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Receptor
PDB id Resolution Class Description Source Keywords
3ACA 2.05 Å EC: 3.6.1.13 CRYSTAL STRUCTURE OF HUMAN NUDT5 COMPLEXED WITH 8-OXO-DADP 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
8DD A:2;
B:209;
Valid;
Valid;
none;
none;
submit data
427.201 C10 H15 N5 O10 P2 c1nc(...
MN A:3;
A:4;
A:5;
B:1;
B:2;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
submit data
54.938 Mn [Mn+2...
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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 5 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 5 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 5 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
Ligand no: 1; Ligand: 8DD; Similar ligands found: 16
No: Ligand ECFP6 Tc MDL keys Tc
1 8DD 1 1
2 8OD 0.629214 0.934211
3 H6Y 0.574468 0.934211
4 8GD 0.520833 0.845238
5 8OP 0.505376 0.921053
6 8OX 0.5 0.805195
7 TYD 0.473118 0.8125
8 8DG 0.470588 0.845238
9 DUD 0.467391 0.844156
10 YYY 0.457447 0.835443
11 TTP 0.424242 0.8125
12 DAT 0.42 0.921053
13 DUT 0.418367 0.844156
14 6U4 0.415094 0.841463
15 DCP 0.41 0.835443
16 8OG 0.4 0.833333
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: 47
This union binding pocket(no: 1) in the query (biounit: 5nqr.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 1KSK URA 1.36986
2 2VEG PMM 1.82648
3 1L7N AF3 1.89573
4 3R7F CP 2.28311
5 4JX1 CAM 2.73973
6 3UB7 ACM 2.76243
7 4JGP PYR 2.76498
8 2UVO NAG 2.92398
9 5YBL AKG 3.19635
10 5CGE 51F 3.19635
11 3FSM 2NC 3.44828
12 5J8Q ALA 3.65297
13 5HWK BEZ 3.65297
14 5LV1 78T 4.28571
15 5UC4 83S 4.54545
16 5IXB LGA 4.62963
17 1LNX URI 4.93827
18 5BRP PNG 5.02283
19 3W9F I3P 5.47945
20 2XHK AKG 5.47945
21 4J7H TLO 5.93607
22 4K7O EKZ 5.95238
23 5E13 5J9 6.8323
24 1UP7 G6P 6.84932
25 3JU6 ARG 7.30594
26 5W6Y TRP 7.30594
27 5XLS URA 7.30594
28 2V95 HCY 7.30594
29 1APZ ASP 7.40741
30 1MID LAP 7.69231
31 5HGZ MLA 7.76256
32 5GG9 8GT 7.76256
33 1WUU GLA 7.76256
34 2QJT AMP 9.13242
35 2AZC 3TL 10.101
36 2F7A BEZ 10.5023
37 2O1C PPV 10.6667
38 5ODQ 9SB 10.8696
39 3O5N BR0 15.1786
40 6EHH 2GE 18.75
41 2DC1 CIT 19.6347
42 5ANU 58T 20.2532
43 5GP0 GPP 22.1477
44 3O61 GDD 27.2251
45 1VHZ APR 34.8485
46 5C8L GLC 39.5604
47 2YVO AMP 41.7582
Pocket No.: 2; Query (leader) PDB : 5NQR; Ligand: 958; Similar sites found with APoc: 21
This union binding pocket(no: 2) in the query (biounit: 5nqr.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 1H6H PIB None
2 4RJD TFP None
3 4Y4V DAL 2.28311
4 5X80 SAL 2.5
5 3UEC ALA ARG TPO LYS 2.73973
6 2YKX AKG 3.19635
7 4CCW VKC 3.19635
8 3QRY DMJ 3.19635
9 1YXM ADE 3.65297
10 4Y7U 491 3.65297
11 3RKR NAP 3.65297
12 2IV2 2MD 4.10959
13 2AJ4 GLA 4.56621
14 5D3X 4IP 4.79042
15 3VPB GLU 5.35714
16 1EYQ NAR 5.47945
17 5OES 3GC 5.47945
18 5NCB JZ3 8.21918
19 3ZIA ADP 9.52381
20 2XKO AKG 10.1124
21 1KNY KAN 10.5023
Pocket No.: 3; Query (leader) PDB : 5NQR; Ligand: 958; Similar sites found with APoc: 9
This union binding pocket(no: 3) in the query (biounit: 5nqr.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 1Q19 SSC 2.28311
2 1LAN LEU 2.73973
3 4LIK CIT 3.19635
4 3TWO NDP 4.10959
5 5OUH L0B 4.87805
6 3HQ9 OXL 5.93607
7 2P3C 3TL 9.09091
8 5OCQ CIT 10.9589
9 2P3B 3TL 15.1515
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