Receptor
PDB id Resolution Class Description Source Keywords
6R1K 1.94 Å NON-ENZYME: OTHER CEREBLON ISOFORM 4 FROM MAGNETOSPIRILLUM GRYPHISWALDENSE IN WITH COMPOUND 7C 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;
C:201;
A:201;
 Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
 submit data
65.409 Zn [Zn+2...
JPB B:203;
B:202;
C:202;
A:202;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 Ki = 9 uM
321.544 C11 H7 Cl3 N2 O3 c1c(c...
PO4 A:203;
 Invalid;
 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: JPB; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 JPB 1 1
2 JO8 0.460317 0.82
Similar Ligands (3D)
Ligand no: 1; Ligand: JPB; Similar ligands found: 91
No: Ligand Similarity coefficient
1 TCL 0.9281
2 27M 0.9178
3 XYP XYP 0.9084
4 GXG 0.9042
5 FT3 0.9012
6 KUP 0.9012
7 D1Y 0.8984
8 1FL 0.8958
9 GXD 0.8949
10 KYN 0.8944
11 LOX XYP 0.8941
12 FT2 0.8938
13 FT1 0.8915
14 VIB 0.8915
15 TCC 0.8912
16 FB4 0.8903
17 8OE 0.8899
18 C4F 0.8893
19 4Z1 0.8889
20 TYP 0.8880
21 ADN 0.8877
22 848 0.8856
23 22F 0.8823
24 TPM 0.8814
25 3IP 0.8797
26 LVY 0.8787
27 J47 0.8785
28 8OB 0.8782
29 A6H 0.8776
30 DCN 0.8762
31 4GU 0.8761
32 SCE 0.8761
33 QRP 0.8759
34 GAL FUC 0.8758
35 4EU 0.8749
36 9ME 0.8743
37 XIF XYP 0.8741
38 XYP XIF 0.8741
39 9W7 0.8741
40 A4V 0.8740
41 VBC 0.8735
42 U4J 0.8726
43 JOE 0.8722
44 NEU 0.8722
45 C6Z 0.8717
46 1HR 0.8716
47 12R 0.8716
48 TCT 0.8710
49 XYP XIM 0.8709
50 AX6 0.8708
51 XYS XYS 0.8706
52 JSX 0.8695
53 F91 0.8674
54 S1D 0.8668
55 WDW 0.8667
56 VXM 0.8665
57 CUH 0.8665
58 4YE 0.8649
59 CC7 0.8648
60 XDL XYP 0.8647
61 RE4 0.8645
62 JCQ 0.8644
63 B5A 0.8634
64 DBE 0.8631
65 EMU 0.8631
66 DX6 0.8630
67 EXG 0.8615
68 1YO 0.8611
69 CHV 0.8610
70 Q9P 0.8607
71 CMP 0.8605
72 6SY 0.8599
73 2L2 0.8593
74 XYP XDN 0.8587
75 2L1 0.8586
76 7XX 0.8583
77 S0F 0.8583
78 PMM 0.8581
79 BZM 0.8576
80 PLP 0.8574
81 HA6 0.8572
82 C2M 0.8570
83 TL5 0.8569
84 5AD 0.8565
85 XDN XYP 0.8564
86 H0V 0.8560
87 EAJ 0.8549
88 MTP 0.8548
89 FCW 0.8546
90 9RK 0.8521
91 XEV 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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