Receptor
PDB id Resolution Class Description Source Keywords
6XEC 1.7 Å EC: 3.5.1.98 STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH KETONE INHIBITOR (C HOMO SAPIENS HISTONE DEACETYLASE HYDROLASE HYDROLASE-HYDROLASE INHIBITO
Ref.: DEVELOPMENT OF A SELECTIVE HDAC INHIBITOR AIMED AT REACTIVATING THE HIV LATENT RESERVOIR. BIOORG.MED.CHEM.LETT. V. 30 27367 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA C:407;
C:406;
B:405;
A:406;
A:407;
B:404;
 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
40.078 Ca [Ca+2...
V1S B:408;
A:411;
C:410;
 Valid;
Valid;
Valid;
 none;
none;
none;
 submit data
511.631 C28 H38 F N5 O3 CCC(C...
SO4 C:403;
C:402;
A:403;
C:404;
A:402;
A:405;
C:405;
A:404;
B:403;
B:402;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
96.063 O4 S [O-]S...
PEG B:407;
C:409;
A:410;
C:408;
A:408;
A:409;
B:406;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
 submit data
106.12 C4 H10 O3 C(COC...
ZN A:401;
C:401;
B:401;
 Part of Protein;
Part of Protein;
Part of Protein;
 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
6XDM 1.56 Å EC: 3.5.1.98 STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH AN ARYL KETONE INHI HOMO SAPIENS HISTONE DEACETYLASE HYDROLASE HYDROLASE-HYDROLASE INHIBITO
Ref.: SELECTIVE CLASS I HDAC INHIBITORS BASED ON ARYL KET BINDING INDUCE HIV-1 PROTEIN FOR CLEARANCE. ACS MED.CHEM.LETT. V. 11 1476 2020
Members (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 5IX0 Ki = 0.519 uM 6EZ C20 H21 F N2 O2 c1cc(ccc1c....
2 6XDM ic50 = 0.1 nM V1D C24 H30 F N5 O4 CN1CC(C1)C....
3 7KBG ic50 = 29 nM WBA C29 H26 F N5 O3 S c1ccc2cc(c....
4 6XEC - V1S C28 H38 F N5 O3 CCC(CCCCC[....
5 4LY1 Kd = 0.0552 uM 20Y C19 H17 N3 O2 S CC(=O)Nc1c....
6 4LXZ Kd = 0.182 uM SHH C14 H20 N2 O3 c1ccc(cc1)....
7 6XEB - V1P C24 H35 N5 O4 CCC(CCCCC[....
8 6WBW - TV1 C27 H37 N5 O4 CCC(CCCCC[....
9 6G3O - EL8 C18 H20 F3 N3 O5 C[C@H](CCC....
10 5IWG Ki = 0.346 uM IWX C18 H19 F N2 O2 c1cc(ccc1c....
11 6WBZ - TV7 C32 H45 N5 O4 CCC(CCCCC[....
12 3MAX ic50 = 0.027 uM LLX C19 H16 N2 O c1ccc(cc1)....
70% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 5IX0 Ki = 0.519 uM 6EZ C20 H21 F N2 O2 c1cc(ccc1c....
2 6XDM ic50 = 0.1 nM V1D C24 H30 F N5 O4 CN1CC(C1)C....
3 7KBG ic50 = 29 nM WBA C29 H26 F N5 O3 S c1ccc2cc(c....
4 6XEC - V1S C28 H38 F N5 O3 CCC(CCCCC[....
5 4LY1 Kd = 0.0552 uM 20Y C19 H17 N3 O2 S CC(=O)Nc1c....
6 4LXZ Kd = 0.182 uM SHH C14 H20 N2 O3 c1ccc(cc1)....
7 6XEB - V1P C24 H35 N5 O4 CCC(CCCCC[....
8 6WBW - TV1 C27 H37 N5 O4 CCC(CCCCC[....
9 6G3O - EL8 C18 H20 F3 N3 O5 C[C@H](CCC....
10 5IWG Ki = 0.346 uM IWX C18 H19 F N2 O2 c1cc(ccc1c....
11 6WBZ - TV7 C32 H45 N5 O4 CCC(CCCCC[....
12 3MAX ic50 = 0.027 uM LLX C19 H16 N2 O 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 5THU - B3N C16 H25 N3 O3 CN(C)c1ccc....
2 5D1D - ACE ARG HIS ALY ALY MCM n/a n/a
3 5DC7 - ACE ARG HIS ALY ALY MCM n/a n/a
4 4QA4 - B3N C16 H25 N3 O3 CN(C)c1ccc....
5 2V5X Kd = 220 nM V5X C36 H41 N5 O5 Cc1c(c2cc(....
6 4QA6 - ACE ARG HIS ALY ALY MCM n/a n/a
7 5THT - B3N C16 H25 N3 O3 CN(C)c1ccc....
8 4QA0 - SHH C14 H20 N2 O3 c1ccc(cc1)....
9 4QA2 - SHH C14 H20 N2 O3 c1ccc(cc1)....
10 3SFF ic50 = 200 nM 0DI C20 H20 Cl F2 N3 O2 c1cc(cc(c1....
11 7JVU - SHH C14 H20 N2 O3 c1ccc(cc1)....
12 1W22 ic50 = 175.5 nM NHB C17 H15 N3 O4 S2 CN(c1ccc(c....
13 3RQD - 02G GLY BB9 03Y VAL n/a n/a
14 3MZ4 - B3N C16 H25 N3 O3 CN(C)c1ccc....
15 5THV - B3N C16 H25 N3 O3 CN(C)c1ccc....
16 5DC6 - ACE ARG HIS ALY ALY MCM n/a n/a
17 3EW8 - B3N C16 H25 N3 O3 CN(C)c1ccc....
18 1VKG - CRI C24 H23 N3 O4 Cc1ccc(cc1....
19 3MZ6 - B3N C16 H25 N3 O3 CN(C)c1ccc....
20 5THS - B3N C16 H25 N3 O3 CN(C)c1ccc....
21 7JVW - B3N C16 H25 N3 O3 CN(C)c1ccc....
22 3EWF - ACE ARG HIS ALY ALY MCM n/a n/a
23 3MZ7 - B3N C16 H25 N3 O3 CN(C)c1ccc....
24 5DC5 - B3N C16 H25 N3 O3 CN(C)c1ccc....
25 4QA5 - ACE ARG HIS ALY ALY MCM n/a n/a
26 1T64 - TSN C17 H22 N2 O3 C[C@H](C=C....
27 4QA7 - ACE ARG HIS ALY ALY MCM n/a n/a
28 4RN2 ic50 = 1500 nM L7G C23 H31 N5 O3 S2 CC(C)[C@H]....
29 7JVV - ACE ARG HIS ALY ALY MCM n/a n/a
30 1T67 - B3N C16 H25 N3 O3 CN(C)c1ccc....
31 6HSK - GOK C21 H26 N6 O2 Cn1cc(c2c1....
32 4RN1 - L8G C23 H31 N5 O3 S2 CC(C)[C@H]....
33 4QA1 - B3N C16 H25 N3 O3 CN(C)c1ccc....
34 5VI6 - PHE PHE CPI 5OM n/a n/a
35 5FCW ic50 = 0.3 uM 5YA C17 H13 N O2 c1ccc2c(c1....
36 5D1C - ACE ARG HIS ALY ALY MCM n/a n/a
37 5DC8 - ACE ARG HIS ALY ALY MCM n/a n/a
38 2V5W - ACE ARG HIS ALY ALY MCM n/a n/a
39 4RN0 ic50 = 255 nM L6G C21 H29 N5 O3 S3 CC(C)[C@H]....
40 5IX0 Ki = 0.519 uM 6EZ C20 H21 F N2 O2 c1cc(ccc1c....
41 6XDM ic50 = 0.1 nM V1D C24 H30 F N5 O4 CN1CC(C1)C....
42 7KBG ic50 = 29 nM WBA C29 H26 F N5 O3 S c1ccc2cc(c....
43 6XEC - V1S C28 H38 F N5 O3 CCC(CCCCC[....
44 4LY1 Kd = 0.0552 uM 20Y C19 H17 N3 O2 S CC(=O)Nc1c....
45 4LXZ Kd = 0.182 uM SHH C14 H20 N2 O3 c1ccc(cc1)....
46 6XEB - V1P C24 H35 N5 O4 CCC(CCCCC[....
47 6WBW - TV1 C27 H37 N5 O4 CCC(CCCCC[....
48 6G3O - EL8 C18 H20 F3 N3 O5 C[C@H](CCC....
49 5IWG Ki = 0.346 uM IWX C18 H19 F N2 O2 c1cc(ccc1c....
50 6WBZ - TV7 C32 H45 N5 O4 CCC(CCCCC[....
51 3MAX ic50 = 0.027 uM LLX C19 H16 N2 O c1ccc(cc1)....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: V1S; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 V1S 1 1
2 TV7 0.412587 0.839506
3 V1P 0.406504 0.77381
Similar Ligands (3D)
Ligand no: 1; Ligand: V1S; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6XDM; Ligand: V1D; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 6xdm.bio3) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 6FYZ EBE 34.8404
2 5G0H E1Z 43.617
Pocket No.: 2; Query (leader) PDB : 6XDM; Ligand: V1D; Similar sites found with APoc: 2
This union binding pocket(no: 2) in the query (biounit: 6xdm.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 6FYZ EBE 34.8404
2 5G0H E1Z 43.617
Pocket No.: 3; Query (leader) PDB : 6XDM; Ligand: V1D; Similar sites found with APoc: 2
This union binding pocket(no: 3) in the query (biounit: 6xdm.bio2) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 6FYZ EBE 34.8404
2 5G0H E1Z 43.617
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