Receptor
PDB id Resolution Class Description Source Keywords
6R0Q 1.5 Å NON-ENZYME: OTHER MUTANT CEREBLON ISOFORM 4 FROM MAGNETOSPIRILLUM GRYPHISWALDE COMPLEX WITH THALIDOMIDE METABOLITE ALPHA-(O-CARBOXYBENZAMIG LUTARIMIDE MAGNETOSPIRILLUM GRYPHISWALDENSE MSR-1ORGANISM_TAXID: 431944 SIGNALING PROTEIN PROTEOLYSIS TARGETING CHIMERA PROTAC PRDEGRADATION HYDROLYSIS PRODUCT
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;
D:201;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
 submit data
65.409 Zn [Zn+2...
UNK UNK UNK UNK H:1;
 Invalid;
 none;
 submit data
n/a n/a
UNK UNK UNK F:1;
G:1;
E:1;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
n/a n/a
JNW D:202;
C:202;
A:202;
B:202;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 submit data
276.245 C13 H12 N2 O5 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: JNW; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 JNW 1 1
2 JO8 0.414286 0.76
Similar Ligands (3D)
Ligand no: 1; Ligand: JNW; Similar ligands found: 207
No: Ligand Similarity coefficient
1 MHB 0.9232
2 H32 0.9198
3 BNY 0.9194
4 QC1 0.9173
5 1V8 0.9169
6 A63 0.9143
7 WLH 0.9138
8 3WK 0.9135
9 NU3 0.9132
10 P2C 0.9132
11 4K2 0.9112
12 CMG 0.9108
13 20D 0.9106
14 6TJ 0.9087
15 1V1 0.9076
16 3G1 0.9072
17 LVY 0.9058
18 697 0.9056
19 A73 0.9048
20 C5Q 0.9043
21 6BK 0.9038
22 5WW 0.9029
23 DFL 0.9025
24 AGI 0.9001
25 UN4 0.8999
26 JZ8 0.8996
27 7FZ 0.8993
28 MRE 0.8991
29 1UZ 0.8990
30 IMK 0.8985
31 AEY 0.8973
32 FLF 0.8963
33 ZRL 0.8955
34 1V0 0.8951
35 25K 0.8951
36 1FL 0.8951
37 E9L 0.8949
38 AJ4 0.8947
39 A4V 0.8946
40 W8L 0.8942
41 FHI 0.8940
42 53X 0.8937
43 1UR 0.8936
44 1UT 0.8933
45 EMU 0.8921
46 AJ6 0.8919
47 9CE 0.8912
48 LI4 0.8900
49 NKI 0.8900
50 3F4 0.8896
51 RGK 0.8894
52 5AV 0.8893
53 CDJ 0.8892
54 XYP XYP 0.8890
55 TH1 0.8888
56 WCU 0.8887
57 SZ5 0.8887
58 MBP 0.8885
59 4GU 0.8880
60 ZRK 0.8878
61 CJZ 0.8874
62 NAR 0.8871
63 NW1 0.8870
64 J5Z 0.8870
65 08C 0.8869
66 H2W 0.8867
67 A64 0.8861
68 27F 0.8860
69 DFV 0.8860
70 KMP 0.8853
71 GAT 0.8848
72 TGW 0.8845
73 91F 0.8840
74 25F 0.8839
75 H35 0.8835
76 I0D 0.8830
77 ISX 0.8826
78 1Q4 0.8823
79 ZMG 0.8819
80 L3L 0.8817
81 XYS XYS 0.8811
82 9E3 0.8810
83 BBY 0.8808
84 6MD 0.8805
85 9JT 0.8803
86 3WJ 0.8796
87 Q5M 0.8796
88 LU2 0.8795
89 3D8 0.8792
90 M3W 0.8791
91 9FN 0.8788
92 AYS 0.8787
93 TLF 0.8785
94 8UY 0.8784
95 LJ1 0.8784
96 O53 0.8782
97 7ZO 0.8780
98 IKY 0.8779
99 97K 0.8777
100 7L4 0.8777
101 FY8 0.8776
102 GPK 0.8775
103 GEN 0.8773
104 47X 0.8771
105 BK1 0.8770
106 VT3 0.8769
107 O9Z 0.8769
108 Y70 0.8767
109 HHV 0.8764
110 KS5 0.8761
111 MHD GAL 0.8760
112 1V3 0.8753
113 3WN 0.8752
114 3WO 0.8752
115 5E4 0.8751
116 F18 0.8748
117 U13 0.8748
118 IW1 0.8743
119 6J3 0.8742
120 AOY 0.8741
121 7WD 0.8740
122 3IP 0.8736
123 8BD 0.8735
124 LI7 0.8731
125 4ZF 0.8725
126 NBZ GLA 0.8724
127 V15 0.8724
128 FE5 0.8724
129 5CE 0.8723
130 FSE 0.8717
131 AUY 0.8714
132 U19 0.8713
133 47V 0.8713
134 GLA BEZ 0.8705
135 DS8 0.8703
136 5TU 0.8702
137 8M5 0.8701
138 F40 0.8699
139 AKD 0.8699
140 4F8 0.8698
141 PCQ 0.8697
142 XYP XIM 0.8697
143 83D 0.8694
144 12R 0.8691
145 0SY 0.8689
146 5NN 0.8685
147 XYS XYP 0.8681
148 XYP XDN 0.8681
149 F1T 0.8678
150 BK2 0.8675
151 BGC BGC 0.8670
152 DDC 0.8670
153 5S9 0.8667
154 XDL XYP 0.8666
155 XIL 0.8666
156 QUE 0.8663
157 ZAR 0.8662
158 CWE 0.8660
159 57D 0.8654
160 3JC 0.8654
161 U4J 0.8651
162 ADN 0.8650
163 WST 0.8649
164 88X 0.8647
165 0X2 0.8646
166 DK4 0.8645
167 7LU 0.8644
168 3CA 0.8637
169 ARJ 0.8634
170 IEE 0.8630
171 GPQ 0.8627
172 UKW 0.8619
173 TYP 0.8617
174 38E 0.8617
175 1V4 0.8615
176 JFS 0.8614
177 BVB 0.8613
178 MJW 0.8612
179 P4L 0.8612
180 7VF 0.8612
181 0OP 0.8608
182 Q2S 0.8606
183 0DJ 0.8605
184 15Q 0.8602
185 6XC 0.8598
186 3GX 0.8596
187 FUZ 0.8594
188 EDZ 0.8593
189 121 0.8586
190 Z15 0.8585
191 8HH 0.8580
192 STL 0.8570
193 IXM 0.8568
194 NE2 0.8558
195 5N5 0.8557
196 Z57 0.8556
197 MZR 0.8555
198 041 0.8552
199 GJB 0.8551
200 88R 0.8549
201 78P 0.8544
202 P2L 0.8541
203 XYP XIF 0.8541
204 C4F 0.8538
205 DKX 0.8532
206 PRH 0.8520
207 BGC GAL 0.8514
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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