Receptor
PDB id Resolution Class Description Source Keywords
6FYZ 2.15 Å EC: 3.-.-.- DEVELOPMENT AND CHARACTERIZATION OF A CNS-PENETRANT BENZHYDR HYDROXAMIC ACID CLASS IIA HISTONE DEACETYLASE INHIBITOR HOMO SAPIENS HYDROXAMIC ACID CNS-PENETRANT HDAC4 INHIBITION CLASS IIA INHIBITOR HYDROLASE
Ref.: DEVELOPMENT AND CHARACTERIZATION OF A CNS-PENETRANT BENZHYDRYL HYDROXAMIC ACID CLASS IIA HISTONE DEACET INHIBITOR. BIOORG. MED. CHEM. LETT. V. 29 83 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EBE A:2001;
C:2001;
B:2001;
 Valid;
Valid;
Valid;
 none;
none;
none;
 Kd = 0.039 uM
337.348 C19 H16 F N3 O2 Cc1nc...
ZN B:2003;
B:2002;
C:2003;
A:2003;
A:2002;
C:2002;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
none;
none;
 submit data
65.409 Zn [Zn+2...
NA B:2004;
A:2004;
C:2004;
 Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
 submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6FYZ 2.15 Å EC: 3.-.-.- DEVELOPMENT AND CHARACTERIZATION OF A CNS-PENETRANT BENZHYDR HYDROXAMIC ACID CLASS IIA HISTONE DEACETYLASE INHIBITOR HOMO SAPIENS HYDROXAMIC ACID CNS-PENETRANT HDAC4 INHIBITION CLASS IIA INHIBITOR HYDROLASE
Ref.: DEVELOPMENT AND CHARACTERIZATION OF A CNS-PENETRANT BENZHYDRYL HYDROXAMIC ACID CLASS IIA HISTONE DEACET INHIBITOR. BIOORG. MED. CHEM. LETT. V. 29 83 2019
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 312 families.
1 2VQM ic50 = 978 nM HA3 C18 H16 N4 O3 S c1ccc(cc1)....
2 6FYZ Kd = 0.039 uM EBE C19 H16 F N3 O2 Cc1ncc(cn1....
3 2VQQ ic50 = 367 nM TFG C19 H16 F3 N3 O3 S c1ccc(cc1)....
4 2VQJ - TFG C19 H16 F3 N3 O3 S c1ccc(cc1)....
5 2VQO ic50 = 317 nM TFG C19 H16 F3 N3 O3 S c1ccc(cc1)....
70% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 3ZNS Ki = 0.039 uM NU7 C26 H24 F3 N5 O2 S CN1CCC(CC1....
2 3C0Z ic50 = 113 uM SHH C14 H20 N2 O3 c1ccc(cc1)....
3 3C10 ic50 = 0.3 uM TSN C17 H22 N2 O3 C[C@H](C=C....
4 3ZNR Ki = 0.036 uM NU9 C25 H21 F3 N4 O3 S c1ccc(cc1)....
5 2VQM ic50 = 978 nM HA3 C18 H16 N4 O3 S c1ccc(cc1)....
6 6FYZ Kd = 0.039 uM EBE C19 H16 F N3 O2 Cc1ncc(cn1....
7 2VQQ ic50 = 367 nM TFG C19 H16 F3 N3 O3 S c1ccc(cc1)....
8 2VQJ - TFG C19 H16 F3 N3 O3 S c1ccc(cc1)....
9 2VQO ic50 = 317 nM TFG C19 H16 F3 N3 O3 S c1ccc(cc1)....
50% Homology Family (51)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 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 6Q0Z - P7V C10 H7 Br N2 O3 c1cc(ccc1c....
4 5EEK - TSN C17 H22 N2 O3 C[C@H](C=C....
5 6PZS - P7J C18 H26 N2 O2 CC1([C@@H]....
6 6PZU - A6I C25 H32 N4 O6 C[C@@H](C(....
7 6CSQ Kd = 410 nM F9P C7 H13 N O2 C1CCC(CC1)....
8 5WGK - AGJ C18 H20 N2 O4 c1ccc(cc1)....
9 5EFN - ARG GLY 5OL MCM n/a n/a
10 6R0K ic50 = 12 nM JNN C13 H11 Cl2 N3 O4 c1cc(c(cc1....
11 5EEI - SHH C14 H20 N2 O3 c1ccc(cc1)....
12 6CSS Kd = 25 nM FBJ C6 H9 N O2 C1CC=C(C1)....
13 6CGP ic50 = 0.058 uM F1Y C17 H18 N4 O2 CCCc1c(n2c....
14 6V7A ic50 = 264.4 nM QQG C21 H25 N3 O2 CN1CC2(CCN....
15 5WGL - AH4 C24 H27 N5 O3 c1ccc(cc1)....
16 6CSP Kd = 3 nM FBM C7 H11 N O2 C1CCC(=CC1....
17 5WGI - TSN C17 H22 N2 O3 C[C@H](C=C....
18 6PZO - P6Y C15 H12 F3 N3 O3 c1cc(c(nc1....
19 6DVM ic50 = 3 nM HBJ C26 H28 N4 O4 Cc1ccc(cc1....
20 6CSR Kd = 144 nM BHO C7 H7 N O2 c1ccc(cc1)....
21 5EFK - SER ASP ALY MCM n/a n/a
22 6PYE ic50 = 0.03 uM P5Y C25 H21 F3 N6 O3 c1ccc(cc1)....
23 6DVO ic50 = 60 nM HBV C20 H27 F N2 O2 CN(Cc1ccc(....
24 6DVL ic50 = 11 nM HBG C25 H31 N3 O4 Cc1cc(cc(c....
25 5EFJ Ki = 0.35 uM 5OM DPR ALA DAL n/a n/a
26 6PZR - P7D C16 H19 N3 O4 S CN(C)Cc1cc....
27 6DVN ic50 = 14 nM HB7 C26 H28 N4 O4 CN(C)c1ccc....
28 5EF7 Ki = 1 nM 5OJ C17 H18 N2 O4 c1ccc(cc1)....
29 5WGM - AH7 C17 H18 F2 N4 O2 c1ccc(cc1)....
30 6VNR - R5G C17 H15 N3 O4 c1cc(ccc1C....
31 6UO5 - QCP C18 H20 N2 O3 CC(C)[C@@H....
32 6UO2 - TSN C17 H22 N2 O3 C[C@H](C=C....
33 6UO7 - QCP C18 H20 N2 O3 CC(C)[C@@H....
34 6UO4 - TSN C17 H22 N2 O3 C[C@H](C=C....
35 6UOC - QCM C24 H27 N3 O4 CCN(CC)Cc1....
36 6UOB - P7D C16 H19 N3 O4 S CN(C)Cc1cc....
37 5G0G ic50 = 5.45 nM TSN C17 H22 N2 O3 C[C@H](C=C....
38 5EEF - TSN C17 H22 N2 O3 C[C@H](C=C....
39 6WYQ - UFJ C14 H19 I N2 O3 c1cc(ccc1N....
40 6UO3 - QCP C18 H20 N2 O3 CC(C)[C@@H....
41 6WYP - UFS C27 H31 N3 O5 C#CCCCC(=O....
42 6WYO - TSN C17 H22 N2 O3 C[C@H](C=C....
43 3ZNS Ki = 0.039 uM NU7 C26 H24 F3 N5 O2 S CN1CCC(CC1....
44 3C0Z ic50 = 113 uM SHH C14 H20 N2 O3 c1ccc(cc1)....
45 3C10 ic50 = 0.3 uM TSN C17 H22 N2 O3 C[C@H](C=C....
46 3ZNR Ki = 0.036 uM NU9 C25 H21 F3 N4 O3 S c1ccc(cc1)....
47 2VQM ic50 = 978 nM HA3 C18 H16 N4 O3 S c1ccc(cc1)....
48 6FYZ Kd = 0.039 uM EBE C19 H16 F N3 O2 Cc1ncc(cn1....
49 2VQQ ic50 = 367 nM TFG C19 H16 F3 N3 O3 S c1ccc(cc1)....
50 2VQJ - TFG C19 H16 F3 N3 O3 S c1ccc(cc1)....
51 2VQO ic50 = 317 nM TFG C19 H16 F3 N3 O3 S c1ccc(cc1)....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: EBE; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 EBE 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: EBE; Similar ligands found: 5
No: Ligand Similarity coefficient
1 TMI 0.9292
2 4U5 0.8924
3 2JR 0.8896
4 4TL 0.8825
5 R5V 0.8728
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6FYZ; Ligand: EBE; Similar sites found with APoc: 5
This union binding pocket(no: 1) in the query (biounit: 6fyz.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 5G1C 9RB 34.0541
2 5G1C 9RB 34.0541
3 6XDM V1D 34.8404
4 6XDM V1D 34.8404
5 6XDM V1D 34.8404
Pocket No.: 2; Query (leader) PDB : 6FYZ; Ligand: EBE; 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: 6fyz.bio3) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 6FYZ; Ligand: EBE; Similar sites found with APoc: 2
This union binding pocket(no: 3) in the query (biounit: 6fyz.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 5G1C 9RB 34.0541
2 5G1C 9RB 34.0541
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