Receptor
PDB id Resolution Class Description Source Keywords
4N1T 1.6 Å EC: 3.6.1.55 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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:205;
A:203;
A:202;
A:204;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
96.063 O4 S [O-]S...
2GD A:201;
 Valid;
 none;
 ic50 = 0.8 nM
269.13 C11 H10 Cl2 N4 CNc1c...
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: 2GD; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 2GD 1 1
2 2GE 0.649123 0.860465
Similar Ligands (3D)
Ligand no: 1; Ligand: 2GD; Similar ligands found: 328
No: Ligand Similarity coefficient
1 B2T 0.9691
2 X11 0.9467
3 WOE 0.9451
4 28A 0.9376
5 IA2 0.9343
6 6PB 0.9335
7 M3E 0.9334
8 TI7 0.9299
9 Q4G 0.9298
10 L5D 0.9290
11 BZE 0.9282
12 WVV 0.9277
13 IQQ 0.9268
14 6J3 0.9260
15 ID8 0.9252
16 BP3 0.9252
17 H70 0.9233
18 KCH 0.9226
19 4GU 0.9225
20 AUV 0.9224
21 EZN 0.9224
22 28B 0.9217
23 PBQ 0.9209
24 TLF 0.9205
25 BBY 0.9188
26 5F8 0.9186
27 AVA 0.9184
28 NE1 0.9167
29 1ZC 0.9156
30 4E5 0.9153
31 B4O 0.9149
32 XEV 0.9147
33 XYP AHR 0.9143
34 43F 0.9143
35 CTN 0.9139
36 W29 0.9136
37 Z16 0.9135
38 BQ5 0.9130
39 FHI 0.9123
40 GN6 0.9115
41 6HX 0.9111
42 A4G 0.9111
43 P9I 0.9109
44 XZ8 0.9106
45 43S 0.9101
46 BPY 0.9101
47 X6P 0.9099
48 JMS 0.9096
49 LJ3 0.9090
50 EAJ 0.9084
51 3C5 0.9075
52 QKU 0.9073
53 XDK 0.9071
54 CK2 0.9070
55 1ER 0.9065
56 79W 0.9064
57 4FF 0.9061
58 5FL 0.9060
59 DCZ 0.9053
60 URI 0.9052
61 5E4 0.9051
62 AH6 0.9050
63 JSX 0.9050
64 1SF 0.9049
65 AVX 0.9048
66 P4L 0.9047
67 FCD 0.9046
68 36Z 0.9044
69 3AD 0.9042
70 5AE 0.9042
71 9CE 0.9041
72 FC2 0.9040
73 2D2 0.9018
74 YE6 0.9012
75 S1D 0.9012
76 7ZL 0.9010
77 M1Z 0.9006
78 5P3 0.9002
79 VBC 0.8998
80 27M 0.8995
81 5C1 0.8991
82 5N5 0.8986
83 17C 0.8984
84 25O 0.8983
85 PCQ 0.8983
86 ADN 0.8982
87 DKZ 0.8981
88 DIF 0.8980
89 6ZW 0.8980
90 6J9 0.8979
91 BP6 0.8976
92 DBQ 0.8976
93 49P 0.8972
94 7VF 0.8967
95 5FD 0.8966
96 CK1 0.8963
97 TCC 0.8962
98 ZYW 0.8959
99 977 0.8958
100 DKX 0.8957
101 VAO 0.8949
102 NE2 0.8949
103 3D1 0.8948
104 TR4 0.8948
105 DXK 0.8948
106 CJB 0.8948
107 AZZ 0.8943
108 5F5 0.8943
109 7L4 0.8942
110 XYP XDN 0.8942
111 VM1 0.8940
112 NOS 0.8935
113 AJD 0.8934
114 CJZ 0.8934
115 MZR 0.8930
116 THM 0.8926
117 5E5 0.8925
118 MIL 0.8924
119 DBS 0.8924
120 0LO 0.8917
121 43U 0.8917
122 LL1 0.8916
123 TIZ 0.8916
124 XYP XIF 0.8914
125 XDN XYP 0.8911
126 AD3 0.8910
127 6EN 0.8906
128 TH4 0.8904
129 6NZ 0.8902
130 GPQ 0.8901
131 XIF XYP 0.8900
132 NIR 0.8899
133 5CD 0.8899
134 A73 0.8896
135 4G2 0.8895
136 3RP 0.8894
137 6DQ 0.8894
138 GPU 0.8893
139 683 0.8893
140 DK4 0.8887
141 TJM 0.8886
142 4GP 0.8884
143 B86 0.8882
144 OX2 0.8881
145 GPK 0.8880
146 3D8 0.8878
147 XYP XYP 0.8878
148 K48 0.8877
149 5AD 0.8875
150 LFQ 0.8874
151 ARJ 0.8874
152 C53 0.8862
153 3Y7 0.8862
154 BP7 0.8861
155 XDL XYP 0.8861
156 X48 0.8858
157 AKD 0.8855
158 1FL 0.8854
159 6DE 0.8851
160 4AU 0.8850
161 Z15 0.8850
162 Z57 0.8849
163 8HH 0.8847
164 AV4 0.8846
165 H7S 0.8845
166 1A7 0.8844
167 2JM 0.8843
168 4F8 0.8843
169 K3Y 0.8841
170 20D 0.8838
171 NKI 0.8835
172 KWB 0.8832
173 M0Y 0.8831
174 Z2T 0.8826
175 Y3J 0.8826
176 1V1 0.8824
177 5F1 0.8822
178 BNY 0.8820
179 ZME 0.8820
180 K80 0.8819
181 9UL 0.8818
182 MUK 0.8817
183 VCE 0.8817
184 1DA 0.8817
185 NOC 0.8814
186 DUR 0.8814
187 SQV 0.8812
188 5B2 0.8811
189 64I 0.8807
190 X29 0.8801
191 X6W 0.8799
192 9FG 0.8798
193 2LT 0.8795
194 2TU 0.8794
195 AQ1 0.8793
196 TIA 0.8792
197 1XS 0.8792
198 GZV 0.8789
199 THU 0.8786
200 TT4 0.8786
201 MEX 0.8785
202 IK1 0.8783
203 1V4 0.8780
204 3GX 0.8776
205 XIL 0.8771
206 C0H 0.8771
207 G30 0.8768
208 TRP 0.8768
209 L1T 0.8767
210 PUR 0.8766
211 RVB 0.8764
212 3DT 0.8763
213 C4E 0.8759
214 UN3 0.8759
215 ABJ 0.8758
216 MTA 0.8757
217 F16 0.8757
218 5BT 0.8757
219 DDC 0.8755
220 2LX 0.8753
221 L2K 0.8753
222 MXD 0.8751
223 WLH 0.8750
224 V2Z 0.8748
225 B23 0.8746
226 ZRK 0.8746
227 MFR 0.8746
228 272 0.8744
229 5NN 0.8743
230 U4J 0.8740
231 MUR 0.8738
232 RVD 0.8731
233 5ID 0.8726
234 2B4 0.8724
235 22L 0.8724
236 AYS 0.8723
237 BNL 0.8722
238 B21 0.8721
239 EAT 0.8720
240 HH6 0.8720
241 P2L 0.8720
242 UA2 0.8707
243 Q2R 0.8705
244 KYN 0.8702
245 GMP 0.8701
246 D3G 0.8700
247 L13 0.8698
248 5I5 0.8697
249 IMH 0.8696
250 ID2 0.8694
251 D2G 0.8694
252 AB3 0.8691
253 0FR 0.8687
254 JGB 0.8687
255 7R4 0.8684
256 A7K 0.8684
257 PRH 0.8683
258 HPR 0.8683
259 NNR 0.8682
260 3L1 0.8681
261 RVC 0.8681
262 VM7 0.8674
263 92G 0.8674
264 JF8 0.8670
265 1Z6 0.8670
266 LWS 0.8669
267 R20 0.8669
268 EWG 0.8669
269 ODK 0.8667
270 BXZ 0.8665
271 89J 0.8662
272 HJH 0.8661
273 145 0.8658
274 II4 0.8656
275 2FA 0.8651
276 9PL 0.8650
277 MMS 0.8649
278 JRB 0.8647
279 0DN 0.8647
280 6KN 0.8643
281 7M2 0.8641
282 WL3 0.8640
283 FMB 0.8638
284 60L 0.8636
285 EVO 0.8634
286 7VP 0.8634
287 7D7 0.8634
288 53X 0.8634
289 5V7 0.8631
290 XI7 0.8630
291 LUR 0.8626
292 6GP 0.8624
293 MG7 0.8620
294 AH9 0.8620
295 A4D 0.8616
296 F01 0.8614
297 TOH 0.8610
298 XYS XYP 0.8608
299 AMR 0.8607
300 1V3 0.8606
301 D1M 0.8599
302 A 0.8599
303 HQJ 0.8587
304 NWW 0.8586
305 A1Y 0.8585
306 9FH 0.8580
307 57D 0.8577
308 LI7 0.8577
309 BIE 0.8576
310 SV4 0.8573
311 5VU 0.8572
312 OA1 0.8567
313 B2Y 0.8565
314 3DE 0.8559
315 8D6 0.8558
316 8UY 0.8557
317 ERZ 0.8555
318 3IL 0.8552
319 N8Z 0.8545
320 2QU 0.8543
321 QQX 0.8540
322 HX4 0.8537
323 W8L 0.8536
324 2KU 0.8536
325 HNK 0.8519
326 NWQ 0.8506
327 I5A 0.8506
328 38E 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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