Receptor
PDB id Resolution Class Description Source Keywords
5IWG 1.66 Å EC: 3.5.1.98 HDAC2 WITH LIGAND BRD4884 HOMO SAPIENS HDAC HISTONE DEACETYLASE HYDROLASE
Ref.: KINETIC AND STRUCTURAL INSIGHTS INTO THE BINDING OF DEACETYLASE 1 AND 2 (HDAC1, 2) INHIBITORS. BIOORG.MED.CHEM. V. 24 4008 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA B:402;
A:402;
C:402;
C:404;
A:404;
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...
IWX C:403;
A:403;
B:403;
 Valid;
Valid;
Valid;
 none;
none;
none;
 Ki = 0.346 uM
314.354 C18 H19 F N2 O2 c1cc(...
PG5 A:405;
 Invalid;
 none;
 submit data
178.226 C8 H18 O4 COCCO...
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...
PGE A:406;
A:407;
 Invalid;
Invalid;
 none;
none;
 submit data
150.173 C6 H14 O4 C(COC...
PEG B:407;
C:405;
B:406;
C:406;
B:405;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
106.12 C4 H10 O3 C(COC...
PG4 B:408;
 Invalid;
 none;
 submit data
194.226 C8 H18 O5 C(COC...
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: IWX; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 IWX 1 1
2 6EZ 0.652174 0.788462
Similar Ligands (3D)
Ligand no: 1; Ligand: IWX; Similar ligands found: 39
No: Ligand Similarity coefficient
1 LLX 0.9760
2 L7A 0.9113
3 SJJ 0.9075
4 3D9 0.9042
5 UUL 0.9034
6 75X 0.9017
7 W64 0.9013
8 EU2 0.9012
9 KK7 0.8996
10 3DV 0.8949
11 3RM 0.8940
12 DN8 0.8929
13 F13 0.8892
14 3Q1 0.8885
15 H65 0.8873
16 3DL 0.8868
17 PVP 0.8838
18 WTI 0.8834
19 3Q2 0.8823
20 95N 0.8809
21 8QB 0.8793
22 QSJ 0.8790
23 0BX 0.8735
24 GQE 0.8720
25 L0B 0.8712
26 3O0 0.8701
27 A1H 0.8698
28 YL3 0.8697
29 IFB 0.8689
30 WI2 0.8676
31 0BY 0.8652
32 0X5 0.8649
33 QZZ 0.8642
34 HHW 0.8625
35 LZA 0.8611
36 JE8 0.8585
37 E7Q 0.8561
38 20Y 0.8549
39 D4Z 0.8540
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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