Receptor
PDB id Resolution Class Description Source Keywords
6R0V 1.6 Å NON-ENZYME: OTHER CEREBLON ISOFORM 4 FROM MAGNETOSPIRILLUM GRYPHISWALDENSE IN WITH HYDROLYSIS PRODUCT OF COMPOUND 4B 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...
PO4 A:204;
A:205;
C:203;
B:203;
A:203;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
94.971 O4 P [O-]P...
JO2 B:202;
A:202;
C:202;
 Valid;
Valid;
Valid;
 none;
none;
none;
 submit data
307.216 C12 H9 N3 O7 c1cc(...
CL B:204;
 Invalid;
 none;
 submit data
35.453 Cl [Cl-]
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: JO2; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 JO2 1 1
2 JOE 0.535211 1
3 JO8 0.438356 0.775862
Similar Ligands (3D)
Ligand no: 1; Ligand: JO2; Similar ligands found: 20
No: Ligand Similarity coefficient
1 UI2 0.8993
2 2J6 0.8957
3 UNM 0.8829
4 74Z 0.8815
5 YJX 0.8757
6 T62 0.8745
7 JYM 0.8745
8 2AM 0.8731
9 EUL 0.8727
10 NAR 0.8724
11 95C 0.8711
12 FYJ 0.8700
13 YK9 0.8696
14 C3G 0.8683
15 WUL 0.8676
16 50R 0.8661
17 K8W 0.8651
18 HY7 0.8610
19 BHF 0.8610
20 T86 0.8590
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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