Receptor
PDB id Resolution Class Description Source Keywords
5VS6 2.27 Å EC: 3.4.19.12 STRUCTURE OF DUB COMPLEX HOMO SAPIENS DEUBIQUITINASE INHIBITOR PROTEIN-INHIBITOR COMPLEX HYDROLINHIBITOR COMPLEX
Ref.: STRUCTURE-GUIDED DEVELOPMENT OF A POTENT AND SELECT NON-COVALENT ACTIVE-SITE INHIBITOR OF USP7. CELL CHEM BIOL V. 24 1490 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
9QD B:601;
A:601;
Valid;
Valid;
none;
none;
Kd = 104 nM
574.714 C32 H42 N6 O4 C[C@H...
GOL B:603;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
ACT B:602;
A:602;
Invalid;
Invalid;
none;
none;
submit data
59.044 C2 H3 O2 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5N9T 1.73 Å EC: 3.4.19.12 CRYSTAL STRUCTURE OF USP7 IN COMPLEX WITH A POTENT, SELECTIV REVERSIBLE SMALL-MOLECULE INHIBITOR HOMO SAPIENS USP7 REVERSIBLE INHIBITOR SELECTIVE HYDROLASE
Ref.: DISCOVERY AND CHARACTERIZATION OF HIGHLY POTENT AND SELECTIVE ALLOSTERIC USP7 INHIBITORS. NAT. CHEM. BIOL. V. 14 118 2018
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 5VS6 Kd = 104 nM 9QD C32 H42 N6 O4 C[C@H](CC(....
2 5NGE Kd = 65 nM 8WK C24 H23 F4 N7 O3 c1cc(ccc1n....
3 5UQX Kd = 246 uM 8JP C20 H20 N4 O2 CCc1c(cnc(....
4 5N9R Kd = 2.6 uM 8RN C22 H24 Br N3 O3 S C[C@H](CC(....
5 6F5H ic50 = 0.087 uM CQ5 C26 H37 N5 O3 C[C@H](CC(....
6 5VSB Kd = 7.614 uM 9QA C23 H24 Cl N3 O3 c1ccc(cc1)....
7 5N9T ic50 = 22 nM 8QQ C29 H31 F3 N6 O3 Cn1c(c2c(n....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 5VS6 Kd = 104 nM 9QD C32 H42 N6 O4 C[C@H](CC(....
2 5NGE Kd = 65 nM 8WK C24 H23 F4 N7 O3 c1cc(ccc1n....
3 5UQX Kd = 246 uM 8JP C20 H20 N4 O2 CCc1c(cnc(....
4 5N9R Kd = 2.6 uM 8RN C22 H24 Br N3 O3 S C[C@H](CC(....
5 6F5H ic50 = 0.087 uM CQ5 C26 H37 N5 O3 C[C@H](CC(....
6 5VSB Kd = 7.614 uM 9QA C23 H24 Cl N3 O3 c1ccc(cc1)....
7 5N9T ic50 = 22 nM 8QQ C29 H31 F3 N6 O3 Cn1c(c2c(n....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 5VS6 Kd = 104 nM 9QD C32 H42 N6 O4 C[C@H](CC(....
2 5NGE Kd = 65 nM 8WK C24 H23 F4 N7 O3 c1cc(ccc1n....
3 5UQX Kd = 246 uM 8JP C20 H20 N4 O2 CCc1c(cnc(....
4 5N9R Kd = 2.6 uM 8RN C22 H24 Br N3 O3 S C[C@H](CC(....
5 6F5H ic50 = 0.087 uM CQ5 C26 H37 N5 O3 C[C@H](CC(....
6 5VSB Kd = 7.614 uM 9QA C23 H24 Cl N3 O3 c1ccc(cc1)....
7 5N9T ic50 = 22 nM 8QQ C29 H31 F3 N6 O3 Cn1c(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 9QD; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 9QD 1 1
2 8RN 0.5 0.789474
3 CQ5 0.467742 0.779221
4 9QA 0.418033 0.816901
Similar Ligands (3D)
Ligand no: 1; Ligand: 9QD; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5N9T; Ligand: 8QQ; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 5n9t.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 5Z84 CHD 10.2041
Pocket No.: 2; Query (leader) PDB : 5N9T; Ligand: 8QQ; 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: 5n9t.bio2) has 37 residues
No: Leader PDB Ligand Sequence Similarity
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