Receptor
PDB id Resolution Class Description Source Keywords
6VNQ 2.05 Å EC: 3.5.1.48 CRYSTAL STRUCTURE OF DANIO RERIO HISTONE DEACETYLASE 10 IN C WITH BISHYDROXAMIC ACID BASED INHIBITOR DANIO RERIO HISTONE DEACETYLASE HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: DESIGN AND SYNTHESIS OF DIHYDROXAMIC ACIDS AS HDAC6 INHIBITORS. CHEMMEDCHEM V. 15 1163 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:703;
A:702;
 Invalid;
Invalid;
 none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
PO4 A:707;
A:708;
 Invalid;
Invalid;
 none;
none;
 submit data
94.971 O4 P [O-]P...
ZN A:704;
 Part of Protein;
 none;
 submit data
65.409 Zn [Zn+2...
K A:705;
A:706;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
39.098 K [K+]
R5G A:701;
 Valid;
 Atoms found MORE than expected: % Diff = 2;
 submit data
325.319 C17 H15 N3 O4 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6WDV 2.4 Å EC: 3.5.1.48 CRYSTAL STRUCTURE OF DANIO RERIO HISTONE DEACETYLASE 10 IN C WITH DIMETHYLAMINOMETHYLINDOLE PHENYLHYDROXAMATE INHIBITOR DANIO RERIO HISTONE DEACETYLASE HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: STRUCTURAL BASIS FOR THE SELECTIVE INHIBITION OF HD CYTOSOLIC POLYAMINE DEACETYLASE. ACS CHEM.BIOL. V. 15 2154 2020
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6WDW ic50 = 20 nM TWV C20 H23 N3 O2 CN(C)CCc1c....
2 6WDV ic50 = 5 nM TWM C19 H21 N3 O2 CN(C)Cc1cn....
3 6VNQ - R5G C17 H15 N3 O4 c1cc(ccc1C....
4 6WBQ ic50 = 12 nM N9W C20 H21 N3 O2 CN1CCc2c(c....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6WDW ic50 = 20 nM TWV C20 H23 N3 O2 CN(C)CCc1c....
2 6WDV ic50 = 5 nM TWM C19 H21 N3 O2 CN(C)Cc1cn....
3 6VNQ - R5G C17 H15 N3 O4 c1cc(ccc1C....
4 6WBQ ic50 = 12 nM N9W C20 H21 N3 O2 CN1CCc2c(c....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6WDW ic50 = 20 nM TWV C20 H23 N3 O2 CN(C)CCc1c....
2 6WDV ic50 = 5 nM TWM C19 H21 N3 O2 CN(C)Cc1cn....
3 6VNQ - R5G C17 H15 N3 O4 c1cc(ccc1C....
4 6WBQ ic50 = 12 nM N9W C20 H21 N3 O2 CN1CCc2c(c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: R5G; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 R5G 1 1
2 GKW 0.766667 0.811321
Similar Ligands (3D)
Ligand no: 1; Ligand: R5G; Similar ligands found: 5
No: Ligand Similarity coefficient
1 JCH 0.9135
2 3QT 0.9112
3 SX8 0.8980
4 MJP 0.8940
5 HY7 0.8539
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6WDV; Ligand: TWM; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 6wdv.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 5G0H E1Z 36.8343
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