Receptor
PDB id Resolution Class Description Source Keywords
6R1X 1.8 Å NON-ENZYME: OTHER CEREBLON ISOFORM 4 FROM MAGNETOSPIRILLUM GRYPHISWALDENSE IN WITH COMPOUND 7A MAGNETOSPIRILLUM GRYPHISWALDENSE MSR-1ORGANISM_TAXID: 431944 PROTEOLYSIS TARGETING CHIMERA PROTAC PROTEIN DEGRADATION HYDROLYSIS PRODUCT SIGNALING PROTEIN
Ref.: DE-NOVO DESIGN OF CEREBLON (CRBN) EFFECTORS GUIDED NATURAL HYDROLYSIS PRODUCTS OF THALIDOMIDE DERIVATI J.MED.CHEM. V. 62 6615 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN B:201;
C:201;
A:201;
 Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
 submit data
65.409 Zn [Zn+2...
JPQ B:202;
A:202;
 Valid;
Valid;
 none;
none;
 submit data
196.203 C9 H12 N2 O3 CC(=C...
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: JPQ; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 JPQ 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: JPQ; Similar ligands found: 283
No: Ligand Similarity coefficient
1 HL4 0.9294
2 I2E 0.9269
3 SOJ 0.9210
4 S8D 0.9186
5 YIP 0.9179
6 TRP 0.9153
7 5O6 0.9142
8 1A5 0.9120
9 FY8 0.9095
10 TYR 0.9090
11 3IP 0.9084
12 IOP 0.9083
13 ZIP 0.9073
14 848 0.9055
15 ZEA 0.9043
16 FCW 0.9037
17 AMR 0.9027
18 NAL 0.9013
19 TB8 0.9013
20 GB4 0.9012
21 C82 0.9010
22 DHC 0.9008
23 EQW 0.9008
24 AVX 0.8996
25 LTN 0.8995
26 6C5 0.8992
27 6ZX 0.8992
28 3TC 0.8991
29 HC4 0.8987
30 GOE 0.8982
31 2JX 0.8975
32 5TO 0.8972
33 9BF 0.8965
34 363 0.8964
35 PLP 0.8964
36 PFF 0.8961
37 7VY 0.8960
38 4Z9 0.8954
39 LZ5 0.8953
40 ENO 0.8950
41 MJ5 0.8949
42 6J5 0.8946
43 LVD 0.8941
44 92G 0.8939
45 QME 0.8935
46 RE4 0.8933
47 P80 0.8930
48 HX8 0.8930
49 C0H 0.8929
50 PLR 0.8929
51 MMS 0.8925
52 FMQ 0.8924
53 ARG 0.8918
54 B41 0.8915
55 H35 0.8913
56 FPL 0.8902
57 TJM 0.8896
58 14W 0.8894
59 GGB 0.8893
60 11X 0.8882
61 KLS 0.8879
62 0OP 0.8873
63 CH8 0.8872
64 DAH 0.8868
65 YOF 0.8867
66 0NX 0.8867
67 TCL 0.8866
68 LSQ 0.8863
69 1YO 0.8860
70 DTY 0.8860
71 HXY 0.8858
72 9F8 0.8855
73 16Z 0.8854
74 9VQ 0.8852
75 ZZA 0.8850
76 P81 0.8845
77 G14 0.8840
78 4BF 0.8840
79 27K 0.8839
80 TYE 0.8839
81 KWB 0.8837
82 TYC 0.8834
83 ENG 0.8834
84 SNV 0.8828
85 N2Y 0.8828
86 TPM 0.8826
87 50C 0.8826
88 F06 0.8823
89 CBE 0.8822
90 NNH 0.8818
91 JX7 0.8817
92 CFA 0.8816
93 ILO 0.8814
94 B3U 0.8813
95 TZP 0.8813
96 V15 0.8811
97 FT6 0.8807
98 263 0.8806
99 4Z3 0.8805
100 HL6 0.8801
101 0K7 0.8801
102 N9M 0.8799
103 HNH 0.8799
104 3IL 0.8799
105 XIF XYP 0.8798
106 M01 0.8795
107 EAT 0.8793
108 FCD 0.8792
109 6Q3 0.8791
110 CS2 0.8790
111 QH3 0.8789
112 D1Y 0.8789
113 RKV 0.8787
114 KPV 0.8787
115 AHL 0.8785
116 6C8 0.8784
117 A9K 0.8783
118 FER 0.8783
119 TOH 0.8780
120 5OO 0.8778
121 PF1 0.8776
122 EQA 0.8776
123 A7K 0.8775
124 4XF 0.8773
125 5C1 0.8773
126 4Z1 0.8772
127 F90 0.8770
128 LTT 0.8770
129 A4N 0.8769
130 JFS 0.8768
131 26C 0.8766
132 NIY 0.8762
133 KDG 0.8762
134 AVA 0.8758
135 HPP 0.8756
136 J27 0.8754
137 DFL 0.8753
138 WA2 0.8752
139 NK5 0.8751
140 NFA 0.8750
141 N9J 0.8750
142 TG6 0.8749
143 T07 0.8749
144 VJJ 0.8749
145 PMP 0.8747
146 XYP XIF 0.8745
147 ALE 0.8742
148 LYS 0.8742
149 Y3L 0.8741
150 CIY 0.8740
151 2LT 0.8739
152 HNK 0.8739
153 JFM 0.8737
154 GLR 0.8736
155 RVE 0.8735
156 0OK 0.8735
157 3H2 0.8734
158 NPI 0.8733
159 FF2 0.8732
160 QUS 0.8732
161 BMC 0.8732
162 YPN 0.8731
163 Z70 0.8730
164 Q4G 0.8725
165 2UB 0.8724
166 RQD 0.8724
167 7L4 0.8722
168 PHE 0.8722
169 PBA 0.8721
170 K80 0.8721
171 API 0.8721
172 XEV 0.8719
173 9FH 0.8718
174 LOT 0.8717
175 4CF 0.8714
176 BPW 0.8710
177 PAL 0.8707
178 8OB 0.8705
179 4AF 0.8703
180 VBC 0.8703
181 2KU 0.8701
182 S1D 0.8701
183 1PS 0.8701
184 DAR 0.8699
185 TCC 0.8696
186 HHV 0.8692
187 H4B 0.8692
188 1BW 0.8692
189 A4T 0.8691
190 A7Q 0.8691
191 A18 0.8690
192 XRS 0.8689
193 HJH 0.8686
194 8MP 0.8685
195 D8Q 0.8685
196 OHJ 0.8684
197 7O4 0.8684
198 5LD 0.8683
199 GF7 0.8681
200 PHI 0.8680
201 AOT 0.8680
202 JSX 0.8679
203 PUE 0.8678
204 TCA 0.8674
205 0ON 0.8673
206 6PR 0.8673
207 S0W 0.8672
208 CC5 0.8672
209 IYR 0.8671
210 SWX 0.8671
211 MLY 0.8669
212 P7Y 0.8667
213 4MP 0.8664
214 A4Q 0.8663
215 L13 0.8662
216 HIC 0.8661
217 GB5 0.8657
218 HVE 0.8655
219 96Z 0.8653
220 SSY 0.8653
221 PQS 0.8650
222 BPY 0.8649
223 RPN 0.8647
224 J6W 0.8646
225 HFA 0.8644
226 F4E 0.8642
227 SQ4 0.8642
228 CIR 0.8641
229 6P3 0.8637
230 ERZ 0.8635
231 ZZU 0.8633
232 AJG 0.8632
233 XQI 0.8632
234 5RP 0.8631
235 N7I 0.8630
236 OJD 0.8628
237 XYP XYP 0.8626
238 OOG 0.8626
239 K82 0.8624
240 68B 0.8622
241 BRH 0.8619
242 GJG 0.8618
243 KYN 0.8617
244 RP3 0.8616
245 AZY 0.8615
246 XYP XDN 0.8614
247 H7S 0.8614
248 SQ7 0.8614
249 PPY 0.8613
250 4FP 0.8612
251 9J6 0.8611
252 54E 0.8610
253 D6G 0.8609
254 9UL 0.8609
255 HCI 0.8605
256 UN1 0.8599
257 GNW 0.8597
258 8OE 0.8590
259 4I8 0.8581
260 XDL XYP 0.8577
261 2NP 0.8576
262 PAN 0.8575
263 JOV 0.8575
264 T2D 0.8572
265 7EH 0.8572
266 BZM 0.8566
267 AWE 0.8566
268 1EB 0.8564
269 R9J 0.8562
270 QUB 0.8562
271 TU0 0.8558
272 F4K 0.8556
273 11C 0.8551
274 EXY 0.8551
275 4ZD 0.8549
276 J1K 0.8545
277 TIH 0.8538
278 XDN XYP 0.8534
279 R5P 0.8529
280 XDK 0.8528
281 PBN 0.8525
282 2OR 0.8519
283 37E 0.8515
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
APoc FAQ
Feedback