Receptor
PDB id Resolution Class Description Source Keywords
5FSK 1.56 Å EC: 3.6.1.- MTH1 SUBSTRATE RECOGNITION: COMPLEX WITH 8-OXO-DGTP. HOMO SAPIENS HYDROLASE NUDT1
Ref.: MTH1 SUBSTRATE RECOGNITION--AN EXAMPLE OF SPECIFIC PROMISCUITY. PLOS ONE V. 11 51154 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
H6Y A:1157;
Valid;
none;
submit data
523.18 C10 H16 N5 O14 P3 c1nc(...
ACT A:1158;
Invalid;
none;
submit data
59.044 C2 H3 O2 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4N1T 1.6 Å EC: 3.6.1.- STRUCTURE OF HUMAN MTH1 IN COMPLEX WITH TH287 HOMO SAPIENS OXIDISED NUCLEOTIDE DEGRADATION HYDROLASE-HYDROLASE INHIBITCOMPLEX
Ref.: MTH1 INHIBITION ERADICATES CANCER BY PREVENTING SAN OF THE DNTP POOL. NATURE V. 508 215 2014
Members (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 27 families.
1 4C9X Kd = 48 nM VHS C21 H22 Cl2 F N5 O C[C@@H](c1....
2 5ANW ic50 = 0.009 uM 9CQ C18 H18 N4 O CN(C)C(=O)....
3 5ANV ic50 = 0.0009 uM RGJ C19 H17 Cl F N3 O3 CNC(=O)c1c....
4 4N1T ic50 = 0.8 nM 2GD C11 H10 Cl2 N4 CNc1cc(nc(....
5 5WS7 - 6U4 C10 H16 N5 O13 P3 C1[C@@H]([....
6 3ZR0 - 8OG C10 H14 N5 O8 P C1[C@@H]([....
7 4C9W Kd = 781 nM VGH C21 H22 Cl2 F N5 O C[C@H](c1c....
8 5GHJ - 6U4 C10 H16 N5 O13 P3 C1[C@@H]([....
9 5GHI - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
10 5NHY ic50 = 2.3 nM 8XT C15 H20 N4 O2 CCNC(=O)c1....
11 5GHQ - 6U4 C10 H16 N5 O13 P3 C1[C@@H]([....
12 5ANU ic50 = 0.5 nM 58T C17 H19 N5 O4 CNc1c2c3nc....
13 4N1U ic50 = 5 nM 2GE C13 H12 Cl2 N4 c1cc(c(c(c....
14 5FSM Kd = 95 uM N91 C10 H11 N3 O CC(=O)Nc1c....
15 5ANS ic50 = 2.056 uM RX8 C17 H22 N4 O2 CCOCc1nc2c....
16 5FSN ic50 = 4.5 uM 6Q3 C8 H13 N3 O2 Cc1cc(nc(n....
17 5GHO - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
18 5FSO ic50 = 1.5 uM S76 C5 H7 N3 O2 CNC1=CC(=O....
19 5FSK - H6Y C10 H16 N5 O14 P3 c1nc(c2c(n....
20 5GHN - 6U4 C10 H16 N5 O13 P3 C1[C@@H]([....
21 5ANT ic50 = 0.536 uM RJE C16 H19 N5 O3 CNc1c2c(nc....
22 5FSI - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
23 5GHM - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
24 5FSL ic50 = 59 uM UAN C7 H9 N5 O CNC1=Nc2c(....
70% Homology Family (25)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 25 families.
1 4C9X Kd = 48 nM VHS C21 H22 Cl2 F N5 O C[C@@H](c1....
2 5ANW ic50 = 0.009 uM 9CQ C18 H18 N4 O CN(C)C(=O)....
3 5ANV ic50 = 0.0009 uM RGJ C19 H17 Cl F N3 O3 CNC(=O)c1c....
4 4N1T ic50 = 0.8 nM 2GD C11 H10 Cl2 N4 CNc1cc(nc(....
5 5WS7 - 6U4 C10 H16 N5 O13 P3 C1[C@@H]([....
6 3ZR0 - 8OG C10 H14 N5 O8 P C1[C@@H]([....
7 4C9W Kd = 781 nM VGH C21 H22 Cl2 F N5 O C[C@H](c1c....
8 5GHJ - 6U4 C10 H16 N5 O13 P3 C1[C@@H]([....
9 5GHI - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
10 5NHY ic50 = 2.3 nM 8XT C15 H20 N4 O2 CCNC(=O)c1....
11 5GHQ - 6U4 C10 H16 N5 O13 P3 C1[C@@H]([....
12 5ANU ic50 = 0.5 nM 58T C17 H19 N5 O4 CNc1c2c3nc....
13 4N1U ic50 = 5 nM 2GE C13 H12 Cl2 N4 c1cc(c(c(c....
14 5FSM Kd = 95 uM N91 C10 H11 N3 O CC(=O)Nc1c....
15 5ANS ic50 = 2.056 uM RX8 C17 H22 N4 O2 CCOCc1nc2c....
16 5FSN ic50 = 4.5 uM 6Q3 C8 H13 N3 O2 Cc1cc(nc(n....
17 5GHO - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
18 5FSO ic50 = 1.5 uM S76 C5 H7 N3 O2 CNC1=CC(=O....
19 5FSK - H6Y C10 H16 N5 O14 P3 c1nc(c2c(n....
20 5GHN - 6U4 C10 H16 N5 O13 P3 C1[C@@H]([....
21 5ANT ic50 = 0.536 uM RJE C16 H19 N5 O3 CNc1c2c(nc....
22 5FSI - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
23 5GHM - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
24 5FSL ic50 = 59 uM UAN C7 H9 N5 O CNC1=Nc2c(....
25 5HZX ic50 = 2.8 nM 2GE C13 H12 Cl2 N4 c1cc(c(c(c....
50% Homology Family (25)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 4C9X Kd = 48 nM VHS C21 H22 Cl2 F N5 O C[C@@H](c1....
2 5ANW ic50 = 0.009 uM 9CQ C18 H18 N4 O CN(C)C(=O)....
3 5ANV ic50 = 0.0009 uM RGJ C19 H17 Cl F N3 O3 CNC(=O)c1c....
4 4N1T ic50 = 0.8 nM 2GD C11 H10 Cl2 N4 CNc1cc(nc(....
5 5WS7 - 6U4 C10 H16 N5 O13 P3 C1[C@@H]([....
6 3ZR0 - 8OG C10 H14 N5 O8 P C1[C@@H]([....
7 4C9W Kd = 781 nM VGH C21 H22 Cl2 F N5 O C[C@H](c1c....
8 5GHJ - 6U4 C10 H16 N5 O13 P3 C1[C@@H]([....
9 5GHI - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
10 5NHY ic50 = 2.3 nM 8XT C15 H20 N4 O2 CCNC(=O)c1....
11 5GHQ - 6U4 C10 H16 N5 O13 P3 C1[C@@H]([....
12 5ANU ic50 = 0.5 nM 58T C17 H19 N5 O4 CNc1c2c3nc....
13 4N1U ic50 = 5 nM 2GE C13 H12 Cl2 N4 c1cc(c(c(c....
14 5FSM Kd = 95 uM N91 C10 H11 N3 O CC(=O)Nc1c....
15 5ANS ic50 = 2.056 uM RX8 C17 H22 N4 O2 CCOCc1nc2c....
16 5FSN ic50 = 4.5 uM 6Q3 C8 H13 N3 O2 Cc1cc(nc(n....
17 5GHO - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
18 5FSO ic50 = 1.5 uM S76 C5 H7 N3 O2 CNC1=CC(=O....
19 5FSK - H6Y C10 H16 N5 O14 P3 c1nc(c2c(n....
20 5GHN - 6U4 C10 H16 N5 O13 P3 C1[C@@H]([....
21 5ANT ic50 = 0.536 uM RJE C16 H19 N5 O3 CNc1c2c(nc....
22 5FSI - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
23 5GHM - 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
24 5FSL ic50 = 59 uM UAN C7 H9 N5 O CNC1=Nc2c(....
25 5HZX ic50 = 2.8 nM 2GE C13 H12 Cl2 N4 c1cc(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: H6Y; Similar ligands found: 26
No: Ligand ECFP6 Tc MDL keys Tc
1 H6Y 1 1
2 8OD 0.907895 1
3 8OP 0.794872 0.986111
4 8OX 0.675325 0.863014
5 8DD 0.574468 0.934211
6 8GT 0.536842 0.85
7 UTP 0.48913 0.851351
8 G8D 0.484536 0.85
9 CTP 0.463158 0.855263
10 7DT 0.444444 0.931507
11 NUP 0.428571 0.855263
12 MGT 0.428571 0.77907
13 UDP 0.425532 0.851351
14 ATP 0.42 0.945205
15 GTP 0.419048 0.946667
16 BMP 0.417582 0.828947
17 5FA 0.415842 0.945205
18 AQP 0.415842 0.945205
19 UP5 0.411765 0.921053
20 OMP 0.410526 0.815789
21 6AU 0.410526 0.815789
22 7D4 0.41 0.857143
23 JW5 0.408602 0.805195
24 S5P 0.402174 0.7875
25 CDP 0.402062 0.855263
26 BMQ 0.4 0.837838
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4N1T; Ligand: 2GD; Similar sites found: 87
This union binding pocket(no: 1) in the query (biounit: 4n1t.bio1) has 33 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2GQS C2R 0.004923 0.4366 None
2 4REI 3MV 0.03475 0.41011 None
3 4V2O CLQ 0.03444 0.40574 None
4 2YIP YIO 0.03624 0.40637 0.724638
5 3H7J PPY 0.01679 0.41064 1.25786
6 1DZK PRZ 0.004466 0.43464 1.27389
7 3A16 PXO 0.01465 0.41956 2.51572
8 4B1L FRU 0.01801 0.41447 2.51572
9 4ITH RCM 0.01073 0.40369 2.51572
10 4WVW SLT 0.01978 0.42637 2.77778
11 4GQP B40 0.004738 0.45721 3.14465
12 4FFG LBS 0.002278 0.4376 3.14465
13 4IAW LIZ 0.01437 0.42571 3.14465
14 5CAD PCA 0.02622 0.41578 3.14465
15 5KEW 6SB 0.009571 0.44229 3.19149
16 3AVR OGA 0.004835 0.45688 3.77358
17 2D6M LBT 0.00821 0.44933 3.77358
18 4FE2 AIR 0.006756 0.43827 3.77358
19 4ZS4 ATP 0.004329 0.4278 3.77358
20 3NZ1 3NY 0.01752 0.42286 3.77358
21 4NAE 1GP 0.0484 0.4034 3.77358
22 1MJT ITU 0.02542 0.40269 3.77358
23 1J3R 6PG 0.03565 0.40127 3.77358
24 3NBC LAT 0.03492 0.40803 4.05405
25 3PUN FUC GAL NDG FUC 0.01311 0.43554 4.40252
26 5MX4 HPA 0.01319 0.43361 4.40252
27 4BWL MN9 0.03151 0.41267 4.40252
28 4OCT AKG 0.02256 0.41151 4.40252
29 4CQB MLI 0.0352 0.40614 4.40252
30 4NS0 PIO 0.003978 0.45325 4.51128
31 4XBT 3ZQ 0.006696 0.42262 4.51613
32 4XBT FLC 0.009129 0.41634 4.51613
33 1OGX EQU 0.004125 0.44034 4.58015
34 4UY1 TJM 0.03501 0.40168 4.58015
35 5AIG VPR 0.01664 0.41829 4.8
36 1GT4 UNA 0.007476 0.42398 5.03145
37 4DSU BZI 0.02948 0.41592 5.03145
38 4GK9 MAN BMA MAN MAN MAN 0.02444 0.4158 5.03145
39 2Q8E OGA 0.02863 0.41426 5.03145
40 2OS2 OGA 0.02892 0.41405 5.03145
41 2YBP 2HG 0.0338 0.40995 5.03145
42 4P7X YCP 0.0171 0.4036 5.03145
43 4P7X AKG 0.0171 0.4036 5.03145
44 1IA9 ANP 0.005854 0.42182 5.66038
45 4GYI ADP 0.01798 0.41277 5.66038
46 5KBE IPH 0.03135 0.41189 5.66038
47 4ZXA H8N 0.0299 0.40898 5.66038
48 5C79 PBU 0.02639 0.41712 6
49 2IVD ACJ 0.0238 0.40666 6.28931
50 3JQ3 ADP 0.03203 0.40367 6.28931
51 2XEM SSV 0.02175 0.41232 6.66667
52 1VRP ADP 0.01247 0.41695 6.91824
53 4DFU QUE 0.03435 0.40579 6.91824
54 4ZGR NGA GAL 0.04678 0.40153 6.91824
55 2PA7 TYD 0.02543 0.41789 7.0922
56 3VV1 GAL FUC 0.01448 0.43535 7.54717
57 2XG5 EC2 0.02825 0.4057 7.54717
58 2XG5 EC5 0.02825 0.4057 7.54717
59 5H2U 1N1 0.02566 0.4016 7.54717
60 3LQV ADE 0.01889 0.42321 7.69231
61 2HKA C3S 0.01588 0.40199 7.69231
62 5LKC FUC GLA A2G 0.001467 0.49332 8.1761
63 5NBW 8SK 0.002278 0.45744 8.1761
64 3UYW TAU 0.01852 0.42764 8.1761
65 1Y7P RIP 0.01642 0.4263 8.80503
66 4K55 H6P 0.008254 0.43289 8.87097
67 2PHT MAN MAN MAN 0.03044 0.41448 9.43396
68 4BG4 ADP 0.01138 0.41187 9.43396
69 2GND MAN 0.0408 0.40711 9.43396
70 3WV6 GAL BGC 0.005574 0.46251 10.0629
71 2VDF OCT 0.005441 0.43449 10.0629
72 2ICK DMA 0.001022 0.47473 10.6918
73 1I1E DM2 0.01088 0.43666 10.6918
74 1USI PHE 0.02733 0.41755 10.6918
75 4IFP MAL 0.03136 0.40789 10.6918
76 5TVF CGQ 0.02784 0.40324 11.7647
77 3HO6 IHP 0.009562 0.43497 12.5786
78 4BCM T7Z 0.02289 0.41928 12.5786
79 3B6R ADP 0.01027 0.41741 12.5786
80 2BOS GLA GAL GLC NBU 0.005638 0.45681 13.2353
81 2BOS GLA GAL GLC 0.007168 0.45083 13.2353
82 1KHZ ADV 0.008037 0.40069 16.3522
83 3GZ8 APR 0.0002764 0.47332 17.6101
84 4KBA 1QM 0.01356 0.41517 17.6101
85 2QJT AMP 0.001104 0.51385 20.7547
86 3I7V ATP 0.002719 0.46011 38.806
87 5LPG 71V 0.00009735 0.53872 40.2516
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