AHX 0.8630
12 AGS 0.8579
13 ACP 0.8558
14 8DG 0.8512
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5HVA; Ligand: DUP; 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: 5hva.bio1) has 49 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5HVA; Ligand: DUP; 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: 5hva.bio2) has 47 residues
No: Leader PDB Ligand Sequence Similarity
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