Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN B:201;
A:201;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
JP5 A:202;
B:202;
Valid;
Valid;
none;
none;
Ki = 4 uM
248.235 C12 H12 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: JP5; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 JP5 1 1
2 JOQ 0.689655 0.94
3 JOW 0.571429 0.886792
4 JOT 0.542373 0.833333
5 JOK 0.516129 0.795918
6 JON 0.484375 0.818182
7 4UZ 0.416667 0.672727
Similar Ligands (3D)
Ligand no: 1; Ligand: JP5; Similar ligands found: 82
No: Ligand Similarity coefficient
1 SVG 0.9367
2 IPJ 0.9248
3 WDU 0.9190
4 OGY 0.9185
5 N0H 0.9124
6 JP8 0.9111
7 HCC 0.9105
8 Q86 0.9063
9 QTK 0.9054
10 1V6 0.9045
11 S45 0.9034
12 F41 0.9021
13 41L 0.9007
14 BZM 0.9001
15 REG 0.8996
16 L02 0.8992
17 PHQ ALA 0.8990
18 00G 0.8989
19 PHQ THR 0.8963
20 0OM 0.8945
21 4Z0 0.8934
22 0MB 0.8930
23 PB2 0.8928
24 OA5 0.8927
25 JPW 0.8910
26 HPX 0.8901
27 CT0 0.8900
28 TBJ 0.8882
29 OH4 0.8869
30 JF5 0.8865
31 4KN 0.8858
32 NX6 0.8851
33 BUN 0.8846
34 BSU 0.8845
35 ZW2 0.8841
36 4P9 0.8839
37 5WK 0.8832
38 1Q2 0.8831
39 4VC 0.8829
40 A21 0.8821
41 HL6 0.8817
42 9W8 0.8816
43 U73 0.8809
44 CMZ 0.8798
45 20P 0.8791
46 G50 0.8784
47 S0B 0.8776
48 8WW 0.8774
49 5NR 0.8771
50 F7L 0.8757
51 HPK 0.8753
52 GYZ 0.8742
53 PHQ DTH 0.8741
54 L12 0.8734
55 JVB 0.8730
56 A0R 0.8720
57 9RK 0.8714
58 N5B 0.8713
59 HPZ 0.8709
60 F91 0.8705
61 H6E 0.8693
62 SU7 0.8690
63 M62 0.8686
64 BP5 0.8681
65 PHQ ASP 0.8679
66 BXB 0.8678
67 2OX 0.8675
68 HRS 0.8673
69 DI9 0.8661
70 CIU 0.8659
71 A9E 0.8650
72 F6W 0.8622
73 RE2 0.8617
74 IGP 0.8606
75 F5N 0.8606
76 D25 0.8570
77 QTD 0.8569
78 4V5 0.8558
79 0QR 0.8557
80 87F 0.8546
81 UMP 0.8535
82 BFL 0.8534
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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