Receptor
PDB id Resolution Class Description Source Keywords
5AMH 1.2 Å NON-ENZYME: OTHER CEREBLON ISOFORM 4 FROM MAGNETOSPIRILLUM GRYPHISWALDENSE IN COMPLEX WITH THALIDOMIDE, TRIGONAL CRYSTAL FORM MAGNETOSPIRILLUM GRYPHISWALDENSE SIGNALING PROTEIN TERATOGENICITY AROMATIC CAGE
Ref.: STRUCTURAL DYNAMICS OF THE CEREBLON LIGAND BINDING PLOS ONE V. 10 28342 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:1130;
A:1127;
A:1132;
A:1128;
A:1133;
A:1129;
A:1131;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
 submit data
35.453 Cl [Cl-]
ZN A:150;
 Part of Protein;
 none;
 submit data
65.409 Zn [Zn+2...
NI A:1134;
 Part of Protein;
 none;
 submit data
58.693 Ni [Ni+2...
CA A:1126;
 Part of Protein;
 none;
 submit data
40.078 Ca [Ca+2...
EF2 A:151;
 Valid;
 none;
 submit data
258.229 C13 H10 N2 O4 c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6R1D 1.1 Å NON-ENZYME: OTHER CEREBLON ISOFORM 4 FROM MAGNETOSPIRILLUM GRYPHISWALDENSE IN WITH COMPOUND 7D, CO-CRYSTALLIZED MAGNETOSPIRILLUM GRYPHISWALDENSE MSR-1ORGANISM_TAXID: 431944 PROTEOLYSIS TARGETING CHIMERA PROTAC PROTEIN DEGRADATION PROTEIN
Ref.: DE-NOVO DESIGN OF CEREBLON (CRBN) EFFECTORS GUIDED NATURAL HYDROLYSIS PRODUCTS OF THALIDOMIDE DERIVATI J.MED.CHEM. V. 62 6615 2019
Members (23)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 4V2Z - Y70 C13 H11 N3 O4 c1cc2c(c(c....
2 6R11 Ki = 12 uM JOB C12 H9 N3 O4 c1cc2c(cc1....
3 5AMJ - EF2 C13 H10 N2 O4 c1ccc2c(c1....
4 6R0V - JO2 C12 H9 N3 O7 c1cc(c(cc1....
5 6R19 - EF2 C13 H10 N2 O4 c1ccc2c(c1....
6 6R0U - JO8 C12 H11 N3 O5 c1cc(c(c(c....
7 6R0Q - JNW C13 H12 N2 O5 c1ccc(c(c1....
8 6R0S - EF2 C13 H10 N2 O4 c1ccc2c(c1....
9 6R12 - EF2 C13 H10 N2 O4 c1ccc2c(c1....
10 6R1C - EF2 C13 H10 N2 O4 c1ccc2c(c1....
11 6R1X - JPQ C9 H12 N2 O3 CC(=CC(=O)....
12 6R1K Ki = 9 uM JPB C11 H7 Cl3 N2 O3 c1c(cc(c(c....
13 4V2Y - EF2 C13 H10 N2 O4 c1ccc2c(c1....
14 5AMI - EF2 C13 H10 N2 O4 c1ccc2c(c1....
15 6R1A - JP8 C11 H17 N3 O4 C1C[C@@H](....
16 6R1D Ki = 4 uM JP5 C12 H12 N2 O4 c1ccc(cc1)....
17 4V30 - LVY C13 H13 N3 O3 c1cc2c(c(c....
18 6R18 - EF2 C13 H10 N2 O4 c1ccc2c(c1....
19 4V32 - EF2 C13 H10 N2 O4 c1ccc2c(c1....
20 6R13 - EF2 C13 H10 N2 O4 c1ccc2c(c1....
21 6R1W - EF2 C13 H10 N2 O4 c1ccc2c(c1....
22 5AMH - EF2 C13 H10 N2 O4 c1ccc2c(c1....
23 4V31 - DUR C9 H12 N2 O5 C1[C@@H]([....
70% Homology Family (23)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 4V2Z - Y70 C13 H11 N3 O4 c1cc2c(c(c....
2 6R11 Ki = 12 uM JOB C12 H9 N3 O4 c1cc2c(cc1....
3 5AMJ - EF2 C13 H10 N2 O4 c1ccc2c(c1....
4 6R0V - JO2 C12 H9 N3 O7 c1cc(c(cc1....
5 6R19 - EF2 C13 H10 N2 O4 c1ccc2c(c1....
6 6R0U - JO8 C12 H11 N3 O5 c1cc(c(c(c....
7 6R0Q - JNW C13 H12 N2 O5 c1ccc(c(c1....
8 6R0S - EF2 C13 H10 N2 O4 c1ccc2c(c1....
9 6R12 - EF2 C13 H10 N2 O4 c1ccc2c(c1....
10 6R1C - EF2 C13 H10 N2 O4 c1ccc2c(c1....
11 6R1X - JPQ C9 H12 N2 O3 CC(=CC(=O)....
12 6R1K Ki = 9 uM JPB C11 H7 Cl3 N2 O3 c1c(cc(c(c....
13 4V2Y - EF2 C13 H10 N2 O4 c1ccc2c(c1....
14 5AMI - EF2 C13 H10 N2 O4 c1ccc2c(c1....
15 6R1A - JP8 C11 H17 N3 O4 C1C[C@@H](....
16 6R1D Ki = 4 uM JP5 C12 H12 N2 O4 c1ccc(cc1)....
17 4V30 - LVY C13 H13 N3 O3 c1cc2c(c(c....
18 6R18 - EF2 C13 H10 N2 O4 c1ccc2c(c1....
19 4V32 - EF2 C13 H10 N2 O4 c1ccc2c(c1....
20 6R13 - EF2 C13 H10 N2 O4 c1ccc2c(c1....
21 6R1W - EF2 C13 H10 N2 O4 c1ccc2c(c1....
22 5AMH - EF2 C13 H10 N2 O4 c1ccc2c(c1....
23 4V31 - DUR C9 H12 N2 O5 C1[C@@H]([....
50% Homology Family (23)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 4V2Z - Y70 C13 H11 N3 O4 c1cc2c(c(c....
2 6R11 Ki = 12 uM JOB C12 H9 N3 O4 c1cc2c(cc1....
3 5AMJ - EF2 C13 H10 N2 O4 c1ccc2c(c1....
4 6R0V - JO2 C12 H9 N3 O7 c1cc(c(cc1....
5 6R19 - EF2 C13 H10 N2 O4 c1ccc2c(c1....
6 6R0U - JO8 C12 H11 N3 O5 c1cc(c(c(c....
7 6R0Q - JNW C13 H12 N2 O5 c1ccc(c(c1....
8 6R0S - EF2 C13 H10 N2 O4 c1ccc2c(c1....
9 6R12 - EF2 C13 H10 N2 O4 c1ccc2c(c1....
10 6R1C - EF2 C13 H10 N2 O4 c1ccc2c(c1....
11 6R1X - JPQ C9 H12 N2 O3 CC(=CC(=O)....
12 6R1K Ki = 9 uM JPB C11 H7 Cl3 N2 O3 c1c(cc(c(c....
13 4V2Y - EF2 C13 H10 N2 O4 c1ccc2c(c1....
14 5AMI - EF2 C13 H10 N2 O4 c1ccc2c(c1....
15 6R1A - JP8 C11 H17 N3 O4 C1C[C@@H](....
16 6R1D Ki = 4 uM JP5 C12 H12 N2 O4 c1ccc(cc1)....
17 4V30 - LVY C13 H13 N3 O3 c1cc2c(c(c....
18 6R18 - EF2 C13 H10 N2 O4 c1ccc2c(c1....
19 4V32 - EF2 C13 H10 N2 O4 c1ccc2c(c1....
20 6R13 - EF2 C13 H10 N2 O4 c1ccc2c(c1....
21 6R1W - EF2 C13 H10 N2 O4 c1ccc2c(c1....
22 5AMH - EF2 C13 H10 N2 O4 c1ccc2c(c1....
23 4V31 - DUR C9 H12 N2 O5 C1[C@@H]([....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: EF2; 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: EF2; Similar ligands found: 338
No: Ligand Similarity coefficient
1 H4B 1.0000
2 JO5 0.9631
3 TGW 0.9548
4 JOB 0.9541
5 0OK 0.9536
6 H75 0.9443
7 KW7 0.9428
8 J84 0.9426
9 EES 0.9377
10 EI1 0.9357
11 789 0.9354
12 6WR 0.9351
13 GEN 0.9329
14 Q0K 0.9313
15 4NR 0.9312
16 5OR 0.9294
17 TC8 0.9275
18 IQW 0.9272
19 A4T 0.9239
20 397 0.9238
21 4EU 0.9222
22 J27 0.9218
23 38B 0.9215
24 47X 0.9214
25 2P3 0.9208
26 A4N 0.9194
27 9FH 0.9176
28 OA4 0.9171
29 9FG 0.9166
30 7EL 0.9152
31 QME 0.9149
32 DFL 0.9148
33 C2M 0.9147
34 26C 0.9147
35 S0G 0.9141
36 KMP 0.9135
37 XIF XYP 0.9132
38 AUT 0.9131
39 CP6 0.9126
40 CC5 0.9126
41 XYP XIF 0.9126
42 ADN 0.9119
43 NYJ 0.9115
44 8D6 0.9108
45 4MP 0.9106
46 1CY 0.9105
47 WCU 0.9105
48 27M 0.9097
49 KP2 0.9096
50 7L4 0.9095
51 STZ 0.9094
52 YX1 0.9094
53 XYP XYP 0.9094
54 2JX 0.9089
55 TCL 0.9088
56 A4Q 0.9086
57 AJ6 0.9085
58 15Q 0.9077
59 3WJ 0.9076
60 1HP 0.9076
61 7EH 0.9074
62 6DQ 0.9070
63 MEX 0.9064
64 PQS 0.9061
65 AU8 0.9059
66 JFS 0.9058
67 FCW 0.9055
68 C93 0.9053
69 XYS XYS 0.9052
70 KF5 0.9052
71 1SF 0.9051
72 TRP 0.9047
73 FMQ 0.9045
74 42R 0.9041
75 AGI 0.9040
76 BGN 0.9038
77 6DE 0.9034
78 5DE 0.9034
79 3QI 0.9029
80 5AD 0.9025
81 64I 0.9019
82 A5K 0.9014
83 PZ8 0.9014
84 5VU 0.9013
85 AJ4 0.9006
86 LZJ 0.8997
87 54E 0.8989
88 H7S 0.8988
89 ARJ 0.8986
90 NOC 0.8986
91 A9K 0.8979
92 22L 0.8974
93 1A5 0.8973
94 3UG 0.8971
95 CU8 0.8966
96 XIL 0.8966
97 5C1 0.8961
98 HMO 0.8958
99 9JT 0.8958
100 EV2 0.8956
101 72E 0.8955
102 PQM 0.8952
103 3DE 0.8951
104 XYP XDN 0.8946
105 XYP XYS 0.8946
106 51Y 0.8944
107 D64 0.8937
108 7FZ 0.8935
109 FHI 0.8934
110 5FD 0.8934
111 EAT 0.8934
112 XDN XYP 0.8933
113 CUT 0.8931
114 1FL 0.8924
115 TCC 0.8922
116 7G0 0.8921
117 XDL XYP 0.8920
118 7G1 0.8918
119 FB4 0.8914
120 GFE 0.8910
121 NAL 0.8909
122 5I5 0.8909
123 3WK 0.8908
124 AFX 0.8906
125 Y3J 0.8906
126 92O 0.8904
127 LP8 0.8902
128 DFV 0.8901
129 0DF 0.8900
130 CBE 0.8900
131 HBI 0.8899
132 W23 0.8899
133 96Z 0.8896
134 5S9 0.8893
135 H2B 0.8891
136 0J4 0.8884
137 G14 0.8881
138 LU2 0.8881
139 1Q4 0.8877
140 IMH 0.8876
141 ZTW 0.8875
142 BHS 0.8873
143 4AB 0.8873
144 7GY 0.8872
145 XYS XYP 0.8870
146 AOJ 0.8869
147 KWB 0.8866
148 OSP 0.8865
149 CUH 0.8865
150 3JC 0.8865
151 RFZ 0.8861
152 L1T 0.8854
153 DKX 0.8853
154 FT1 0.8851
155 BMC 0.8843
156 DK4 0.8842
157 CJB 0.8841
158 4DE 0.8840
159 DKZ 0.8837
160 4AF 0.8836
161 CP7 0.8835
162 FY8 0.8831
163 9KZ 0.8830
164 Y0V 0.8829
165 AVX 0.8827
166 FT6 0.8825
167 40N 0.8825
168 AUV 0.8825
169 5UD 0.8824
170 AWE 0.8824
171 GPK 0.8823
172 NE1 0.8823
173 C4E 0.8822
174 8OB 0.8820
175 FMC 0.8820
176 5CK 0.8820
177 JSX 0.8819
178 2GQ 0.8817
179 4L2 0.8815
180 ESE 0.8813
181 A7K 0.8811
182 16Z 0.8810
183 57D 0.8808
184 5CD 0.8807
185 X29 0.8807
186 NAR 0.8806
187 TI7 0.8805
188 0FR 0.8802
189 RSV 0.8800
190 B52 0.8795
191 GPQ 0.8793
192 Z15 0.8787
193 BIO 0.8783
194 A18 0.8783
195 C5Q 0.8780
196 MZR 0.8776
197 M77 0.8776
198 WVV 0.8773
199 FPL 0.8773
200 3WL 0.8768
201 RAB 0.8768
202 CX5 0.8767
203 SJK 0.8765
204 RKN 0.8764
205 3AD 0.8762
206 1GM 0.8760
207 L3L 0.8760
208 MTA 0.8759
209 7QV 0.8757
210 Z57 0.8755
211 KXN 0.8755
212 P2L 0.8754
213 FT3 0.8752
214 GPU 0.8752
215 H52 0.8751
216 NOS 0.8750
217 NIY 0.8750
218 GJB 0.8749
219 A4D 0.8749
220 MJ5 0.8747
221 AD3 0.8747
222 7R7 0.8746
223 M2E 0.8744
224 CTN 0.8744
225 2L2 0.8741
226 MQR 0.8741
227 F5F 0.8739
228 BP3 0.8737
229 GJG 0.8736
230 TBN 0.8736
231 FMB 0.8732
232 5N5 0.8731
233 78U 0.8730
234 5F1 0.8729
235 EST 0.8727
236 LOT 0.8727
237 B2L 0.8725
238 NVS 0.8724
239 CWE 0.8724
240 CTE 0.8721
241 BC5 0.8721
242 6QT 0.8721
243 DBE 0.8720
244 6WU 0.8720
245 A4B 0.8719
246 2L1 0.8717
247 MQ1 0.8716
248 4K2 0.8713
249 1OT 0.8711
250 FM2 0.8707
251 U4J 0.8703
252 0ON 0.8702
253 3WN 0.8700
254 3WO 0.8700
255 VIB 0.8699
256 0J2 0.8697
257 Q4G 0.8695
258 TYP 0.8695
259 68B 0.8693
260 Q8G 0.8693
261 Q8D 0.8690
262 RVD 0.8689
263 A8Q 0.8688
264 50C 0.8687
265 BPY 0.8686
266 AUG 0.8684
267 VJJ 0.8681
268 MIL 0.8680
269 JOH 0.8680
270 BG8 0.8678
271 FM1 0.8674
272 RPP 0.8674
273 0X2 0.8671
274 6MD 0.8671
275 3AK 0.8671
276 3L1 0.8669
277 A6H 0.8668
278 EZB 0.8665
279 A 0.8663
280 1DA 0.8662
281 FWD 0.8662
282 AVA 0.8659
283 89J 0.8659
284 K80 0.8658
285 S1D 0.8657
286 DCN 0.8656
287 FT2 0.8653
288 3D1 0.8651
289 4FC 0.8650
290 AUE 0.8647
291 JA3 0.8643
292 CH8 0.8642
293 72D 0.8642
294 RVB 0.8641
295 U3P 0.8639
296 QUE 0.8639
297 EQU 0.8633
298 35G 0.8633
299 K48 0.8632
300 GF7 0.8630
301 CWD 0.8630
302 5NB 0.8629
303 J47 0.8627
304 26A 0.8623
305 CX6 0.8622
306 H4B NO 0.8621
307 DBS 0.8617
308 7VF 0.8617
309 VBC 0.8612
310 GMP 0.8609
311 458 0.8608
312 KMY 0.8603
313 8OE 0.8601
314 CMP 0.8599
315 NWD 0.8598
316 0OL 0.8595
317 3BH 0.8595
318 PRH 0.8592
319 7M5 0.8586
320 ESZ 0.8584
321 BP6 0.8576
322 IMK 0.8575
323 NXB 0.8572
324 9H2 0.8571
325 TMC 0.8569
326 2FA 0.8551
327 MTP 0.8551
328 OSY 0.8550
329 5ID 0.8550
330 205 0.8550
331 4FP 0.8546
332 ZAR 0.8544
333 5CQ 0.8540
334 URI 0.8538
335 BWD 0.8536
336 XEV 0.8528
337 3NF 0.8526
338 CHQ 0.8519
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6R1D; Ligand: JP5; 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: 6r1d.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6R1D; Ligand: JP5; 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: 6r1d.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
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