Receptor
PDB id Resolution Class Description Source Keywords
4v2z 1.45 Å NON-ENZYME: OTHER CEREBLON ISOFORM 4 FROM MAGNETOSPIRILLUM GRYPHISWALDENSE IN COMPLEX WITH POMALIDOMIDE MAGNETOSPIRILLUM GRYPHISWALDENSE SIGNALING PROTEIN TERATOGENICITY AROMATIC CAGE CC-4047 P
Ref.: THALIDOMIDE MIMICS URIDINE BINDING TO AN AROMATIC C CEREBLON. J.STRUCT.BIOL. V. 188 225 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN C:150;
A:150;
B:150;
 Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
 submit data
65.409 Zn [Zn+2...
Y70 A:151;
B:151;
C:151;
 Valid;
Valid;
Valid;
 none;
none;
none;
 submit data
273.244 C13 H11 N3 O4 c1cc2...
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: Y70; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 Y70 1 1
2 JO5 0.666667 0.90566
3 EF2 0.561404 0.903846
4 6EL 0.561404 0.903846
5 LVY 0.485294 0.910714
6 F4U 0.441176 0.857143
7 JOH 0.408451 0.730159
Similar Ligands (3D)
Ligand no: 1; Ligand: Y70; Similar ligands found: 253
No: Ligand Similarity coefficient
1 GEN 0.9438
2 0OK 0.9380
3 TGW 0.9376
4 JOB 0.9341
5 3WJ 0.9317
6 1FL 0.9298
7 KMP 0.9274
8 NYJ 0.9207
9 OA4 0.9204
10 EES 0.9197
11 AJ6 0.9186
12 AGI 0.9184
13 6WR 0.9178
14 H4B 0.9164
15 H75 0.9163
16 3QI 0.9142
17 KW7 0.9119
18 AJ4 0.9117
19 TC8 0.9114
20 J84 0.9113
21 Q0K 0.9106
22 0GA 0.9097
23 1HP 0.9095
24 789 0.9095
25 NAR 0.9094
26 5OR 0.9088
27 47X 0.9083
28 64I 0.9082
29 CC5 0.9079
30 L3L 0.9077
31 ADN 0.9074
32 D64 0.9053
33 7L4 0.9048
34 4NR 0.9046
35 IQW 0.9043
36 2P3 0.9033
37 EI1 0.9032
38 FHI 0.9028
39 MEX 0.9013
40 ARJ 0.9008
41 697 0.8995
42 J27 0.8988
43 DFL 0.8987
44 5AD 0.8985
45 S0G 0.8985
46 CC6 0.8983
47 QME 0.8983
48 H7S 0.8982
49 15Q 0.8980
50 3WK 0.8977
51 XIF XYP 0.8968
52 AP6 0.8964
53 4L2 0.8963
54 42R 0.8962
55 96Z 0.8957
56 1Q4 0.8950
57 C93 0.8950
58 4EU 0.8947
59 JFS 0.8944
60 3WL 0.8941
61 92O 0.8941
62 XYP XIF 0.8939
63 6DE 0.8934
64 7EL 0.8934
65 XYP XYP 0.8924
66 WCU 0.8920
67 DH2 0.8920
68 1SF 0.8920
69 DBS 0.8917
70 7EH 0.8914
71 9FH 0.8911
72 KXN 0.8910
73 Y3J 0.8910
74 AFX 0.8907
75 H2B 0.8906
76 NOC 0.8906
77 5I5 0.8904
78 TRP 0.8902
79 3JC 0.8897
80 57D 0.8892
81 4K2 0.8892
82 MZR 0.8891
83 2JX 0.8890
84 0DF 0.8890
85 C2M 0.8889
86 LP8 0.8889
87 BHS 0.8887
88 DKX 0.8887
89 CWE 0.8885
90 6DQ 0.8884
91 EV2 0.8883
92 KWB 0.8881
93 DKZ 0.8881
94 LU2 0.8881
95 CJB 0.8878
96 B2L 0.8877
97 4MP 0.8874
98 KP2 0.8869
99 RFZ 0.8864
100 CP6 0.8862
101 GPU 0.8859
102 STZ 0.8855
103 YX1 0.8855
104 5DE 0.8855
105 GPK 0.8853
106 TCL 0.8852
107 XIL 0.8851
108 LZJ 0.8851
109 DK4 0.8848
110 DQH 0.8848
111 H52 0.8845
112 X29 0.8841
113 XDL XYP 0.8841
114 1GM 0.8841
115 5FD 0.8836
116 FCW 0.8836
117 XYS XYS 0.8834
118 HBI 0.8831
119 XYP XDN 0.8830
120 MIL 0.8827
121 DFV 0.8825
122 XYP XYS 0.8822
123 CU8 0.8821
124 NOS 0.8817
125 0J4 0.8816
126 AOJ 0.8814
127 GMP 0.8811
128 A4T 0.8808
129 QUE 0.8807
130 0HY 0.8806
131 GPQ 0.8806
132 4AB 0.8805
133 AUG 0.8802
134 Z15 0.8798
135 JSX 0.8797
136 3WN 0.8795
137 3WO 0.8795
138 BGN 0.8792
139 B52 0.8791
140 AUE 0.8786
141 40N 0.8785
142 1CY 0.8784
143 CBE 0.8783
144 3DE 0.8783
145 XDN XYP 0.8783
146 TYP 0.8780
147 5CD 0.8777
148 Z57 0.8776
149 X0T 0.8774
150 A4N 0.8770
151 JNW 0.8767
152 IMH 0.8763
153 EAT 0.8758
154 AUT 0.8757
155 XYS XYP 0.8753
156 5C1 0.8752
157 GFE 0.8749
158 4DE 0.8748
159 MTA 0.8745
160 BIE 0.8745
161 NIY 0.8743
162 TBN 0.8743
163 7FZ 0.8741
164 2FA 0.8737
165 A5K 0.8733
166 NWD 0.8732
167 26C 0.8724
168 EZB 0.8724
169 WVV 0.8718
170 A4Q 0.8717
171 A4D 0.8711
172 AU8 0.8709
173 IMK 0.8706
174 7A9 0.8703
175 FT6 0.8701
176 51Y 0.8698
177 Y0V 0.8695
178 8UY 0.8694
179 FMQ 0.8693
180 M77 0.8692
181 FY8 0.8689
182 BG8 0.8689
183 U4J 0.8687
184 22L 0.8687
185 5N5 0.8682
186 W23 0.8682
187 0J2 0.8682
188 2QV 0.8680
189 7VF 0.8676
190 RAB 0.8674
191 2L2 0.8674
192 OJ7 0.8672
193 2AN 0.8670
194 CUH 0.8668
195 AUV 0.8667
196 22T 0.8667
197 EUN 0.8660
198 Q4G 0.8656
199 TI7 0.8656
200 5F1 0.8655
201 NAL 0.8651
202 P2L 0.8650
203 G14 0.8648
204 RPP 0.8645
205 OUA 0.8641
206 JA3 0.8640
207 35G 0.8639
208 FM2 0.8638
209 6MD 0.8636
210 B2X 0.8635
211 NVS 0.8635
212 FMB 0.8633
213 CTN 0.8632
214 TH1 0.8632
215 AD3 0.8632
216 AVA 0.8630
217 RSV 0.8630
218 4GP 0.8629
219 PQS 0.8628
220 9KZ 0.8626
221 FMC 0.8625
222 6XC 0.8620
223 MQ1 0.8618
224 S1D 0.8615
225 A 0.8610
226 3L1 0.8610
227 3BH 0.8608
228 26A 0.8602
229 6WU 0.8599
230 EST 0.8597
231 2L1 0.8597
232 89J 0.8596
233 DBE 0.8595
234 5NB 0.8590
235 3RP 0.8587
236 UX0 0.8578
237 Q9G 0.8574
238 MG7 0.8573
239 LJ4 0.8571
240 5XM 0.8568
241 69K 0.8563
242 BP3 0.8560
243 XDH 0.8559
244 TVZ 0.8559
245 FM1 0.8556
246 7G1 0.8550
247 MDR 0.8547
248 3AD 0.8546
249 OSY 0.8540
250 5ID 0.8535
251 GJB 0.8529
252 54E 0.8528
253 PRH 0.8518
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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