Receptor
PDB id Resolution Class Description Source Keywords
5YJ1 2 Å NON-ENZYME: OTHER MOUSE CEREBLON THALIDOMIDE BINDING DOMAIN COMPLEXED WITH R-F THALIDOMIDE MUS MUSCULUS ZINC BINDING PROTEIN METAL BINDING PROTEIN
Ref.: STRUCTURAL BASIS OF THALIDOMIDE ENANTIOMER BINDING CEREBLON SCI REP V. 8 1294 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN K:502;
H:502;
E:502;
A:502;
S:502;
Q:502;
P:502;
B:502;
G:502;
T:502;
M:502;
J:502;
D:502;
V:502;
N:502;
Y:502;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
SO4 T:504;
B:503;
T:503;
M:503;
S:504;
J:504;
S:503;
H:503;
A:503;
Y:504;
M:504;
K:504;
D:504;
K:503;
A:504;
P:503;
N:503;
M:505;
E:504;
N:504;
N:505;
V:504;
D:503;
J:503;
V:503;
B:504;
E:503;
Q:503;
Y:505;
Y:503;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
6EL M:501;
Y:501;
T:501;
D:501;
Q:501;
A:501;
S:501;
P:501;
H:501;
V:501;
E:501;
G:501;
N:501;
K:501;
B:501;
J:501;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
Kd = 50.3 uM
258.229 C13 H10 N2 O4 c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5YJ0 1.8 Å NON-ENZYME: OTHER MOUSE CEREBLON THALIDOMIDE BINDING DOMAIN COMPLEXED WITH S-F THALIDOMIDE MUS MUSCULUS ZINC BINDING PROTEIN METAL BINDING PROTEIN
Ref.: STRUCTURAL BASIS OF THALIDOMIDE ENANTIOMER BINDING CEREBLON SCI REP V. 8 1294 2018
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 5YJ0 Kd = 5.7 uM EF2 C13 H10 N2 O4 c1ccc2c(c1....
2 5YIZ - EF2 C13 H10 N2 O4 c1ccc2c(c1....
3 5YJ1 Kd = 50.3 uM 6EL C13 H10 N2 O4 c1ccc2c(c1....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 5YJ0 Kd = 5.7 uM EF2 C13 H10 N2 O4 c1ccc2c(c1....
2 5YIZ - EF2 C13 H10 N2 O4 c1ccc2c(c1....
3 5YJ1 Kd = 50.3 uM 6EL C13 H10 N2 O4 c1ccc2c(c1....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 5YJ0 Kd = 5.7 uM EF2 C13 H10 N2 O4 c1ccc2c(c1....
2 5YIZ - EF2 C13 H10 N2 O4 c1ccc2c(c1....
3 5YJ1 Kd = 50.3 uM 6EL C13 H10 N2 O4 c1ccc2c(c1....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 6EL; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 EF2 1 1
2 6EL 1 1
3 F4U 0.611111 0.903846
4 Y70 0.561404 0.903846
5 LVY 0.451613 0.854545
Similar Ligands (3D)
Ligand no: 1; Ligand: 6EL; Similar ligands found: 259
No: Ligand Similarity coefficient
1 0OK 0.9480
2 H75 0.9455
3 789 0.9422
4 KW7 0.9413
5 EES 0.9390
6 J84 0.9377
7 TGW 0.9369
8 6WR 0.9316
9 JO5 0.9280
10 GEN 0.9252
11 JOB 0.9246
12 EI1 0.9241
13 47X 0.9238
14 4NR 0.9211
15 Q0K 0.9209
16 5OR 0.9177
17 TC8 0.9167
18 A4T 0.9152
19 A4N 0.9146
20 7EL 0.9145
21 KP2 0.9137
22 26C 0.9132
23 2P3 0.9131
24 KF5 0.9116
25 397 0.9112
26 J27 0.9109
27 QME 0.9094
28 9FH 0.9090
29 C2M 0.9088
30 38B 0.9084
31 S0G 0.9081
32 7EH 0.9076
33 STZ 0.9076
34 YX1 0.9076
35 8D6 0.9075
36 IQW 0.9073
37 64I 0.9072
38 ADN 0.9061
39 9FG 0.9059
40 PQS 0.9057
41 2JX 0.9054
42 1CY 0.9054
43 KMP 0.9049
44 0J4 0.9028
45 1HP 0.9025
46 CP6 0.9023
47 OA4 0.9018
48 AJ4 0.9015
49 H4B 0.9007
50 XYP XYP 0.9001
51 CC5 0.9000
52 FCW 0.9000
53 6DE 0.8988
54 3WJ 0.8986
55 ARJ 0.8976
56 3WK 0.8974
57 EAT 0.8970
58 4MP 0.8969
59 LZJ 0.8969
60 PQM 0.8966
61 AFX 0.8960
62 XDL XYP 0.8956
63 5DE 0.8955
64 54E 0.8955
65 WCU 0.8954
66 5AD 0.8946
67 15Q 0.8945
68 RVE 0.8937
69 3UG 0.8936
70 HMO 0.8936
71 C93 0.8933
72 7L4 0.8931
73 XYP XIF 0.8930
74 XIF XYP 0.8930
75 FMQ 0.8922
76 42R 0.8921
77 9KZ 0.8918
78 FT6 0.8913
79 XYS XYS 0.8912
80 XYP XDN 0.8912
81 XDN XYP 0.8911
82 AJ6 0.8910
83 3QI 0.8908
84 A9K 0.8903
85 7FZ 0.8903
86 AGI 0.8899
87 51Y 0.8897
88 4EU 0.8896
89 3DE 0.8894
90 GFE 0.8893
91 XIL 0.8891
92 7G1 0.8887
93 MEX 0.8883
94 B52 0.8881
95 PZ8 0.8880
96 NOC 0.8878
97 DK4 0.8871
98 CJB 0.8867
99 72E 0.8867
100 6DQ 0.8867
101 DKZ 0.8865
102 1SF 0.8865
103 NAL 0.8864
104 GPK 0.8863
105 4AB 0.8860
106 DKX 0.8859
107 CU8 0.8859
108 H2B 0.8857
109 TRP 0.8857
110 AUT 0.8857
111 XYP XYS 0.8854
112 1FL 0.8850
113 NYJ 0.8849
114 4AF 0.8848
115 5VU 0.8848
116 FHI 0.8847
117 HBI 0.8841
118 EV2 0.8839
119 27M 0.8838
120 DFL 0.8838
121 AU8 0.8837
122 0DF 0.8830
123 78U 0.8829
124 D64 0.8829
125 5I5 0.8820
126 GPQ 0.8818
127 JFS 0.8813
128 RKN 0.8805
129 A7K 0.8805
130 XYS XYP 0.8800
131 BHS 0.8797
132 FWD 0.8794
133 5CK 0.8793
134 Z15 0.8793
135 XYA 0.8790
136 4DE 0.8788
137 7G0 0.8788
138 68B 0.8788
139 92O 0.8786
140 GPU 0.8785
141 A4Q 0.8777
142 OSP 0.8776
143 SJK 0.8772
144 M77 0.8772
145 AWE 0.8770
146 Z57 0.8763
147 ZTW 0.8761
148 LU2 0.8759
149 5CD 0.8758
150 MZR 0.8755
151 NE1 0.8753
152 3JC 0.8749
153 P2L 0.8748
154 BC5 0.8746
155 1Q4 0.8746
156 5FD 0.8745
157 3WO 0.8744
158 3WN 0.8744
159 LOT 0.8742
160 0FR 0.8742
161 22L 0.8735
162 96Z 0.8731
163 CTN 0.8730
164 EST 0.8729
165 50C 0.8724
166 TBN 0.8721
167 U3P 0.8718
168 1A5 0.8717
169 CWD 0.8716
170 NOS 0.8710
171 H4B NO 0.8710
172 Y0V 0.8708
173 L3L 0.8708
174 CP7 0.8707
175 BG8 0.8706
176 57D 0.8706
177 A4B 0.8706
178 BP3 0.8703
179 35G 0.8703
180 W23 0.8702
181 0ON 0.8699
182 1GM 0.8698
183 TCL 0.8698
184 RAB 0.8696
185 Y3J 0.8692
186 A8Q 0.8691
187 RSV 0.8690
188 G14 0.8689
189 40N 0.8688
190 PRH 0.8687
191 4L2 0.8682
192 IMK 0.8677
193 F5F 0.8677
194 CMP 0.8676
195 AVX 0.8669
196 EZB 0.8668
197 5F1 0.8668
198 AUG 0.8665
199 3AD 0.8664
200 FM2 0.8662
201 2L1 0.8661
202 HWD 0.8660
203 GJG 0.8659
204 FMB 0.8658
205 C5Q 0.8654
206 DFV 0.8653
207 6MD 0.8651
208 KWB 0.8651
209 458 0.8650
210 6WU 0.8648
211 B2L 0.8646
212 6SX 0.8645
213 BIO 0.8640
214 FMC 0.8637
215 72D 0.8637
216 NWD 0.8636
217 A4D 0.8635
218 0X2 0.8635
219 BWD 0.8632
220 NAR 0.8625
221 5N5 0.8623
222 DBS 0.8621
223 MQR 0.8616
224 IWD 0.8615
225 CBE 0.8613
226 HA6 0.8610
227 CX5 0.8610
228 3WL 0.8609
229 A18 0.8608
230 NIY 0.8607
231 KMY 0.8605
232 JSX 0.8605
233 IMH 0.8601
234 OCZ 0.8599
235 A 0.8597
236 EQU 0.8592
237 H7S 0.8592
238 KXN 0.8592
239 ESZ 0.8589
240 5NB 0.8583
241 L1T 0.8581
242 AD3 0.8572
243 CGW 0.8567
244 3BH 0.8563
245 NPS 0.8563
246 RFZ 0.8562
247 BP6 0.8561
248 5B2 0.8558
249 FM1 0.8557
250 H52 0.8557
251 VIB 0.8556
252 EYY 0.8555
253 Q8G 0.8555
254 MDR 0.8544
255 NAG 0.8542
256 QUE 0.8539
257 3D1 0.8539
258 BGC GAL 0.8532
259 SOJ 0.8512
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5YJ0; Ligand: EF2; 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: 5yj0.bio3) has 7 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5YJ0; Ligand: EF2; 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: 5yj0.bio5) has 7 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5YJ0; Ligand: EF2; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5yj0.bio6) has 7 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5YJ0; Ligand: EF2; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5yj0.bio1) has 7 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5YJ0; Ligand: EF2; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 5yj0.bio8) has 7 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 5YJ0; Ligand: EF2; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5yj0.bio2) has 7 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 5YJ0; Ligand: EF2; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 5yj0.bio4) has 7 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 5YJ0; Ligand: EF2; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 5yj0.bio7) has 7 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 5YJ0; Ligand: EF2; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 9) in the query (biounit: 5yj0.bio9) has 7 residues
No: Leader PDB Ligand Sequence Similarity
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