Receptor
PDB id Resolution Class Description Source Keywords
3ZR0 1.8 Å EC: 3.6.1.55 CRYSTAL STRUCTURE OF HUMAN MTH1 IN COMPLEX WITH 8-OXO-DGMP HOMO SAPIENS HYDROLASE DNA REPAIR
Ref.: CRYSTAL STRUCTURE OF HUMAN MTH1 AND THE 8-OXO-DGMP PRODUCT COMPLEX. FEBS LETT. V. 585 2617 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
8OG A:1157;
B:1157;
Valid;
Valid;
none;
none;
submit data
363.221 C10 H14 N5 O8 P C1[C@...
SO4 A:1158;
A:1159;
B:1158;
B:1159;
B:1160;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6US2 1.8 Å EC: 3.6.1.55 MTH1 IN COMPLEX WITH COMPOUND 5 HOMO SAPIENS HYDROLASE NUDT1 NUDIX HYDROLASE INHIBITOR HYDROLASE-HYDRINHIBITOR COMPLEX
Ref.: DISCOVERY OF POTENT AND SELECTIVE MTH1 INHIBITORS F ONCOLOGY: ENABLING RAPID TARGET (IN)VALIDATION. ACS MED.CHEM.LETT. V. 11 358 2020
Members (38)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 6US4 ic50 = 13 nM GN6 C12 H8 Cl2 N4 c1cc(c(c(c....
2 4C9X Kd = 48 nM VHS C21 H22 Cl2 F N5 O C[C@@H](c1....
3 5ANW Kd = 0.003 uM 9CQ C18 H18 N4 O CN(C)C(=O)....
4 6F23 ic50 = 0.005 uM C8Z C17 H17 N3 c1ccc(cc1)....
5 5ANV Kd = 0.0005 uM RGJ C19 H17 Cl F N3 O3 CNC(=O)c1c....
6 4N1T ic50 = 0.8 nM 2GD C11 H10 Cl2 N4 CNc1cc(nc(....
7 6AA4 ic50 = 0.47 uM MKS C24 H26 O6 CC(=CCc1c(....
8 5WS7 - 6U4 C10 H16 N5 O13 P3 C1[C@@H]([....
9 3ZR0 - 8OG C10 H14 N5 O8 P C1[C@@H]([....
10 6ILI - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
11 5NGS ic50 = 170 nM 8WW C13 H13 N5 S c1ccc(cc1)....
12 6US3 ic50 = 81 nM 8JF C18 H17 N3 O Cc1cccc(c1....
13 4C9W Kd = 781 nM VGH C21 H22 Cl2 F N5 O C[C@H](c1c....
14 5GHJ - 6U4 C10 H16 N5 O13 P3 C1[C@@H]([....
15 5GHI - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
16 5NHY ic50 = 2.3 nM 8XT C15 H20 N4 O2 CCNC(=O)c1....
17 6F20 Kd = 49.5 uM C9E C10 H10 N2 O2 CCOC(=O)c1....
18 5GHQ - 6U4 C10 H16 N5 O13 P3 C1[C@@H]([....
19 5ANU Kd = 0.0004 uM 58T C17 H19 N5 O4 CNc1c2c3nc....
20 4N1U ic50 = 5 nM 2GE C13 H12 Cl2 N4 c1cc(c(c(c....
21 6F22 ic50 = 0.002 uM C9B C16 H16 N4 O c1ccc(cc1)....
22 5FSM Kd > 40 uM N91 C10 H11 N3 O CC(=O)Nc1c....
23 5NGR ic50 = 24 uM 8WT C6 H7 N5 S CSc1[nH]c2....
24 5OTM - 6OG C11 H16 N5 O7 P COc1c2c(nc....
25 6F1X ic50 = 0.02 uM C9Q C16 H14 Cl N3 O CCNC(=O)c1....
26 5ANS ic50 = 2.056 uM RX8 C17 H22 N4 O2 CCOCc1nc2c....
27 5FSN Kd = 1.7 uM 6Q3 C8 H13 N3 O2 Cc1cc(nc(n....
28 5GHO - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
29 5FSO Kd = 0.81 uM S76 C5 H7 N3 O2 CNC1=CC(=O....
30 5FSK - H6Y C10 H16 N5 O14 P3 c1nc(c2c(n....
31 6AA5 ic50 = 0.052 uM MKU C24 H26 O6 CC(=CCc1c2....
32 5GHN - 6U4 C10 H16 N5 O13 P3 C1[C@@H]([....
33 5ANT Kd = 0.44 uM RJE C16 H19 N5 O3 CNc1c2c(nc....
34 5FSI - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
35 6US2 Ki = 5.2 pM S3O C18 H21 N3 O Cc1cccc(c1....
36 5GHM - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
37 5NGT - 8WZ C12 H10 N2 O2 Cc1cc(c2c(....
38 5FSL Kd = 24 uM UAN C7 H9 N5 O CNC1=Nc2c(....
70% Homology Family (44)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 6EHH ic50 = 32 nM 2GE C13 H12 Cl2 N4 c1cc(c(c(c....
2 5MZG ic50 = 138 nM 2GE C13 H12 Cl2 N4 c1cc(c(c(c....
3 5MZE - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
4 6US4 ic50 = 13 nM GN6 C12 H8 Cl2 N4 c1cc(c(c(c....
5 4C9X Kd = 48 nM VHS C21 H22 Cl2 F N5 O C[C@@H](c1....
6 5ANW Kd = 0.003 uM 9CQ C18 H18 N4 O CN(C)C(=O)....
7 6F23 ic50 = 0.005 uM C8Z C17 H17 N3 c1ccc(cc1)....
8 5ANV Kd = 0.0005 uM RGJ C19 H17 Cl F N3 O3 CNC(=O)c1c....
9 4N1T ic50 = 0.8 nM 2GD C11 H10 Cl2 N4 CNc1cc(nc(....
10 6AA4 ic50 = 0.47 uM MKS C24 H26 O6 CC(=CCc1c(....
11 5WS7 - 6U4 C10 H16 N5 O13 P3 C1[C@@H]([....
12 3ZR0 - 8OG C10 H14 N5 O8 P C1[C@@H]([....
13 6ILI - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
14 5NGS ic50 = 170 nM 8WW C13 H13 N5 S c1ccc(cc1)....
15 6US3 ic50 = 81 nM 8JF C18 H17 N3 O Cc1cccc(c1....
16 4C9W Kd = 781 nM VGH C21 H22 Cl2 F N5 O C[C@H](c1c....
17 5GHJ - 6U4 C10 H16 N5 O13 P3 C1[C@@H]([....
18 5GHI - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
19 5NHY ic50 = 2.3 nM 8XT C15 H20 N4 O2 CCNC(=O)c1....
20 6F20 Kd = 49.5 uM C9E C10 H10 N2 O2 CCOC(=O)c1....
21 5GHQ - 6U4 C10 H16 N5 O13 P3 C1[C@@H]([....
22 5ANU Kd = 0.0004 uM 58T C17 H19 N5 O4 CNc1c2c3nc....
23 4N1U ic50 = 5 nM 2GE C13 H12 Cl2 N4 c1cc(c(c(c....
24 6F22 ic50 = 0.002 uM C9B C16 H16 N4 O c1ccc(cc1)....
25 5FSM Kd > 40 uM N91 C10 H11 N3 O CC(=O)Nc1c....
26 5NGR ic50 = 24 uM 8WT C6 H7 N5 S CSc1[nH]c2....
27 5OTM - 6OG C11 H16 N5 O7 P COc1c2c(nc....
28 6F1X ic50 = 0.02 uM C9Q C16 H14 Cl N3 O CCNC(=O)c1....
29 5ANS ic50 = 2.056 uM RX8 C17 H22 N4 O2 CCOCc1nc2c....
30 5FSN Kd = 1.7 uM 6Q3 C8 H13 N3 O2 Cc1cc(nc(n....
31 5GHO - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
32 5FSO Kd = 0.81 uM S76 C5 H7 N3 O2 CNC1=CC(=O....
33 5FSK - H6Y C10 H16 N5 O14 P3 c1nc(c2c(n....
34 6AA5 ic50 = 0.052 uM MKU C24 H26 O6 CC(=CCc1c2....
35 5GHN - 6U4 C10 H16 N5 O13 P3 C1[C@@H]([....
36 5ANT Kd = 0.44 uM RJE C16 H19 N5 O3 CNc1c2c(nc....
37 5FSI - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
38 6US2 Ki = 5.2 pM S3O C18 H21 N3 O Cc1cccc(c1....
39 5GHM - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
40 5NGT - 8WZ C12 H10 N2 O2 Cc1cc(c2c(....
41 5FSL Kd = 24 uM UAN C7 H9 N5 O CNC1=Nc2c(....
42 6QVO - 6MA C11 H16 N5 O6 P CNc1c2c(nc....
43 5HZX ic50 = 2.8 nM 2GE C13 H12 Cl2 N4 c1cc(c(c(c....
44 5OTN - 6OG C11 H16 N5 O7 P COc1c2c(nc....
50% Homology Family (44)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 6EHH ic50 = 32 nM 2GE C13 H12 Cl2 N4 c1cc(c(c(c....
2 5MZG ic50 = 138 nM 2GE C13 H12 Cl2 N4 c1cc(c(c(c....
3 5MZE - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
4 6US4 ic50 = 13 nM GN6 C12 H8 Cl2 N4 c1cc(c(c(c....
5 4C9X Kd = 48 nM VHS C21 H22 Cl2 F N5 O C[C@@H](c1....
6 5ANW Kd = 0.003 uM 9CQ C18 H18 N4 O CN(C)C(=O)....
7 6F23 ic50 = 0.005 uM C8Z C17 H17 N3 c1ccc(cc1)....
8 5ANV Kd = 0.0005 uM RGJ C19 H17 Cl F N3 O3 CNC(=O)c1c....
9 4N1T ic50 = 0.8 nM 2GD C11 H10 Cl2 N4 CNc1cc(nc(....
10 6AA4 ic50 = 0.47 uM MKS C24 H26 O6 CC(=CCc1c(....
11 5WS7 - 6U4 C10 H16 N5 O13 P3 C1[C@@H]([....
12 3ZR0 - 8OG C10 H14 N5 O8 P C1[C@@H]([....
13 6ILI - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
14 5NGS ic50 = 170 nM 8WW C13 H13 N5 S c1ccc(cc1)....
15 6US3 ic50 = 81 nM 8JF C18 H17 N3 O Cc1cccc(c1....
16 4C9W Kd = 781 nM VGH C21 H22 Cl2 F N5 O C[C@H](c1c....
17 5GHJ - 6U4 C10 H16 N5 O13 P3 C1[C@@H]([....
18 5GHI - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
19 5NHY ic50 = 2.3 nM 8XT C15 H20 N4 O2 CCNC(=O)c1....
20 6F20 Kd = 49.5 uM C9E C10 H10 N2 O2 CCOC(=O)c1....
21 5GHQ - 6U4 C10 H16 N5 O13 P3 C1[C@@H]([....
22 5ANU Kd = 0.0004 uM 58T C17 H19 N5 O4 CNc1c2c3nc....
23 4N1U ic50 = 5 nM 2GE C13 H12 Cl2 N4 c1cc(c(c(c....
24 6F22 ic50 = 0.002 uM C9B C16 H16 N4 O c1ccc(cc1)....
25 5FSM Kd > 40 uM N91 C10 H11 N3 O CC(=O)Nc1c....
26 5NGR ic50 = 24 uM 8WT C6 H7 N5 S CSc1[nH]c2....
27 5OTM - 6OG C11 H16 N5 O7 P COc1c2c(nc....
28 6F1X ic50 = 0.02 uM C9Q C16 H14 Cl N3 O CCNC(=O)c1....
29 5ANS ic50 = 2.056 uM RX8 C17 H22 N4 O2 CCOCc1nc2c....
30 5FSN Kd = 1.7 uM 6Q3 C8 H13 N3 O2 Cc1cc(nc(n....
31 5GHO - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
32 5FSO Kd = 0.81 uM S76 C5 H7 N3 O2 CNC1=CC(=O....
33 5FSK - H6Y C10 H16 N5 O14 P3 c1nc(c2c(n....
34 6AA5 ic50 = 0.052 uM MKU C24 H26 O6 CC(=CCc1c2....
35 5GHN - 6U4 C10 H16 N5 O13 P3 C1[C@@H]([....
36 5ANT Kd = 0.44 uM RJE C16 H19 N5 O3 CNc1c2c(nc....
37 5FSI - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
38 6US2 Ki = 5.2 pM S3O C18 H21 N3 O Cc1cccc(c1....
39 5GHM - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
40 5NGT - 8WZ C12 H10 N2 O2 Cc1cc(c2c(....
41 5FSL Kd = 24 uM UAN C7 H9 N5 O CNC1=Nc2c(....
42 6QVO - 6MA C11 H16 N5 O6 P CNc1c2c(nc....
43 5HZX ic50 = 2.8 nM 2GE C13 H12 Cl2 N4 c1cc(c(c(c....
44 5OTN - 6OG C11 H16 N5 O7 P COc1c2c(nc....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 8OG; Similar ligands found: 23
No: Ligand ECFP6 Tc MDL keys Tc
1 8OG 1 1
2 8GD 0.815789 0.9875
3 8DG 0.775 0.9875
4 8HG 0.742857 0.888889
5 8GM 0.585366 0.949367
6 G8D 0.494505 0.9375
7 8GT 0.483871 0.9375
8 DC 0.44186 0.873418
9 DCM 0.44186 0.873418
10 QBT 0.435294 0.780488
11 UMP 0.435294 0.835443
12 DU 0.435294 0.835443
13 UFP 0.430233 0.807229
14 TMP 0.425287 0.82716
15 BRU 0.425287 0.807229
16 5HU 0.425287 0.817073
17 UMC 0.423529 0.790123
18 5IU 0.420455 0.807229
19 5CM 0.411111 0.864198
20 DDN 0.406977 0.835443
21 DGP 0.404255 0.855422
22 DG 0.404255 0.855422
23 8DD 0.4 0.833333
Similar Ligands (3D)
Ligand no: 1; Ligand: 8OG; Similar ligands found: 101
No: Ligand Similarity coefficient
1 6OG 0.9614
2 DA 0.9448
3 5GP 0.9444
4 6MA 0.9439
5 XMP 0.9434
6 G 0.9429
7 DI 0.9408
8 71V 0.9407
9 D5M 0.9404
10 G7M 0.9368
11 45A 0.9358
12 AMP 0.9356
13 8OP 0.9337
14 IMU 0.9328
15 BVP 0.9322
16 8BR 0.9250
17 IMP 0.9230
18 CNU 0.9230
19 6CG 0.9226
20 EO7 0.9190
21 5HM 0.9189
22 AS 0.9186
23 NYM 0.9143
24 6MZ 0.9137
25 FMP 0.9132
26 93A 0.9117
27 ABM 0.9117
28 Z8B 0.9106
29 FDM 0.9098
30 5FU 0.9080
31 O8M 0.9078
32 TKW 0.9065
33 5BU 0.9062
34 LMS 0.9061
35 JLN 0.9061
36 N5O 0.9059
37 IRP 0.9045
38 SRA 0.9034
39 PCG 0.9006
40 2DT 0.8999
41 FNU 0.8989
42 M2T 0.8977
43 ZAS 0.8967
44 7D5 0.8955
45 C 0.8941
46 NEC 0.8940
47 CMP 0.8936
48 NMN 0.8916
49 AOC 0.8899
50 3F5 0.8892
51 SSI 0.8890
52 KB7 0.8885
53 U 0.8874
54 N8M 0.8866
55 FEU 0.8851
56 6SW 0.8825
57 3DH 0.8808
58 35G 0.8804
59 U5P 0.8796
60 MTA 0.8796
61 MTM 0.8789
62 A8M 0.8786
63 C2R 0.8774
64 A3N 0.8761
65 C5P 0.8758
66 T3S 0.8757
67 DUS 0.8753
68 ATM 0.8753
69 AMZ 0.8739
70 NUP 0.8736
71 0NH 0.8736
72 16B 0.8736
73 C8M 0.8722
74 NIA 0.8721
75 SP1 0.8717
76 NCN 0.8712
77 H2U 0.8707
78 S5P 0.8707
79 UP6 0.8701
80 PFU 0.8698
81 6RE 0.8693
82 100 0.8686
83 GMP 0.8680
84 NWQ 0.8676
85 MTH 0.8663
86 BMP 0.8659
87 6SZ 0.8659
88 U6M 0.8650
89 IXF 0.8650
90 J7C 0.8649
91 BMQ 0.8649
92 HDU 0.8640
93 OMP 0.8623
94 6J7 0.8623
95 T3P 0.8617
96 IMG 0.8616
97 581 0.8608
98 RP1 0.8592
99 7CH 0.8587
100 43H 0.8564
101 9RA 0.8545
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6US2; Ligand: S3O; 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: 6us2.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback