Receptor
PDB id Resolution Class Description Source Keywords
3MAX 2.05 Å EC: 3.5.1.98 CRYSTAL STRUCTURE OF HUMAN HDAC2 COMPLEXED WITH AN N-(2-AMIN BENZAMIDE HOMO SAPIENS CLASS 2 HDAC FOOT POCKET HYDROLASE
Ref.: EXPLORATION OF THE HDAC2 FOOT POCKET: SYNTHESIS AND SUBSTITUTED N-(2-AMINOPHENYL)BENZAMIDES. BIOORG.MED.CHEM.LETT. V. 20 3142 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:380;
B:380;
C:380;
 Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
 submit data
40.078 Ca [Ca+2...
LLX A:400;
B:400;
C:400;
 Valid;
Valid;
Valid;
 none;
none;
none;
 ic50 = 0.027 uM
288.343 C19 H16 N2 O c1ccc...
NA A:381;
B:381;
C:381;
 Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
 submit data
22.99 Na [Na+]
NHE A:383;
 Invalid;
 none;
 submit data
207.29 C8 H17 N O3 S C1CCC...
ZN A:379;
B:379;
C:379;
 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: LLX; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 LLX 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: LLX; Similar ligands found: 44
No: Ligand Similarity coefficient
1 IWX 0.9760
2 L7A 0.9546
3 GOW 0.9524
4 6EZ 0.9379
5 DN8 0.9300
6 3Q2 0.9174
7 3DV 0.9100
8 T61 0.9092
9 KK7 0.9083
10 T34 0.9082
11 T86 0.9075
12 EU2 0.9055
13 WI2 0.9045
14 3Q1 0.9038
15 F13 0.9000
16 HHW 0.8972
17 3DL 0.8964
18 KK3 0.8951
19 43J 0.8943
20 PVP 0.8936
21 GQE 0.8926
22 3D9 0.8914
23 8QB 0.8860
24 0J6 0.8836
25 QZZ 0.8829
26 UV4 0.8819
27 XK3 0.8811
28 W64 0.8777
29 43G 0.8746
30 4VB 0.8741
31 3RM 0.8734
32 20Y 0.8726
33 UUL 0.8666
34 QSJ 0.8657
35 0RA 0.8652
36 QLV 0.8650
37 GQZ 0.8648
38 J8G 0.8624
39 3XL 0.8614
40 8JS 0.8608
41 A1H 0.8603
42 0BX 0.8601
43 E7Q 0.8560
44 0FZ 0.8525
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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