Receptor
PDB id Resolution Class Description Source Keywords
5NGT 1.54 Å EC: 3.6.1.55 CRYSTAL STRUCTURE OF HUMAN MTH1 IN COMPLEX WITH INHIBITOR 7- YL)-5-METHYL-1,3-BENZOXAZOL-2-AMINE HOMO SAPIENS INHIBITOR FRAGMENT OXIDISED NUCLEOTIDES HYDROLASE
Ref.: FRAGMENT-BASED DISCOVERY AND OPTIMIZATION OF ENZYME INHIBITORS BY DOCKING OF COMMERCIAL CHEMICAL SPACE. J. MED. CHEM. V. 60 8160 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:203;
A:202;
 Invalid;
Invalid;
 none;
none;
 submit data
96.063 O4 S [O-]S...
8WZ A:201;
 Valid;
 none;
 submit data
214.22 C12 H10 N2 O2 Cc1cc...
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: 8WZ; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 8WZ 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: 8WZ; Similar ligands found: 303
No: Ligand Similarity coefficient
1 JR2 0.9737
2 25O 0.9713
3 TQU 0.9619
4 96R 0.9509
5 QZ8 0.9445
6 1X8 0.9430
7 SYR 0.9408
8 DNC 0.9359
9 TNF 0.9326
10 7I2 0.9323
11 96U 0.9297
12 9AP 0.9293
13 6PB 0.9286
14 LDR 0.9282
15 8GK 0.9244
16 TNL 0.9242
17 M4B 0.9220
18 A1Y 0.9216
19 8G6 0.9215
20 692 0.9212
21 4ME 0.9192
22 7WR 0.9170
23 2JK 0.9163
24 1Z8 0.9161
25 ZME 0.9149
26 3Y7 0.9133
27 A9O 0.9130
28 W8G 0.9120
29 AY4 0.9118
30 QPR 0.9116
31 OKM 0.9115
32 HLD 0.9111
33 HNQ 0.9109
34 9UG 0.9108
35 K3Y 0.9108
36 BQ5 0.9106
37 DK1 0.9095
38 XQK 0.9090
39 0GZ 0.9083
40 IBM 0.9064
41 C9E 0.9060
42 XZ8 0.9052
43 4KL 0.9050
44 878 0.9048
45 XFE 0.9048
46 DXK 0.9047
47 X0W 0.9040
48 P9I 0.9039
49 8XQ 0.9035
50 CKA 0.9032
51 VYM 0.9029
52 6XI 0.9029
53 5P3 0.9023
54 5V7 0.9020
55 1X7 0.9019
56 OTD 0.9017
57 X8D 0.9017
58 5OF 0.9011
59 O2A 0.9010
60 6J9 0.9009
61 0GY 0.9000
62 EDM 0.8996
63 6DP 0.8994
64 5JT 0.8991
65 NLA 0.8986
66 ONR 0.8986
67 AM1 0.8981
68 M1Z 0.8971
69 F2W 0.8967
70 SNY 0.8967
71 JKZ 0.8966
72 UAN 0.8966
73 11G 0.8964
74 2LX 0.8962
75 49N 0.8959
76 OMD 0.8956
77 0F9 0.8955
78 OAI 0.8949
79 7ZL 0.8949
80 DNF 0.8944
81 AIN 0.8943
82 BZE 0.8934
83 RB2 0.8933
84 EWG 0.8926
85 GV9 0.8926
86 OX2 0.8914
87 2D3 0.8910
88 F12 0.8909
89 NBG 0.8907
90 I6G 0.8905
91 5VJ 0.8903
92 EYM 0.8900
93 QMS 0.8898
94 6BL 0.8897
95 EYA 0.8896
96 BPU 0.8895
97 APZ 0.8892
98 54X 0.8892
99 MOK 0.8888
100 22L 0.8888
101 G1P 0.8881
102 226 0.8877
103 F95 0.8877
104 FBG 0.8876
105 BK9 0.8876
106 FLV 0.8874
107 VXX 0.8871
108 XM5 0.8868
109 AMR 0.8865
110 7FF 0.8864
111 EY7 0.8860
112 2LY 0.8859
113 SRO 0.8856
114 GN6 0.8855
115 CR1 0.8855
116 4MU 0.8851
117 M3Q 0.8850
118 NVU 0.8847
119 9UL 0.8844
120 H5B 0.8843
121 M5H 0.8842
122 KYA 0.8840
123 EVO 0.8840
124 FGZ 0.8839
125 T6Z 0.8837
126 772 0.8836
127 582 0.8830
128 8HH 0.8827
129 GDE 0.8827
130 5WY 0.8826
131 FWB 0.8825
132 KED 0.8824
133 BPS 0.8822
134 C2Y 0.8822
135 TWO 0.8822
136 B4O 0.8822
137 8NX 0.8820
138 M6Z 0.8819
139 89J 0.8819
140 LEL 0.8818
141 92P 0.8818
142 YO5 0.8817
143 IPT 0.8813
144 QSH 0.8813
145 2GQ 0.8812
146 7ZE 0.8810
147 ELH 0.8810
148 JP2 0.8807
149 TNG 0.8807
150 I7A 0.8806
151 7MX 0.8805
152 28S 0.8804
153 90J 0.8801
154 AO6 0.8801
155 4NO 0.8799
156 H33 0.8798
157 NPL 0.8798
158 67Y 0.8794
159 UFO 0.8792
160 TDH 0.8791
161 2ZQ 0.8788
162 PEY 0.8785
163 UXH 0.8784
164 0W1 0.8779
165 209 0.8777
166 MHK 0.8774
167 5F5 0.8772
168 64C 0.8772
169 VNL 0.8771
170 K25 0.8769
171 PRZ 0.8768
172 HQJ 0.8767
173 Z5P 0.8766
174 II4 0.8764
175 ESI 0.8764
176 VM1 0.8763
177 0FK 0.8763
178 43U 0.8763
179 K3Q 0.8762
180 774 0.8760
181 AKH 0.8760
182 X11 0.8758
183 JTA 0.8757
184 30G 0.8756
185 O2Y 0.8753
186 MIL 0.8752
187 B2T 0.8749
188 67X 0.8747
189 8VE 0.8741
190 42C 0.8738
191 N7I 0.8737
192 5F8 0.8736
193 V1T 0.8736
194 BZJ 0.8734
195 WUB 0.8728
196 HA5 0.8727
197 KFN 0.8727
198 TWB 0.8723
199 1QP 0.8721
200 5FL 0.8719
201 EGR 0.8718
202 DBQ 0.8718
203 H05 0.8718
204 8W9 0.8717
205 7M5 0.8717
206 9F8 0.8717
207 7ME 0.8709
208 Q6T 0.8706
209 SXX 0.8706
210 HMD 0.8705
211 D07 0.8704
212 NID 0.8703
213 49O 0.8702
214 9FE 0.8701
215 GHM 0.8701
216 9GP 0.8699
217 6KN 0.8697
218 F69 0.8696
219 AX3 0.8695
220 KOM 0.8694
221 WOE 0.8692
222 28N 0.8692
223 BPY 0.8691
224 K44 0.8691
225 EXD 0.8690
226 S3P 0.8690
227 MXX 0.8689
228 2O6 0.8687
229 FOT 0.8686
230 YJD 0.8685
231 UFV 0.8684
232 60Q 0.8683
233 512 0.8678
234 IOS 0.8676
235 PDC 0.8676
236 ISJ 0.8675
237 IJZ 0.8674
238 7M2 0.8671
239 DRG 0.8671
240 B56 0.8669
241 6TZ 0.8667
242 MXD 0.8664
243 LZB 0.8662
244 M3E 0.8661
245 KDO 0.8660
246 A5H 0.8658
247 3TJ 0.8653
248 LF5 0.8651
249 HJ8 0.8649
250 CCV 0.8645
251 KLK 0.8640
252 DNA 0.8639
253 KTW 0.8638
254 ORO 0.8637
255 RD4 0.8635
256 9X5 0.8633
257 GI3 0.8629
258 3E2 0.8627
259 4XS 0.8626
260 5NS 0.8625
261 6R8 0.8623
262 CKU 0.8623
263 39O 0.8623
264 GRX 0.8621
265 4XV 0.8616
266 B23 0.8615
267 LT8 0.8613
268 MNP 0.8612
269 BN1 0.8608
270 1A7 0.8606
271 LZ2 0.8601
272 K6B 0.8600
273 9KQ 0.8599
274 2J9 0.8597
275 HQD 0.8596
276 2KU 0.8595
277 BOQ 0.8591
278 VAR 0.8591
279 GZ2 0.8590
280 5PX 0.8590
281 KB8 0.8580
282 0XT 0.8579
283 463 0.8577
284 SG2 0.8576
285 CRB 0.8575
286 ANC 0.8575
287 6QF 0.8573
288 CH9 0.8573
289 61M 0.8572
290 F5C 0.8566
291 34D 0.8558
292 T28 0.8558
293 NIG 0.8555
294 C2U 0.8554
295 7M6 0.8547
296 CE2 0.8544
297 LJ3 0.8544
298 52C 0.8542
299 PD2 0.8540
300 URC 0.8531
301 2T4 0.8530
302 JG8 0.8530
303 E35 0.8527
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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