Receptor
PDB id Resolution Class Description Source Keywords
5EF7 1.9 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF DANIO RERIO HISTONE DEACETYLASE 6 CATAL DOMAIN 2 IN COMPLEX WITH HPOB DANIO RERIO HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: HISTONE DEACETYLASE 6 STRUCTURE AND MOLECULAR BASIS CATALYSIS AND INHIBITION. NAT.CHEM.BIOL. V. 12 741 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN B:801;
A:801;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
K B:803;
A:803;
A:802;
B:802;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
39.098 K [K+]
5OJ A:804;
B:804;
Valid;
Valid;
none;
none;
Ki = 1 nM
314.336 C17 H18 N2 O4 c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5EF7 1.9 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF DANIO RERIO HISTONE DEACETYLASE 6 CATAL DOMAIN 2 IN COMPLEX WITH HPOB DANIO RERIO HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: HISTONE DEACETYLASE 6 STRUCTURE AND MOLECULAR BASIS CATALYSIS AND INHIBITION. NAT.CHEM.BIOL. V. 12 741 2016
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 5EEN - 5OG C15 H14 N2 O4 S c1ccc(cc1)....
2 5EFH Ki = 0.8 uM FKS C10 H21 F3 N2 O2 C(CCC(C(F)....
3 5EEK - TSN C17 H22 N2 O3 C[C@H](C=C....
4 5EFN - ARG GLY 5OL MCM n/a n/a
5 5EEI - SHH C14 H20 N2 O3 c1ccc(cc1)....
6 5EFK - SER ASP ALY MCM n/a n/a
7 5EFJ Ki = 0.35 uM 5OM DPR ALA DAL n/a n/a
8 5EF7 Ki = 1 nM 5OJ C17 H18 N2 O4 c1ccc(cc1)....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 5EEN - 5OG C15 H14 N2 O4 S c1ccc(cc1)....
2 5EFH Ki = 0.8 uM FKS C10 H21 F3 N2 O2 C(CCC(C(F)....
3 5EEK - TSN C17 H22 N2 O3 C[C@H](C=C....
4 5EFN - ARG GLY 5OL MCM n/a n/a
5 5EEI - SHH C14 H20 N2 O3 c1ccc(cc1)....
6 5EFK - SER ASP ALY MCM n/a n/a
7 5EFJ Ki = 0.35 uM 5OM DPR ALA DAL n/a n/a
8 5EF7 Ki = 1 nM 5OJ C17 H18 N2 O4 c1ccc(cc1)....
50% Homology Family (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 5EEN - 5OG C15 H14 N2 O4 S c1ccc(cc1)....
2 5EFH Ki = 0.8 uM FKS C10 H21 F3 N2 O2 C(CCC(C(F)....
3 5EEK - TSN C17 H22 N2 O3 C[C@H](C=C....
4 5EFN - ARG GLY 5OL MCM n/a n/a
5 5EEI - SHH C14 H20 N2 O3 c1ccc(cc1)....
6 5EFK - SER ASP ALY MCM n/a n/a
7 5EFJ Ki = 0.35 uM 5OM DPR ALA DAL n/a n/a
8 5EF7 Ki = 1 nM 5OJ C17 H18 N2 O4 c1ccc(cc1)....
9 5G0G ic50 = 5.45 nM TSN C17 H22 N2 O3 C[C@H](C=C....
10 5EEF - TSN C17 H22 N2 O3 C[C@H](C=C....
11 3ZNS Ki = 0.039 uM NU7 C26 H24 F3 N5 O2 S CN1CCC(CC1....
12 3C0Z ic50 = 113 uM SHH C14 H20 N2 O3 c1ccc(cc1)....
13 3C10 ic50 = 0.3 uM TSN C17 H22 N2 O3 C[C@H](C=C....
14 3ZNR Ki = 0.036 uM NU9 C25 H21 F3 N4 O3 S c1ccc(cc1)....
15 2VQM ic50 = 975 nM HA3 C18 H16 N4 O3 S c1ccc(cc1)....
16 2VQQ ic50 = 367 nM TFG C19 H16 F3 N3 O3 S c1ccc(cc1)....
17 2VQJ - TFG C19 H16 F3 N3 O3 S c1ccc(cc1)....
18 2VQO ic50 = 317 nM TFG C19 H16 F3 N3 O3 S c1ccc(cc1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5OJ; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 5OJ 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5EF7; Ligand: 5OJ; Similar sites found: 11
This union binding pocket(no: 1) in the query (biounit: 5ef7.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4FE2 ASP 0.01534 0.4084 2.35294
2 1ZUW DGL 0.02458 0.40013 2.57353
3 2YKX AKG 0.02394 0.40904 5.21978
4 2CJP VPR 0.02706 0.40396 6.09756
5 3GCM 5GP 0.003744 0.40935 6.31868
6 5TVM PUT 0.01899 0.40593 8.23529
7 4ZUR 7XA 0.0000000001412 0.71816 32.5513
8 5FUE UV4 0.00000003119 0.6448 38.1868
9 1C3R TSN 0.00000002596 0.56325 39.2
10 3MAX LLX 0.00000002842 0.58431 39.5095
11 2V5X V5X 0.0000002497 0.49737 42.5824
Pocket No.: 2; Query (leader) PDB : 5EF7; Ligand: 5OJ; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5ef7.bio2) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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