Receptor
PDB id Resolution Class Description Source Keywords
5U5K 2.33 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF EED IN COMPLEX WITH 3-(3-METHOXYBENZYL) HYDROCHLORIDE HOMO SAPIENS EED FRAGMENT-BASED GENERATION ONCOLOGY TRANSCRIPTION
Ref.: STRUCTURE-GUIDED DESIGN OF EED BINDERS ALLOSTERICAL INHIBITING THE EPIGENETIC POLYCOMB REPRESSIVE COMPL (PRC2) METHYLTRANSFERASE. J. MED. CHEM. V. 60 415 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
7VY A:502;
Valid;
none;
ic50 = 95 uM
205.296 C13 H19 N O COc1c...
FMT A:501;
Invalid;
none;
submit data
46.025 C H2 O2 C(=O)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6W7F 2.2 Å NON-ENZYME: OTHER STRUCTURE OF EED BOUND TO INHIBITOR 5285 HOMO SAPIENS INHIBITOR GENE REGULATION TRANSCRIPTION-INHIBITOR COMPLEX
Ref.: EEDI-5285: AN EXCEPTIONALLY POTENT, EFFICACIOUS, AN ACTIVE SMALL-MOLECULE INHIBITOR OF EMBRYONIC ECTODE DEVELOPMENT. J.MED.CHEM. V. 63 7252 2020
Members (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 6W7G ic50 = 0.5 nM Q3A C23 H22 F N5 O3 S Cc1ccc(c(n....
2 5U8A Ki = 13 nM 82D C22 H25 Br F N3 Cn1cc(c2c1....
3 6W7F ic50 = 0.2 nM Q3D C24 H22 F N5 O3 S CS(=O)(=O)....
4 5TTW Kd = 1.09 uM PRO SER M3L PHE NLW n/a n/a
5 5U69 Ki = 600 nM LQD C23 H29 N3 O Cn1cc(c2c1....
6 5U5H ic50 = 1.3 uM 7VV C18 H24 F N3 O CC(C)c1c2n....
7 3JZG - ALA ARG M3L SER n/a n/a
8 5U8F Ki = 11 nM 82G C24 H28 F N3 Cn1cc(c2c1....
9 5H13 ic50 = 11.58 uM LQA C25 H23 N3 O4 [H]/N=C1/C....
10 5U5K ic50 = 95 uM 7VY C13 H19 N O COc1cccc(c....
11 5U6D Ki = 2.6 nM 7XG C25 H30 F N5 O Cc1cccc(c1....
12 6SFB - L9K C21 H17 N5 O3 S CS(=O)(=O)....
13 6SFC Kd = 5.2 uM L9T C16 H16 N4 O2 S Cc1c(sc(n1....
14 3JZH - ASP PHE M3L THR ASP n/a n/a
15 3K27 - LYS GLN THR ALA ARG M3L SER THR GLY n/a n/a
70% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 6W7G ic50 = 0.5 nM Q3A C23 H22 F N5 O3 S Cc1ccc(c(n....
2 5U8A Ki = 13 nM 82D C22 H25 Br F N3 Cn1cc(c2c1....
3 6W7F ic50 = 0.2 nM Q3D C24 H22 F N5 O3 S CS(=O)(=O)....
4 5TTW Kd = 1.09 uM PRO SER M3L PHE NLW n/a n/a
5 5U69 Ki = 600 nM LQD C23 H29 N3 O Cn1cc(c2c1....
6 5U5H ic50 = 1.3 uM 7VV C18 H24 F N3 O CC(C)c1c2n....
7 3JZG - ALA ARG M3L SER n/a n/a
8 5U8F Ki = 11 nM 82G C24 H28 F N3 Cn1cc(c2c1....
9 5H13 ic50 = 11.58 uM LQA C25 H23 N3 O4 [H]/N=C1/C....
10 5U5K ic50 = 95 uM 7VY C13 H19 N O COc1cccc(c....
11 5U6D Ki = 2.6 nM 7XG C25 H30 F N5 O Cc1cccc(c1....
12 6SFB - L9K C21 H17 N5 O3 S CS(=O)(=O)....
13 6SFC Kd = 5.2 uM L9T C16 H16 N4 O2 S Cc1c(sc(n1....
14 3JZH - ASP PHE M3L THR ASP n/a n/a
15 3K27 - LYS GLN THR ALA ARG M3L SER THR GLY n/a n/a
50% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 6W7G ic50 = 0.5 nM Q3A C23 H22 F N5 O3 S Cc1ccc(c(n....
2 5U8A Ki = 13 nM 82D C22 H25 Br F N3 Cn1cc(c2c1....
3 6W7F ic50 = 0.2 nM Q3D C24 H22 F N5 O3 S CS(=O)(=O)....
4 5TTW Kd = 1.09 uM PRO SER M3L PHE NLW n/a n/a
5 5U69 Ki = 600 nM LQD C23 H29 N3 O Cn1cc(c2c1....
6 5U5H ic50 = 1.3 uM 7VV C18 H24 F N3 O CC(C)c1c2n....
7 3JZG - ALA ARG M3L SER n/a n/a
8 5U8F Ki = 11 nM 82G C24 H28 F N3 Cn1cc(c2c1....
9 5H13 ic50 = 11.58 uM LQA C25 H23 N3 O4 [H]/N=C1/C....
10 5U5K ic50 = 95 uM 7VY C13 H19 N O COc1cccc(c....
11 5U6D Ki = 2.6 nM 7XG C25 H30 F N5 O Cc1cccc(c1....
12 6SFB - L9K C21 H17 N5 O3 S CS(=O)(=O)....
13 6SFC Kd = 5.2 uM L9T C16 H16 N4 O2 S Cc1c(sc(n1....
14 3JZH - ASP PHE M3L THR ASP n/a n/a
15 3K27 - LYS GLN THR ALA ARG M3L SER THR GLY n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 7VY; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 7VY 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: 7VY; Similar ligands found: 242
No: Ligand Similarity coefficient
1 RK4 0.9680
2 536 0.9661
3 531 0.9657
4 VJJ 0.9647
5 0OO 0.9640
6 54F 0.9560
7 0OP 0.9524
8 HHV 0.9478
9 R9G 0.9467
10 H35 0.9431
11 EXG 0.9416
12 TZM 0.9412
13 GNW 0.9397
14 IM4 0.9367
15 6HO 0.9365
16 AX4 0.9306
17 1ZC 0.9296
18 OA1 0.9265
19 A7Q 0.9253
20 11X 0.9241
21 4FP 0.9221
22 LJ4 0.9219
23 4RG 0.9199
24 AX5 0.9186
25 EVO 0.9182
26 9X3 0.9179
27 A4V 0.9178
28 AEY 0.9177
29 TRP 0.9169
30 TH4 0.9161
31 108 0.9161
32 N1Y 0.9152
33 3VW 0.9148
34 FPL 0.9143
35 HLP 0.9139
36 S0F 0.9122
37 9W5 0.9120
38 14W 0.9118
39 PZX 0.9115
40 6C5 0.9113
41 OJD 0.9111
42 3AK 0.9108
43 50Q 0.9105
44 LL2 0.9101
45 DAH 0.9097
46 P2L 0.9096
47 2J5 0.9095
48 4EU 0.9095
49 23N 0.9092
50 NIY 0.9092
51 PW1 0.9091
52 MMS 0.9085
53 XI7 0.9081
54 3QO 0.9068
55 DTR 0.9064
56 HO6 0.9058
57 A18 0.9058
58 NFZ 0.9051
59 ZEZ 0.9051
60 3IP 0.9048
61 IWH 0.9041
62 3IL 0.9037
63 IYR 0.9035
64 ITW 0.9034
65 6C9 0.9034
66 EMU 0.9026
67 MJ5 0.9023
68 L12 0.9022
69 AZY 0.9022
70 SE5 0.9018
71 QTS 0.9013
72 FUZ 0.9010
73 AUY 0.9006
74 C4F 0.9004
75 CH8 0.9002
76 J9Y 0.8998
77 3CX 0.8997
78 0QV 0.8996
79 6MW 0.8990
80 JF5 0.8987
81 YOF 0.8979
82 N2Y 0.8975
83 RCV 0.8973
84 SQV 0.8973
85 KYN 0.8965
86 848 0.8962
87 JPQ 0.8960
88 HX8 0.8955
89 TIZ 0.8954
90 2KU 0.8952
91 S7D 0.8950
92 0QA 0.8947
93 TOH 0.8946
94 DCN 0.8945
95 1YO 0.8945
96 D1Y 0.8945
97 BC3 0.8943
98 ONZ 0.8942
99 9F5 0.8931
100 TPM 0.8930
101 5KJ 0.8929
102 BZQ 0.8926
103 NKI 0.8926
104 9E3 0.8926
105 9PL 0.8922
106 DE7 0.8921
107 22F 0.8915
108 S0I 0.8914
109 RE4 0.8912
110 RDM 0.8911
111 C6Z 0.8910
112 ZIP 0.8907
113 QH3 0.8907
114 JGY 0.8905
115 KWB 0.8904
116 DBE 0.8903
117 YIE 0.8903
118 2LT 0.8901
119 4VT 0.8899
120 B1T 0.8897
121 GZV 0.8896
122 XQI 0.8895
123 6C4 0.8895
124 JCQ 0.8894
125 YIP 0.8892
126 9VQ 0.8885
127 KPV 0.8884
128 8OE 0.8884
129 WL3 0.8881
130 2JX 0.8880
131 P93 0.8880
132 96Z 0.8877
133 1BN 0.8874
134 8CV 0.8867
135 HVE 0.8867
136 BZM 0.8864
137 DCZ 0.8861
138 M02 0.8861
139 9BF 0.8860
140 BDJ 0.8849
141 4Z9 0.8849
142 M01 0.8849
143 0FR 0.8848
144 AX8 0.8843
145 5WN 0.8837
146 5TO 0.8836
147 WA2 0.8833
148 4WF 0.8829
149 MBP 0.8821
150 MH5 0.8809
151 RNK 0.8803
152 AHL 0.8802
153 D8Y 0.8801
154 V15 0.8797
155 TYP 0.8797
156 6NZ 0.8795
157 Z70 0.8793
158 3IB 0.8790
159 ASE 0.8779
160 Q5M 0.8779
161 T07 0.8777
162 BB4 0.8777
163 HWH 0.8776
164 YIH 0.8776
165 6FG 0.8775
166 E9S 0.8774
167 B41 0.8773
168 SB7 0.8768
169 M6H 0.8768
170 CQW 0.8765
171 5PV 0.8764
172 5ER 0.8763
173 DFL 0.8762
174 JE7 0.8760
175 5JT 0.8758
176 LDC 0.8750
177 TIA 0.8748
178 N9M 0.8745
179 X2M 0.8744
180 DDC 0.8742
181 5O5 0.8741
182 E9P 0.8740
183 AC2 0.8735
184 4P8 0.8727
185 ING 0.8726
186 8OB 0.8726
187 DNB 0.8723
188 BZS 0.8722
189 9B3 0.8719
190 XRS 0.8719
191 H48 0.8712
192 6J5 0.8711
193 L21 0.8708
194 LQG 0.8706
195 NPA 0.8705
196 M77 0.8703
197 4Z1 0.8701
198 XOG 0.8697
199 FB4 0.8696
200 B2K 0.8694
201 UN4 0.8693
202 A6H 0.8692
203 4Y2 0.8691
204 BSV 0.8690
205 RP5 0.8684
206 RDY 0.8684
207 F91 0.8682
208 PE2 0.8681
209 KUP 0.8678
210 TA6 0.8674
211 NIP 0.8673
212 6Q3 0.8673
213 5V0 0.8669
214 5AV 0.8664
215 0XR 0.8664
216 IQP 0.8662
217 JA3 0.8658
218 DA3 0.8656
219 NIR 0.8655
220 PQV 0.8654
221 RLG 0.8654
222 6L6 0.8652
223 ML1 0.8651
224 39Z 0.8646
225 TCW 0.8643
226 G6P 0.8633
227 SB9 0.8631
228 XEN 0.8628
229 CHQ 0.8628
230 4OG 0.8610
231 0RY 0.8599
232 GXG 0.8596
233 F1X 0.8587
234 6FR 0.8586
235 STV 0.8585
236 6IP 0.8579
237 0QX 0.8578
238 69K 0.8578
239 GXD 0.8572
240 RGG 0.8571
241 HAR 0.8559
242 7W7 0.8551
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6W7F; Ligand: Q3D; 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: 6w7f.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6W7F; Ligand: Q3D; 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: 6w7f.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
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