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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 (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 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 6CSQ ic50 = 380 nM F9P C7 H13 N O2 C1CCC(CC1)....
5 5WGK - AGJ C18 H20 N2 O4 c1ccc(cc1)....
6 5EFN - ARG GLY 5OL MCM n/a n/a
7 5EEI - SHH C14 H20 N2 O3 c1ccc(cc1)....
8 6CSS ic50 = 30 nM FBJ C6 H9 N O2 C1CC=C(C1)....
9 6CGP ic50 = 0.058 uM F1Y C17 H18 N4 O2 CCCc1c(n2c....
10 5WGL - AH4 C24 H27 N5 O3 c1ccc(cc1)....
11 6CSP ic50 = 12 nM FBM C7 H11 N O2 C1CCC(=CC1....
12 5WGI - TSN C17 H22 N2 O3 C[C@H](C=C....
13 6DVM ic50 = 3 nM HBJ C26 H28 N4 O4 Cc1ccc(cc1....
14 6CSR ic50 = 115 nM BHO C7 H7 N O2 c1ccc(cc1)....
15 5EFK - SER ASP ALY MCM n/a n/a
16 6DVO ic50 = 60 nM HBV C20 H27 F N2 O2 CN(Cc1ccc(....
17 6DVL ic50 = 11 nM HBG C25 H31 N3 O4 Cc1cc(cc(c....
18 5EFJ Ki = 0.35 uM 5OM DPR ALA DAL n/a n/a
19 6DVN ic50 = 14 nM HB7 C26 H28 N4 O4 CN(C)c1ccc....
20 5EF7 Ki = 1 nM 5OJ C17 H18 N2 O4 c1ccc(cc1)....
21 5WGM - AH7 C17 H18 F2 N4 O2 c1ccc(cc1)....
70% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 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 6CSQ ic50 = 380 nM F9P C7 H13 N O2 C1CCC(CC1)....
5 5WGK - AGJ C18 H20 N2 O4 c1ccc(cc1)....
6 5EFN - ARG GLY 5OL MCM n/a n/a
7 5EEI - SHH C14 H20 N2 O3 c1ccc(cc1)....
8 6CSS ic50 = 30 nM FBJ C6 H9 N O2 C1CC=C(C1)....
9 6CGP ic50 = 0.058 uM F1Y C17 H18 N4 O2 CCCc1c(n2c....
10 5WGL - AH4 C24 H27 N5 O3 c1ccc(cc1)....
11 6CSP ic50 = 12 nM FBM C7 H11 N O2 C1CCC(=CC1....
12 5WGI - TSN C17 H22 N2 O3 C[C@H](C=C....
13 6DVM ic50 = 3 nM HBJ C26 H28 N4 O4 Cc1ccc(cc1....
14 6CSR ic50 = 115 nM BHO C7 H7 N O2 c1ccc(cc1)....
15 5EFK - SER ASP ALY MCM n/a n/a
16 6DVO ic50 = 60 nM HBV C20 H27 F N2 O2 CN(Cc1ccc(....
17 6DVL ic50 = 11 nM HBG C25 H31 N3 O4 Cc1cc(cc(c....
18 5EFJ Ki = 0.35 uM 5OM DPR ALA DAL n/a n/a
19 6DVN ic50 = 14 nM HB7 C26 H28 N4 O4 CN(C)c1ccc....
20 5EF7 Ki = 1 nM 5OJ C17 H18 N2 O4 c1ccc(cc1)....
21 5WGM - AH7 C17 H18 F2 N4 O2 c1ccc(cc1)....
50% Homology Family (32)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 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 6CSQ ic50 = 380 nM F9P C7 H13 N O2 C1CCC(CC1)....
5 5WGK - AGJ C18 H20 N2 O4 c1ccc(cc1)....
6 5EFN - ARG GLY 5OL MCM n/a n/a
7 5EEI - SHH C14 H20 N2 O3 c1ccc(cc1)....
8 6CSS ic50 = 30 nM FBJ C6 H9 N O2 C1CC=C(C1)....
9 6CGP ic50 = 0.058 uM F1Y C17 H18 N4 O2 CCCc1c(n2c....
10 5WGL - AH4 C24 H27 N5 O3 c1ccc(cc1)....
11 6CSP ic50 = 12 nM FBM C7 H11 N O2 C1CCC(=CC1....
12 5WGI - TSN C17 H22 N2 O3 C[C@H](C=C....
13 6DVM ic50 = 3 nM HBJ C26 H28 N4 O4 Cc1ccc(cc1....
14 6CSR ic50 = 115 nM BHO C7 H7 N O2 c1ccc(cc1)....
15 5EFK - SER ASP ALY MCM n/a n/a
16 6DVO ic50 = 60 nM HBV C20 H27 F N2 O2 CN(Cc1ccc(....
17 6DVL ic50 = 11 nM HBG C25 H31 N3 O4 Cc1cc(cc(c....
18 5EFJ Ki = 0.35 uM 5OM DPR ALA DAL n/a n/a
19 6DVN ic50 = 14 nM HB7 C26 H28 N4 O4 CN(C)c1ccc....
20 5EF7 Ki = 1 nM 5OJ C17 H18 N2 O4 c1ccc(cc1)....
21 5WGM - AH7 C17 H18 F2 N4 O2 c1ccc(cc1)....
22 5G0G ic50 = 5.45 nM TSN C17 H22 N2 O3 C[C@H](C=C....
23 5EEF - TSN C17 H22 N2 O3 C[C@H](C=C....
24 3ZNS Ki = 0.039 uM NU7 C26 H24 F3 N5 O2 S CN1CCC(CC1....
25 3C0Z ic50 = 113 uM SHH C14 H20 N2 O3 c1ccc(cc1)....
26 3C10 ic50 = 0.3 uM TSN C17 H22 N2 O3 C[C@H](C=C....
27 3ZNR Ki = 0.036 uM NU9 C25 H21 F3 N4 O3 S c1ccc(cc1)....
28 2VQM ic50 = 975 nM HA3 C18 H16 N4 O3 S c1ccc(cc1)....
29 6FYZ ic50 = 0.036 uM EBE C19 H16 F N3 O2 Cc1ncc(cn1....
30 2VQQ ic50 = 367 nM TFG C19 H16 F3 N3 O3 S c1ccc(cc1)....
31 2VQJ - TFG C19 H16 F3 N3 O3 S c1ccc(cc1)....
32 2VQO ic50 = 317 nM TFG C19 H16 F3 N3 O3 S c1ccc(cc1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5OJ; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 5OJ 1 1
2 AGJ 0.522388 0.903846
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5EF7; Ligand: 5OJ; Similar sites found with APoc: 30
This union binding pocket(no: 1) in the query (biounit: 5ef7.bio1) has 40 residues
No: Leader PDB Ligand Sequence Similarity
1 6F5W KG1 1.64835
2 5T63 ALA ALA ALA ALA 1.92308
3 4L77 CNL 1.92308
4 6F92 MVL 2.1978
5 6F90 MVL 2.1978
6 4FE2 ASP 2.35294
7 1ZUW DGL 2.57353
8 2CE7 ADP 3.02198
9 3B8I OXL 3.13589
10 3VOZ 04A 3.49206
11 1XXR MAN 3.72671
12 3WLV AZA 3.84615
13 6FOG OXL 4.01786
14 4LFL TG6 4.32099
15 1TOQ AMG 4.51128
16 2YKX AKG 5.21978
17 6F8N NAG NAG 5.76923
18 2CJP VPR 6.09756
19 3GCM 5GP 6.31868
20 1U4J MAN 6.77966
21 5TVM PUT 8.23529
22 2GL0 ADN 8.98204
23 3GUZ PAF 9.09091
24 5Y02 MXN 10.2804
25 1APZ ASP 11.7284
26 6GXA TB8 37.3626
27 1C3R TSN 39.2
28 3MAX LLX 39.5095
29 2V5X V5X 42.5824
30 5G1C 9RB 43.4066
Pocket No.: 2; Query (leader) PDB : 5EF7; Ligand: 5OJ; Similar sites found with APoc: 4
This union binding pocket(no: 2) in the query (biounit: 5ef7.bio2) has 39 residues
No: Leader PDB Ligand Sequence Similarity
1 3GE7 AFQ 1.64835
2 5A6B OAN 2.74725
3 1V7C HEY 5.98291
4 3I27 SID 7.69231
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