Receptor
PDB id Resolution Class Description Source Keywords
6T0D 1.43 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF YTHDC1 WITH FRAGMENT 27 (DHU_DC1_256) HOMO SAPIENS FRAGMENT COMPLEX YTHDC1 EPITRANSCRIPTOMIC RNA BINDING PR
Ref.: SELECTIVELY DISRUPTING M6A-DEPENDENT PROTEIN-RNA INTERACTIONS WITH FRAGMENTS. ACS CHEM.BIOL. V. 15 618 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 B:602;
B:603;
B:605;
B:604;
B:606;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
96.063 O4 S [O-]S...
M4N B:601;
A:601;
 Valid;
Valid;
 none;
none;
 ic50 = 391 uM
201.225 C11 H11 N3 O CNC(=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6RT7 1.73 Å NON-ENZYME: OTHER THE YTH DOMAIN OF YTHDC1 PROTEIN IN COMPLEX WITH GM6ACU OLIGONUCLEOTIDE HOMO SAPIENS PROTEIN-RNA INTERACTION EPITRANSCRIPTOMICS RNA BINDING PRO
Ref.: FLEXIBLE BINDING OF M6A READER PROTEIN YTHDC1 TO IT PREFERRED RNA MOTIF. J CHEM THEORY COMPUT V. 15 7004 2019
Members (34)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 6T07 ic50 > 1000 uM M45 C6 H11 N5 c1nc([nH]n....
2 6SZ1 ic50 > 1000 uM M0W C9 H9 N3 CNc1c2cccc....
3 6T0O - M6N C8 H7 N3 O CC1=Nc2cnc....
4 6SZY ic50 > 1000 uM M5N C11 H16 N2 O CC(C)C1=NC....
5 6SYZ ic50 > 1000 uM M1E C7 H7 N3 S CNc1c2c(cc....
6 6RT5 - G 6MZ C n/a n/a
7 6T01 ic50 = 2057 uM M4B C11 H9 N3 O3 CC1=C(C(=N....
8 6SZ2 - M0Q C9 H9 N3 CNc1ccnc2c....
9 6SZN ic50 > 1000 uM YZM C8 H8 N2 O2 c1ccc(cc1)....
10 6T04 ic50 > 1000 uM M3H C9 H10 N2 c1ccc(cc1)....
11 6SZT ic50 = 1926 uM M4Q C11 H13 N3 O2 S CN(Cc1ccsc....
12 6T05 ic50 > 1000 uM M6H C10 H14 N2 c1ccc(cc1)....
13 6T0C Kd = 22 uM M4E C9 H9 N3 O CNC(=O)c1c....
14 6SZ7 ic50 = 1615 uM M1Q C8 H10 N2 O2 C1CCC2=NC(....
15 6T08 ic50 > 1000 uM M5B C7 H7 N3 O2 S2 c1cc(sc1)S....
16 6SZL ic50 > 1000 uM M3E C10 H8 N2 O2 c1ccc(cc1)....
17 6T11 ic50 = 402 uM O2A C10 H10 N2 O CNC(=O)c1c....
18 6T0Z ic50 > 1000 uM M75 C6 H9 N3 O2 S c1c(nc[nH]....
19 6SZX Kd = 58 uM M4K C15 H17 N3 O2 c1ccc(cc1)....
20 6T02 ic50 > 1000 uM M5E C11 H15 N O c1ccc(cc1)....
21 6RT4 - 6MZ C U n/a n/a
22 6T03 ic50 > 1000 uM MZY C3 H4 N2 S C1=CNC(=S)....
23 6RT7 Kd = 3.7 uM G 6MZ C U n/a n/a
24 6T0A ic50 = 2040 uM M58 C6 H8 N2 S c1cc(cnc1)....
25 6SZR ic50 > 1000 uM M3Z C13 H15 N3 O2 CN(Cc1cccc....
26 6T10 ic50 = 348 uM M6Z C9 H8 I N3 O CNC(=O)c1c....
27 6RT6 Kd = 11.1 uM G G 6MZ C n/a n/a
28 6SZ3 - M1H C10 H14 N2 CNc1ccnc2c....
29 6T0X ic50 > 1000 uM M6W C6 H12 N2 O CNC(=O)[C@....
30 6T06 ic50 = 2010 uM M5H C10 H12 N4 c1ccc2c(c1....
31 6SZ8 ic50 > 1000 uM M1Z C8 H11 N3 O2 C1CCN(C1)C....
32 6T12 ic50 = 825 uM M78 C12 H14 N2 O Cc1c([nH]c....
33 6T0D ic50 = 391 uM M4N C11 H11 N3 O CNC(=O)c1c....
34 6T09 - M4T C7 H8 N2 O CC(=O)Nc1c....
70% Homology Family (34)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 6T07 ic50 > 1000 uM M45 C6 H11 N5 c1nc([nH]n....
2 6SZ1 ic50 > 1000 uM M0W C9 H9 N3 CNc1c2cccc....
3 6T0O - M6N C8 H7 N3 O CC1=Nc2cnc....
4 6SZY ic50 > 1000 uM M5N C11 H16 N2 O CC(C)C1=NC....
5 6SYZ ic50 > 1000 uM M1E C7 H7 N3 S CNc1c2c(cc....
6 6RT5 - G 6MZ C n/a n/a
7 6T01 ic50 = 2057 uM M4B C11 H9 N3 O3 CC1=C(C(=N....
8 6SZ2 - M0Q C9 H9 N3 CNc1ccnc2c....
9 6SZN ic50 > 1000 uM YZM C8 H8 N2 O2 c1ccc(cc1)....
10 6T04 ic50 > 1000 uM M3H C9 H10 N2 c1ccc(cc1)....
11 6SZT ic50 = 1926 uM M4Q C11 H13 N3 O2 S CN(Cc1ccsc....
12 6T05 ic50 > 1000 uM M6H C10 H14 N2 c1ccc(cc1)....
13 6T0C Kd = 22 uM M4E C9 H9 N3 O CNC(=O)c1c....
14 6SZ7 ic50 = 1615 uM M1Q C8 H10 N2 O2 C1CCC2=NC(....
15 6T08 ic50 > 1000 uM M5B C7 H7 N3 O2 S2 c1cc(sc1)S....
16 6SZL ic50 > 1000 uM M3E C10 H8 N2 O2 c1ccc(cc1)....
17 6T11 ic50 = 402 uM O2A C10 H10 N2 O CNC(=O)c1c....
18 6T0Z ic50 > 1000 uM M75 C6 H9 N3 O2 S c1c(nc[nH]....
19 6SZX Kd = 58 uM M4K C15 H17 N3 O2 c1ccc(cc1)....
20 6T02 ic50 > 1000 uM M5E C11 H15 N O c1ccc(cc1)....
21 6RT4 - 6MZ C U n/a n/a
22 6T03 ic50 > 1000 uM MZY C3 H4 N2 S C1=CNC(=S)....
23 6RT7 Kd = 3.7 uM G 6MZ C U n/a n/a
24 6T0A ic50 = 2040 uM M58 C6 H8 N2 S c1cc(cnc1)....
25 6SZR ic50 > 1000 uM M3Z C13 H15 N3 O2 CN(Cc1cccc....
26 6T10 ic50 = 348 uM M6Z C9 H8 I N3 O CNC(=O)c1c....
27 6RT6 Kd = 11.1 uM G G 6MZ C n/a n/a
28 6SZ3 - M1H C10 H14 N2 CNc1ccnc2c....
29 6T0X ic50 > 1000 uM M6W C6 H12 N2 O CNC(=O)[C@....
30 6T06 ic50 = 2010 uM M5H C10 H12 N4 c1ccc2c(c1....
31 6SZ8 ic50 > 1000 uM M1Z C8 H11 N3 O2 C1CCN(C1)C....
32 6T12 ic50 = 825 uM M78 C12 H14 N2 O Cc1c([nH]c....
33 6T0D ic50 = 391 uM M4N C11 H11 N3 O CNC(=O)c1c....
34 6T09 - M4T C7 H8 N2 O CC(=O)Nc1c....
50% Homology Family (34)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 6T07 ic50 > 1000 uM M45 C6 H11 N5 c1nc([nH]n....
2 6SZ1 ic50 > 1000 uM M0W C9 H9 N3 CNc1c2cccc....
3 6T0O - M6N C8 H7 N3 O CC1=Nc2cnc....
4 6SZY ic50 > 1000 uM M5N C11 H16 N2 O CC(C)C1=NC....
5 6SYZ ic50 > 1000 uM M1E C7 H7 N3 S CNc1c2c(cc....
6 6RT5 - G 6MZ C n/a n/a
7 6T01 ic50 = 2057 uM M4B C11 H9 N3 O3 CC1=C(C(=N....
8 6SZ2 - M0Q C9 H9 N3 CNc1ccnc2c....
9 6SZN ic50 > 1000 uM YZM C8 H8 N2 O2 c1ccc(cc1)....
10 6T04 ic50 > 1000 uM M3H C9 H10 N2 c1ccc(cc1)....
11 6SZT ic50 = 1926 uM M4Q C11 H13 N3 O2 S CN(Cc1ccsc....
12 6T05 ic50 > 1000 uM M6H C10 H14 N2 c1ccc(cc1)....
13 6T0C Kd = 22 uM M4E C9 H9 N3 O CNC(=O)c1c....
14 6SZ7 ic50 = 1615 uM M1Q C8 H10 N2 O2 C1CCC2=NC(....
15 6T08 ic50 > 1000 uM M5B C7 H7 N3 O2 S2 c1cc(sc1)S....
16 6SZL ic50 > 1000 uM M3E C10 H8 N2 O2 c1ccc(cc1)....
17 6T11 ic50 = 402 uM O2A C10 H10 N2 O CNC(=O)c1c....
18 6T0Z ic50 > 1000 uM M75 C6 H9 N3 O2 S c1c(nc[nH]....
19 6SZX Kd = 58 uM M4K C15 H17 N3 O2 c1ccc(cc1)....
20 6T02 ic50 > 1000 uM M5E C11 H15 N O c1ccc(cc1)....
21 6RT4 - 6MZ C U n/a n/a
22 6T03 ic50 > 1000 uM MZY C3 H4 N2 S C1=CNC(=S)....
23 6RT7 Kd = 3.7 uM G 6MZ C U n/a n/a
24 6T0A ic50 = 2040 uM M58 C6 H8 N2 S c1cc(cnc1)....
25 6SZR ic50 > 1000 uM M3Z C13 H15 N3 O2 CN(Cc1cccc....
26 6T10 ic50 = 348 uM M6Z C9 H8 I N3 O CNC(=O)c1c....
27 6RT6 Kd = 11.1 uM G G 6MZ C n/a n/a
28 6SZ3 - M1H C10 H14 N2 CNc1ccnc2c....
29 6T0X ic50 > 1000 uM M6W C6 H12 N2 O CNC(=O)[C@....
30 6T06 ic50 = 2010 uM M5H C10 H12 N4 c1ccc2c(c1....
31 6SZ8 ic50 > 1000 uM M1Z C8 H11 N3 O2 C1CCN(C1)C....
32 6T12 ic50 = 825 uM M78 C12 H14 N2 O Cc1c([nH]c....
33 6T0D ic50 = 391 uM M4N C11 H11 N3 O CNC(=O)c1c....
34 6T09 - M4T C7 H8 N2 O CC(=O)Nc1c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: M4N; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 M4N 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: M4N; Similar ligands found: 441
No: Ligand Similarity coefficient
1 8CC 0.9861
2 A9B 0.9680
3 NK5 0.9652
4 G14 0.9646
5 ZZA 0.9625
6 P7V 0.9607
7 3VQ 0.9566
8 JMG 0.9559
9 KLE 0.9557
10 ODK 0.9556
11 YE6 0.9536
12 KLS 0.9531
13 D25 0.9529
14 47V 0.9520
15 KW7 0.9516
16 5C1 0.9497
17 A6W 0.9487
18 0UL 0.9467
19 PUE 0.9447
20 9FH 0.9419
21 MKN 0.9418
22 7O4 0.9404
23 5E5 0.9393
24 6C8 0.9390
25 D26 0.9371
26 5TT 0.9371
27 FCW 0.9367
28 J38 0.9365
29 L1T 0.9360
30 LZ5 0.9359
31 2D2 0.9346
32 0NX 0.9335
33 7MW 0.9332
34 7EH 0.9321
35 7KE 0.9316
36 7FU 0.9313
37 JCZ 0.9306
38 6FG 0.9300
39 FHV 0.9294
40 SWX 0.9291
41 FZM 0.9291
42 363 0.9290
43 3C5 0.9286
44 5H6 0.9278
45 XI7 0.9270
46 8D6 0.9262
47 6H2 0.9259
48 FCD 0.9257
49 C4E 0.9252
50 PIQ 0.9252
51 7G2 0.9251
52 A98 0.9246
53 68B 0.9245
54 4FF 0.9239
55 1XS 0.9238
56 5TO 0.9237
57 1OT 0.9228
58 5B2 0.9225
59 PQM 0.9223
60 RKV 0.9215
61 4AU 0.9214
62 TJM 0.9214
63 0DF 0.9212
64 L2K 0.9209
65 833 0.9209
66 6C5 0.9206
67 39R 0.9205
68 0OK 0.9203
69 9JT 0.9199
70 PQS 0.9197
71 TMG 0.9191
72 WA1 0.9187
73 6P3 0.9181
74 6MW 0.9180
75 QME 0.9172
76 JGY 0.9172
77 3VS 0.9172
78 J1K 0.9169
79 2FX 0.9166
80 YE7 0.9165
81 M78 0.9164
82 ZRK 0.9164
83 JBZ 0.9162
84 78Y 0.9161
85 Y3L 0.9160
86 VC3 0.9160
87 795 0.9155
88 LR8 0.9155
89 B1J 0.9155
90 BP7 0.9154
91 LL1 0.9154
92 TCR 0.9151
93 0K7 0.9149
94 LR2 0.9144
95 F4K 0.9137
96 0ON 0.9135
97 K48 0.9133
98 2JX 0.9133
99 RF2 0.9129
100 D2G 0.9128
101 D9Z 0.9127
102 6DQ 0.9127
103 BSU 0.9123
104 BVS 0.9121
105 RA7 0.9120
106 F40 0.9117
107 TRP 0.9117
108 S0D 0.9116
109 8YH 0.9112
110 6L6 0.9112
111 245 0.9110
112 54E 0.9109
113 9NB 0.9107
114 LFQ 0.9106
115 AD6 0.9104
116 LO1 0.9101
117 FYR 0.9098
118 LIG 0.9095
119 QIV 0.9094
120 3DE 0.9093
121 EV2 0.9092
122 0SY 0.9088
123 5VU 0.9086
124 6SD 0.9085
125 OLU 0.9083
126 27K 0.9082
127 YZ9 0.9082
128 S8P 0.9079
129 D1G 0.9078
130 1EB 0.9075
131 6C9 0.9074
132 KF5 0.9073
133 0NJ 0.9070
134 AVA 0.9067
135 D3G 0.9065
136 JF5 0.9064
137 CBE 0.9061
138 4G2 0.9059
139 1A5 0.9059
140 5SJ 0.9055
141 VGS 0.9055
142 5F8 0.9053
143 AJ1 0.9051
144 JVD 0.9045
145 1HP 0.9043
146 GOE 0.9043
147 L03 0.9041
148 SOJ 0.9041
149 P4L 0.9040
150 II4 0.9036
151 6C4 0.9036
152 0LO 0.9033
153 F02 0.9031
154 UN3 0.9030
155 VM1 0.9028
156 20N 0.9024
157 PQV 0.9024
158 2PK 0.9023
159 5DE 0.9023
160 2PV 0.9022
161 RSV 0.9019
162 RGK 0.9018
163 H75 0.9014
164 5WK 0.9013
165 4BX 0.9011
166 XCG 0.9010
167 K4T 0.9010
168 1V3 0.9009
169 37E 0.9009
170 JAH 0.9006
171 G2V 0.9006
172 C53 0.9006
173 1V4 0.9005
174 4HB 0.9005
175 397 0.9005
176 X6W 0.9004
177 2P3 0.9004
178 OQC 0.9003
179 1FE 0.9001
180 1Q2 0.8998
181 A5Q 0.8997
182 TID 0.8996
183 7L4 0.8996
184 P93 0.8994
185 KWV 0.8989
186 4CN 0.8988
187 4I8 0.8988
188 9CE 0.8987
189 K7H 0.8980
190 AJG 0.8978
191 JA5 0.8978
192 EQW 0.8976
193 MR6 0.8976
194 GO2 0.8976
195 FC2 0.8973
196 BMZ 0.8966
197 MMJ 0.8965
198 2QC 0.8965
199 8V8 0.8964
200 ERZ 0.8959
201 HL6 0.8958
202 5TZ 0.8954
203 NDD 0.8952
204 BZQ 0.8951
205 90G 0.8949
206 S0A 0.8948
207 PZX 0.8946
208 4FC 0.8945
209 TPM 0.8944
210 2QU 0.8944
211 HNT 0.8941
212 A7H 0.8939
213 B21 0.8933
214 49P 0.8932
215 3D8 0.8931
216 GJG 0.8931
217 5FL 0.8929
218 3F4 0.8929
219 0MB 0.8928
220 VFM 0.8926
221 K0G 0.8926
222 HH6 0.8923
223 60L 0.8922
224 2O8 0.8921
225 36Y 0.8920
226 120 0.8916
227 SZ5 0.8915
228 492 0.8915
229 HX4 0.8910
230 S7D 0.8909
231 AVX 0.8909
232 AP6 0.8906
233 FBC 0.8905
234 3XH 0.8905
235 EWG 0.8904
236 ZTW 0.8904
237 122 0.8903
238 801 0.8899
239 121 0.8899
240 X48 0.8898
241 6KT 0.8897
242 MD6 0.8896
243 RDV 0.8896
244 CPZ 0.8891
245 S45 0.8890
246 3S9 0.8888
247 HC4 0.8887
248 LEL 0.8887
249 CR4 0.8887
250 ZEA 0.8883
251 80G 0.8883
252 0FR 0.8883
253 3CX 0.8882
254 M83 0.8881
255 PRL 0.8881
256 E3X 0.8877
257 25F 0.8877
258 4MB 0.8876
259 BZM 0.8875
260 SSY 0.8875
261 1R5 0.8875
262 549 0.8873
263 A73 0.8872
264 20D 0.8871
265 DFL 0.8870
266 LOT 0.8867
267 83D 0.8867
268 2J1 0.8865
269 SNJ 0.8864
270 7VP 0.8863
271 N9M 0.8862
272 1V1 0.8862
273 OA1 0.8860
274 11X 0.8859
275 6N4 0.8859
276 MGB 0.8857
277 Q4G 0.8856
278 5F5 0.8855
279 6FB 0.8853
280 DXK 0.8853
281 S8G 0.8851
282 272 0.8850
283 124 0.8850
284 4UM 0.8848
285 2QV 0.8848
286 MR4 0.8844
287 I2E 0.8844
288 P81 0.8843
289 1Q1 0.8842
290 IDZ 0.8842
291 P4T 0.8840
292 92O 0.8838
293 VFG 0.8836
294 MR5 0.8836
295 4NP 0.8834
296 CIU 0.8832
297 U7E 0.8831
298 L15 0.8831
299 2GQ 0.8830
300 A51 0.8830
301 D64 0.8827
302 ZRL 0.8827
303 AZM 0.8826
304 H4B 0.8825
305 JMM 0.8824
306 VUP 0.8823
307 WLH 0.8819
308 RCV 0.8815
309 HRM 0.8814
310 5S9 0.8813
311 36M 0.8811
312 N4E 0.8808
313 ITE 0.8806
314 GHQ 0.8806
315 NY4 0.8805
316 X2M 0.8797
317 613 0.8795
318 SNV 0.8793
319 TIA 0.8789
320 NIF 0.8786
321 6QT 0.8784
322 Z21 0.8783
323 52F 0.8783
324 72D 0.8780
325 SJR 0.8778
326 GVY 0.8777
327 4NS 0.8774
328 VFJ 0.8773
329 5NN 0.8771
330 KWB 0.8771
331 6T5 0.8769
332 ZHA 0.8768
333 IWT 0.8767
334 F18 0.8766
335 Q9T 0.8766
336 U13 0.8764
337 PPY 0.8763
338 AOY 0.8761
339 Q8D 0.8760
340 DHC 0.8759
341 5OR 0.8758
342 4V2 0.8757
343 9BF 0.8754
344 3SU 0.8753
345 PNP 0.8751
346 DX2 0.8750
347 WDW 0.8743
348 PTB 0.8743
349 2OX 0.8742
350 4ZF 0.8740
351 1PS 0.8739
352 3GX 0.8739
353 ENO 0.8739
354 STV 0.8730
355 AES 0.8728
356 LC1 0.8725
357 BC5 0.8724
358 W8L 0.8719
359 0XR 0.8718
360 4AF 0.8718
361 REG 0.8717
362 TOH 0.8715
363 0QA 0.8714
364 2WU 0.8707
365 BX4 0.8706
366 JFS 0.8705
367 4Z9 0.8704
368 AMR 0.8704
369 3R4 0.8704
370 IQQ 0.8704
371 S7S 0.8700
372 EES 0.8700
373 S62 0.8700
374 Q8G 0.8699
375 S98 0.8697
376 DAH 0.8696
377 FF2 0.8696
378 UAY 0.8691
379 657 0.8691
380 WG8 0.8690
381 7ZO 0.8688
382 A5H 0.8687
383 M5A 0.8687
384 CDJ 0.8686
385 BVA 0.8684
386 BQ2 0.8681
387 1AJ 0.8680
388 92Y 0.8678
389 IOP 0.8672
390 GT4 0.8671
391 92G 0.8670
392 5NR 0.8667
393 H2W 0.8663
394 IPJ 0.8661
395 HXY 0.8652
396 L02 0.8650
397 BIK 0.8650
398 JSX 0.8650
399 MJW 0.8649
400 4BY 0.8647
401 C82 0.8645
402 2LW 0.8645
403 ZE7 0.8643
404 JCQ 0.8642
405 ZSP 0.8641
406 D8Q 0.8640
407 L5D 0.8640
408 IIH 0.8639
409 5ZM 0.8639
410 EAE 0.8637
411 E9L 0.8637
412 1ER 0.8634
413 EUE 0.8633
414 6FR 0.8624
415 G1L 0.8621
416 3D3 0.8621
417 9KZ 0.8616
418 ESJ 0.8610
419 FZ0 0.8606
420 0F3 0.8604
421 5TU 0.8600
422 Z3R 0.8600
423 CUE 0.8599
424 A8D 0.8598
425 RAY 0.8594
426 L22 0.8593
427 5TY 0.8587
428 S7V 0.8581
429 X0U 0.8575
430 EE8 0.8574
431 HPX 0.8570
432 JGB 0.8562
433 E42 0.8559
434 NEU 0.8558
435 135 0.8551
436 U55 0.8550
437 3QV 0.8532
438 C0V 0.8532
439 TEF 0.8522
440 ZYQ 0.8517
441 4XF 0.8506
Similar Binding Sites (Proteins are less than 50% similar to leader) APoc FAQ
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