Receptor
PDB id Resolution Class Description Source Keywords
3AC9 2.1 Å EC: 3.6.1.13 CRYSTAL STRUCTURE OF HUMAN NUDT5 COMPLEXED WITH 8-OXO-DGDP A MANGANESE HOMO SAPIENS NUDIX MOTIF MAGNESIUM HYDROLASE-HYDROLASE INHIBITOR COMPLE
Ref.: DIVERSE SUBSTRATE RECOGNITION AND HYDROLYSIS MECHAN HUMAN NUDT5 NUCLEIC ACIDS RES. V. 39 8972 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
8GD A:2;
B:1;
 Valid;
Valid;
 none;
none;
 submit data
443.201 C10 H15 N5 O11 P2 C1[C@...
MN B:2;
B:209;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
54.938 Mn [Mn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5NQR 2.2 Å EC: 3.6.1.13 POTENT INHIBITORS OF NUDT5 SILENCE HORMONE SIGNALING IN BREA HOMO SAPIENS NUDIX INHIBITOR HYDROLASE
Ref.: TARGETED NUDT5 INHIBITORS BLOCK HORMONE SIGNALING I CANCER CELLS. NAT COMMUN V. 9 250 2018
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 3AC9 - 8GD C10 H15 N5 O11 P2 C1[C@@H]([....
2 3L85 - 8OG C10 H14 N5 O8 P C1[C@@H]([....
3 3ACA - 8DD C10 H15 N5 O10 P2 c1nc(c2c(n....
4 2DSC - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
5 5NQR ic50 = 70 nM 958 C19 H21 N7 O3 Cc1cccc(c1....
6 3BM4 - ADV C16 H25 N5 O13 P2 c1nc(c2c(n....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 3AC9 - 8GD C10 H15 N5 O11 P2 C1[C@@H]([....
2 3L85 - 8OG C10 H14 N5 O8 P C1[C@@H]([....
3 3ACA - 8DD C10 H15 N5 O10 P2 c1nc(c2c(n....
4 2DSC - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
5 5NQR ic50 = 70 nM 958 C19 H21 N7 O3 Cc1cccc(c1....
6 3BM4 - ADV C16 H25 N5 O13 P2 c1nc(c2c(n....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 3AC9 - 8GD C10 H15 N5 O11 P2 C1[C@@H]([....
2 3L85 - 8OG C10 H14 N5 O8 P C1[C@@H]([....
3 3ACA - 8DD C10 H15 N5 O10 P2 c1nc(c2c(n....
4 2DSC - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
5 5NQR ic50 = 70 nM 958 C19 H21 N7 O3 Cc1cccc(c1....
6 3BM4 - ADV C16 H25 N5 O13 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 8GD; Similar ligands found: 18
No: Ligand ECFP6 Tc MDL keys Tc
1 8GD 1 1
2 8DG 0.897436 1
3 8OG 0.815789 0.9875
4 8HG 0.706667 0.901235
5 G8D 0.613636 0.95
6 8GT 0.565217 0.95
7 8DD 0.520833 0.845238
8 8GM 0.494505 0.9375
9 YYY 0.483516 0.875
10 DUD 0.477778 0.8375
11 F6G 0.473684 0.841463
12 TYD 0.467391 0.829268
13 DGI 0.44 0.857143
14 DCP 0.43299 0.875
15 DUT 0.427083 0.8375
16 TTP 0.418367 0.829268
17 6U4 0.409524 0.95
18 M7G 0.407767 0.872093
Similar Ligands (3D)
Ligand no: 1; Ligand: 8GD; Similar ligands found: 14
No: Ligand Similarity coefficient
1 ADP 0.9252
2 GDP 0.9250
3 GDP MG 0.9049
4 DAT 0.8912
5 IDP 0.8816
6 A12 0.8779
7 O02 0.8740
8 KG4 0.8721
9 ADX 0.8721
10 6AD 0.8715
11 UDP 0.8708
12 DGT 0.8707
13 CA0 0.8698
14 AP2 0.8604
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5NQR; Ligand: 958; 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: 5nqr.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5NQR; Ligand: 958; 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: 5nqr.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5NQR; Ligand: 958; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5nqr.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
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