Receptor
PDB id Resolution Class Description Source Keywords
6QVO 2.45 Å EC: 3.6.1.55 CRYSTAL STRUCTURE OF HUMAN MTH1 IN COMPLEX WITH N6-METHYL-DA HOMO SAPIENS ---- HYDROLASE
Ref.: MUTT HOMOLOGUE 1 (MTH1) REMOVES N6-METHYL-DATP FROM POOL. J.BIOL.CHEM. V. 295 4761 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 B:201;
C:202;
A:203;
A:201;
A:202;
C:201;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
6MA D:201;
B:202;
C:203;
A:204;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
345.248 C11 H16 N5 O6 P CNc1c...
GOL B:203;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6QVO 2.45 Å EC: 3.6.1.55 CRYSTAL STRUCTURE OF HUMAN MTH1 IN COMPLEX WITH N6-METHYL-DA HOMO SAPIENS ---- HYDROLASE
Ref.: MUTT HOMOLOGUE 1 (MTH1) REMOVES N6-METHYL-DATP FROM POOL. J.BIOL.CHEM. V. 295 4761 2020
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 6QVO - 6MA C11 H16 N5 O6 P CNc1c2c(nc....
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: 6MA; Similar ligands found: 24
No: Ligand ECFP6 Tc MDL keys Tc
1 6MA 1 1
2 DA 0.68 0.957747
3 D5M 0.68 0.957747
4 DOI 0.64557 0.90411
5 6MZ 0.580247 0.90411
6 DAT 0.564706 0.931507
7 6OG 0.552941 0.945946
8 DZ4 0.550562 0.906667
9 AS 0.548781 0.906667
10 DTP 0.539326 0.931507
11 G 6MZ C 0.488889 0.851351
12 DGP 0.47191 0.858974
13 DG 0.47191 0.858974
14 6MD 0.468354 0.76
15 MDR 0.4625 0.794521
16 3D1 0.455696 0.797297
17 3L1 0.455696 0.797297
18 DI 0.455556 0.881579
19 HF7 0.443299 0.945205
20 6IA 0.427083 0.8375
21 5F1 0.426829 0.780822
22 CPA 0.424779 0.82716
23 6C6 0.416667 0.906667
24 101 0.404494 0.90411
Similar Ligands (3D)
Ligand no: 1; Ligand: 6MA; Similar ligands found: 110
No: Ligand Similarity coefficient
1 AMP 0.9618
2 ABM 0.9558
3 FMP 0.9516
4 IMP 0.9489
5 AMP MG 0.9487
6 45A 0.9455
7 71V 0.9455
8 8OG 0.9439
9 IRP 0.9438
10 XMP 0.9426
11 8OP 0.9417
12 5GP 0.9412
13 SRA 0.9401
14 LMS 0.9383
15 UMP 0.9373
16 7D5 0.9370
17 G 0.9364
18 UFP 0.9324
19 G7M 0.9295
20 C2R 0.9292
21 AMZ 0.9283
22 ZAS 0.9269
23 5CM 0.9266
24 N5O 0.9265
25 TMP 0.9256
26 8GM 0.9255
27 NEC 0.9248
28 JLN 0.9246
29 93A 0.9242
30 PFU 0.9218
31 IMU 0.9211
32 U5P 0.9211
33 BRU 0.9196
34 J7C 0.9183
35 6RE 0.9182
36 5HU 0.9176
37 DU 0.9138
38 2DT 0.9137
39 D4M 0.9137
40 AOC 0.9133
41 3DH 0.9131
42 8BR 0.9124
43 C 0.9117
44 EO7 0.9106
45 QBT 0.9095
46 DCM 0.9082
47 CNU 0.9081
48 BMQ 0.9079
49 FNU 0.9077
50 UP6 0.9075
51 C5P 0.9074
52 NIA 0.9072
53 BMP 0.9067
54 MCF 0.9055
55 NYM 0.9054
56 Z8B 0.9050
57 5FU 0.9039
58 U 0.9030
59 6CG 0.9025
60 A3N 0.8988
61 5IU 0.8986
62 DUS 0.8975
63 T3S 0.8975
64 NCN 0.8975
65 PSU 0.8970
66 NMN 0.8968
67 TKW 0.8965
68 H2U 0.8962
69 IMO 0.8959
70 NUP 0.8953
71 NWQ 0.8949
72 16B 0.8949
73 FN5 0.8944
74 S5P 0.8938
75 MTA 0.8931
76 5BU 0.8927
77 UMC 0.8897
78 4X2 0.8897
79 DC 0.8896
80 103 0.8892
81 SSI 0.8871
82 PRX 0.8865
83 ATM 0.8858
84 BVP 0.8839
85 MZP 0.8839
86 CAR 0.8835
87 RVP 0.8834
88 3Q1 0.8816
89 DOC 0.8802
90 DSH 0.8792
91 U6M 0.8784
92 FDM 0.8783
93 6CN 0.8781
94 785 0.8756
95 NWW 0.8739
96 ADP 0.8734
97 TXS 0.8732
98 KG4 0.8731
99 CA0 0.8723
100 3Q2 0.8705
101 DDN 0.8696
102 3Q0 0.8662
103 T3P 0.8656
104 GDP 0.8654
105 ADN 0.8646
106 A3P 0.8608
107 ADX 0.8580
108 6AU 0.8555
109 M8Q 0.8547
110 2WF 0.8537
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6QVO; Ligand: 6MA; 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: 6qvo.bio3) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6QVO; Ligand: 6MA; 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: 6qvo.bio2) has 21 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 6QVO; Ligand: 6MA; 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: 6qvo.bio4) has 21 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 6QVO; Ligand: 6MA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 6qvo.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
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