Receptor
PDB id Resolution Class Description Source Keywords
6R11 1.75 Å NON-ENZYME: OTHER CEREBLON ISOFORM 4 FROM MAGNETOSPIRILLUM GRYPHISWALDENSE IN WITH COMPOUND 5B 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...
JOB A:202;
B:202;
 Valid;
Valid;
 none;
none;
 Ki = 12 uM
259.218 C12 H9 N3 O4 c1cc2...
CL B:204;
 Invalid;
 none;
 submit data
35.453 Cl [Cl-]
PO4 B:203;
A:203;
 Invalid;
Invalid;
 none;
none;
 submit data
94.971 O4 P [O-]P...
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: JOB; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 JOB 1 1
2 JO5 0.459016 0.979592
Similar Ligands (3D)
Ligand no: 1; Ligand: JOB; Similar ligands found: 188
No: Ligand Similarity coefficient
1 F4U 0.9615
2 EF2 0.9541
3 Y70 0.9341
4 0OK 0.9308
5 6EL 0.9246
6 7QV 0.9236
7 OA4 0.9170
8 7R7 0.9160
9 J84 0.9159
10 KW7 0.9135
11 TGW 0.9134
12 0J4 0.9129
13 W23 0.9116
14 6DE 0.9115
15 LP8 0.9113
16 3QI 0.9097
17 LVY 0.9089
18 FCW 0.9069
19 0J2 0.9052
20 GEN 0.9050
21 TCL 0.9047
22 2JX 0.9042
23 EV2 0.9036
24 H7S 0.9036
25 TC8 0.9035
26 KP2 0.9027
27 4AB 0.8991
28 Q8G 0.8981
29 38B 0.8967
30 27M 0.8967
31 A4N 0.8957
32 H2B 0.8951
33 HBI 0.8951
34 3DE 0.8949
35 H4B 0.8949
36 WCU 0.8942
37 B52 0.8935
38 JOH 0.8933
39 4RV 0.8932
40 NYJ 0.8930
41 1A5 0.8930
42 9KZ 0.8924
43 NPX 0.8923
44 ARJ 0.8918
45 NPS 0.8905
46 BIO 0.8904
47 4L2 0.8901
48 0GA 0.8892
49 CU8 0.8884
50 XIF XYP 0.8883
51 A5K 0.8881
52 CBE 0.8873
53 BGN 0.8867
54 RSV 0.8857
55 ADN 0.8854
56 EST 0.8854
57 STZ 0.8854
58 5AD 0.8851
59 S0G 0.8849
60 TRP 0.8849
61 PZ8 0.8848
62 92O 0.8846
63 AUT 0.8843
64 BHS 0.8835
65 LZJ 0.8834
66 AJ4 0.8831
67 EQU 0.8830
68 NOC 0.8828
69 Q8D 0.8818
70 3L1 0.8815
71 CUT 0.8810
72 XYP XIF 0.8809
73 CC5 0.8809
74 5FD 0.8808
75 9FH 0.8806
76 51Y 0.8803
77 FT6 0.8801
78 Y0V 0.8800
79 17M 0.8796
80 QME 0.8795
81 47X 0.8787
82 FB4 0.8787
83 RVD 0.8782
84 R18 0.8782
85 AWE 0.8781
86 EI1 0.8781
87 5F1 0.8778
88 CTE 0.8778
89 3WF 0.8777
90 5I5 0.8773
91 DBE 0.8769
92 DFV 0.8766
93 M77 0.8766
94 TCC 0.8763
95 54E 0.8760
96 3AD 0.8758
97 CUH 0.8755
98 0J5 0.8753
99 A4T 0.8750
100 D64 0.8749
101 A18 0.8749
102 KMP 0.8740
103 IQ5 0.8736
104 FM2 0.8735
105 0LA 0.8731
106 AU8 0.8729
107 L3L 0.8729
108 5DE 0.8723
109 5CD 0.8718
110 3D1 0.8718
111 NAL 0.8712
112 L07 0.8711
113 PFT 0.8711
114 H75 0.8710
115 7EL 0.8710
116 7L4 0.8708
117 XYP XYP 0.8702
118 MTA 0.8700
119 RFZ 0.8700
120 PQS 0.8695
121 MDR 0.8691
122 7EH 0.8690
123 RVB 0.8690
124 NAG 0.8689
125 AGI 0.8684
126 FM1 0.8684
127 CHV 0.8683
128 XYP XYS 0.8680
129 6MD 0.8679
130 FT1 0.8677
131 9JT 0.8677
132 KWB 0.8676
133 3JC 0.8676
134 1OT 0.8676
135 IMH 0.8676
136 A4Q 0.8665
137 0OO 0.8664
138 26A 0.8661
139 2L1 0.8659
140 AD3 0.8659
141 KF5 0.8658
142 ASD 0.8657
143 657 0.8657
144 XYS XYS 0.8655
145 DFL 0.8652
146 SJK 0.8650
147 TBN 0.8646
148 J3Z 0.8643
149 LU2 0.8641
150 C93 0.8637
151 1Q4 0.8636
152 NAR 0.8635
153 96Z 0.8635
154 MTP 0.8628
155 57D 0.8628
156 AON 0.8624
157 0SX 0.8621
158 LWS 0.8621
159 5SD 0.8617
160 C4F 0.8609
161 0DF 0.8605
162 KXN 0.8601
163 AOX 0.8600
164 H52 0.8596
165 X6P 0.8586
166 NDG 0.8584
167 FMC 0.8582
168 3XR 0.8579
169 X0T 0.8572
170 8OB 0.8568
171 A9K 0.8567
172 CHQ 0.8565
173 TXW 0.8561
174 XYP XDN 0.8560
175 SDN 0.8560
176 9H2 0.8558
177 Q4G 0.8557
178 3WJ 0.8557
179 ANB 0.8555
180 BMC 0.8552
181 NIY 0.8536
182 GMP 0.8534
183 42R 0.8530
184 RKN 0.8530
185 KLV 0.8529
186 PIC 0.8522
187 NGA 0.8518
188 A8K 0.8508
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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