Receptor
PDB id Resolution Class Description Source Keywords
3C0Z 2.1 Å EC: 3.5.1.98 CRYSTAL STRUCTURE OF CATALYTIC DOMAIN OF HUMAN HISTONE DEACETYLASE HDAC7 IN COMPLEX WITH SAHA HOMO SAPIENS HDAC STRUCTURAL GENOMICS STRUCTURAL GENOMICS CONSORTIUM SGC ALTERNATIVE SPLICING CHROMATIN REGULATOR CYTOPLASM HYDROLASE NUCLEUS PHOSPHOPROTEIN POLYMORPHISM REPRESSOR TRANSCRIPTION TRANSCRIPTION REGULATION
Ref.: HUMAN HDAC7 HARBORS A CLASS IIA HISTONE DEACETYLASE-SPECIFIC ZINC BINDING MOTIF AND CRYPTIC DEACETYLASE ACTIVITY. J.BIOL.CHEM. V. 283 11355 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
K A:201;
A:202;
B:201;
B:202;
C:201;
C:202;
 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
39.098 K [K+]
SHH A:301;
B:301;
C:301;
 Valid;
Valid;
Valid;
 none;
none;
none;
 ic50 = 113 uM
264.32 C14 H20 N2 O3 c1ccc...
ZN A:101;
A:102;
B:101;
B:102;
C:101;
C:102;
 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...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3ZNR 2.4 Å EC: 3.5.1.98 HDAC7 BOUND WITH INHIBITOR TMP269 HOMO SAPIENS HYDROLASE CLASS IIA HDACS TFMO
Ref.: SELECTIVE CLASS IIA HISTONE DEACETYLASE INHIBITION NON-CHELATING ZINC BINDING GROUP NAT.CHEM.BIOL. V. 9 319 2013
Members (4)
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)....
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: SHH; Similar ligands found: 11
No: Ligand ECFP6 Tc MDL keys Tc
1 SHH 1 1
2 CF3 0.673469 0.604167
3 UFJ 0.632653 0.913043
4 6DK 0.622642 0.607843
5 9Z8 0.584906 0.659574
6 UFS 0.516667 0.875
7 7XA 0.466667 0.695652
8 OKS 0.456522 0.695652
9 6XA 0.444444 0.673913
10 SPB 0.403226 0.617021
11 5XA 0.4 0.652174
Similar Ligands (3D)
Ligand no: 1; Ligand: SHH; Similar ligands found: 8
No: Ligand Similarity coefficient
1 B3N 0.8989
2 XH8 0.8791
3 9P1 0.8635
4 ML6 0.8611
5 TSN 0.8606
6 3M5 0.8533
7 QAP 0.8533
8 M7K 0.8526
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3ZNR; Ligand: NU9; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3znr.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
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