Receptor
PDB id Resolution Class Description Source Keywords
6F1X 1.9 Å EC: 3.6.1.55 COMPLEX BETWEEN MTH1 AND COMPOUND 7 (A 7-AZAINDOLE-2-AMIDE D HOMO SAPIENS NUDIX NUCLEOTIDE HYDROLASE INHIBITOR ONCOLOGY HYDROLASE
Ref.: CREATION OF A NOVEL CLASS OF POTENT AND SELECTIVE M HOMOLOGUE 1 (MTH1) INHIBITORS USING FRAGMENT-BASED AND STRUCTURE-BASED DRUG DESIGN. J. MED. CHEM. V. 61 2533 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 B:202;
B:204;
A:202;
B:201;
A:203;
B:203;
B:206;
A:201;
B:205;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
96.063 O4 S [O-]S...
C9Q A:200;
B:200;
 Valid;
Valid;
 none;
none;
 ic50 = 0.02 uM
299.755 C16 H14 Cl N3 O CCNC(...
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: C9Q; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 C9Q 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: C9Q; Similar ligands found: 74
No: Ligand Similarity coefficient
1 8XT 0.9477
2 K6B 0.9412
3 K8W 0.9241
4 K6N 0.9208
5 362 0.9118
6 ZZ6 0.9118
7 4UB 0.9045
8 XEZ 0.9033
9 ZRM 0.9018
10 7WH 0.8986
11 36I 0.8980
12 SNB 0.8961
13 BTD 0.8937
14 2GE 0.8901
15 6JJ 0.8899
16 61Y 0.8896
17 BIT 0.8885
18 1QJ 0.8875
19 9XZ 0.8873
20 4ZK 0.8871
21 6HW 0.8864
22 35X 0.8857
23 4RV 0.8849
24 TDH 0.8841
25 PVP 0.8830
26 J57 0.8824
27 BHF 0.8817
28 4V9 0.8812
29 CK6 0.8807
30 460 0.8804
31 HM5 0.8796
32 RC0 0.8792
33 1TM 0.8789
34 UI2 0.8769
35 25Q 0.8766
36 3D9 0.8762
37 AED 0.8755
38 H3H 0.8752
39 HM4 0.8739
40 7VF 0.8727
41 S2X 0.8723
42 4VB 0.8723
43 8QB 0.8712
44 49K 0.8706
45 PDB 0.8700
46 L7A 0.8692
47 50R 0.8691
48 3DL 0.8676
49 A28 0.8676
50 SW4 0.8662
51 1AV 0.8657
52 9KQ 0.8656
53 499 0.8651
54 5F3 0.8640
55 43L 0.8638
56 T1D 0.8630
57 73U 0.8624
58 UNM 0.8612
59 PLG 0.8612
60 JY7 0.8603
61 PZB 0.8579
62 CQU 0.8569
63 T34 0.8569
64 BN1 0.8567
65 FIL 0.8557
66 3NG 0.8556
67 695 0.8556
68 0H5 0.8555
69 4QX 0.8552
70 KOM 0.8539
71 7M2 0.8527
72 HKK 0.8525
73 6KN 0.8524
74 7M5 0.8504
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
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