Receptor
PDB id Resolution Class Description Source Keywords
5A82 1.86 Å EC: 3.6.1.3 CRYSTAL STRUCTURE OF HUMAN ATAD2 BROMODOMAIN IN COMPLEX WITH 4-(3R,4R)-4-(3-METHYL-2-OXO-1,2-DIHYDRO-1,7- N APHTHYRIDIN-8-YL)AMINOPIPERIDIN-3-YLOXYMETHYL)-1-THIANE-1,1- DIONE HOMO SAPIENS INHIBITOR ATAD2 BROMODOMAIN EPIGENETICS ATPASE FAMILY ADOMAIN-CONTAINING PROTEIN 2
Ref.: STRUCTURE-BASED OPTIMIZATION OF NAPHTHYRIDONES INTO ATAD2 BROMODOMAIN INHIBITORS. J.MED.CHEM. V. 58 6151 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:2109;
A:2111;
A:2110;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
SO4 A:2113;
 Invalid;
 none;
 submit data
96.063 O4 S [O-]S...
YEJ A:2112;
 Valid;
 none;
 ic50 = 2.51 uM
420.526 C20 H28 N4 O4 S CC1=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6HDN 1.9 Å EC: 3.6.1.3 CRYSTAL STRUCTURE OF HUMAN ATAD2 BROMODOMAIN IN COMPLEX WITH 8-((8-METHYL-8-AZABICYCLOOCTAN-3-YL)AMINO)-1,7-NAPHTHYRIDIN HOMO SAPIENS INHIBITOR ATAD2 BROMODOMAIN EPIGENETICS ATPASE FAMILY AACONTAINING PROTEIN 2 TRANSCRIPTION
Ref.: AIMING TO MISS A MOVING TARGET: BROMO AND EXTRA TER DOMAIN (BET) SELECTIVITY IN CONSTRAINED ATAD2 INHIB J. MED. CHEM. V. 61 8321 2018
Members (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 5A5R ic50 = 1.3 uM NP8 C20 H23 N5 O2 CC1=Cc2c(c....
2 5A82 ic50 = 2.51 uM YEJ C20 H28 N4 O4 S CC1=Cc2ccn....
3 5A5Q Kd = 21 uM 6XC C14 H18 N4 O CC1=Cc2ccn....
4 6S55 - KW5 C17 H21 Br N4 O5 S C[C@H]1CCC....
5 5A81 Kd = 2.9 uM 78J C21 H30 N4 O2 CC1=Cc2ccn....
6 5A5P ic50 = 0.1 mM JTF C14 H19 N3 O CC1=Cc2ccc....
7 4TU4 Kd = 175 uM 37N C18 H16 N2 O5 S Cc1c(c(on1....
8 4TZ8 Kd = 500 uM 39U C9 H13 N3 O S CC1(Cc2c(s....
9 5A5O - J5I C10 H9 N O CC1=Cc2ccc....
10 6HDN ic50 = 3.16 uM FZB C17 H22 N4 O CC1=Cc2ccn....
11 6S57 - KVT C20 H28 N4 O5 S Cc1ccc(cc1....
12 5A5N - 8WS C11 H21 N3 O3 CC(=O)NCCC....
13 4TTE Kd = 202 uM 36Z C13 H14 N2 O3 Cc1c(c(on1....
14 4TYL Kd = 600 uM 39O C10 H13 N3 O Cc1cc2c(cc....
15 4TZ2 Kd = 350 uM 39R C14 H12 N4 c1ccc(cc1)....
16 5A83 ic50 = 0.158 uM YD3 C27 H34 N4 O4 S Cc1cc(cnc1....
17 5LJ0 ic50 = 0.00000001 M 6XX C28 H35 F2 N5 O3 Cc1cc(cnc1....
18 6S56 - KVZ C22 H23 Cl N4 O5 S CN(C)S(=O)....
70% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5A5R ic50 = 1.3 uM NP8 C20 H23 N5 O2 CC1=Cc2c(c....
2 5A82 ic50 = 2.51 uM YEJ C20 H28 N4 O4 S CC1=Cc2ccn....
3 5A5Q Kd = 21 uM 6XC C14 H18 N4 O CC1=Cc2ccn....
4 6S55 - KW5 C17 H21 Br N4 O5 S C[C@H]1CCC....
5 5A81 Kd = 2.9 uM 78J C21 H30 N4 O2 CC1=Cc2ccn....
6 5A5P ic50 = 0.1 mM JTF C14 H19 N3 O CC1=Cc2ccc....
7 4TU4 Kd = 175 uM 37N C18 H16 N2 O5 S Cc1c(c(on1....
8 4TZ8 Kd = 500 uM 39U C9 H13 N3 O S CC1(Cc2c(s....
9 5A5O - J5I C10 H9 N O CC1=Cc2ccc....
10 6HDN ic50 = 3.16 uM FZB C17 H22 N4 O CC1=Cc2ccn....
11 6S57 - KVT C20 H28 N4 O5 S Cc1ccc(cc1....
12 5A5N - 8WS C11 H21 N3 O3 CC(=O)NCCC....
13 4TTE Kd = 202 uM 36Z C13 H14 N2 O3 Cc1c(c(on1....
14 4TYL Kd = 600 uM 39O C10 H13 N3 O Cc1cc2c(cc....
15 4TZ2 Kd = 350 uM 39R C14 H12 N4 c1ccc(cc1)....
16 5A83 ic50 = 0.158 uM YD3 C27 H34 N4 O4 S Cc1cc(cnc1....
17 5LJ0 ic50 = 0.00000001 M 6XX C28 H35 F2 N5 O3 Cc1cc(cnc1....
18 6S56 - KVZ C22 H23 Cl N4 O5 S CN(C)S(=O)....
19 6VEO - YD4 C26 H33 N5 O4 S Cc1cc(cnc1....
50% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5A5R ic50 = 1.3 uM NP8 C20 H23 N5 O2 CC1=Cc2c(c....
2 5A82 ic50 = 2.51 uM YEJ C20 H28 N4 O4 S CC1=Cc2ccn....
3 5A5Q Kd = 21 uM 6XC C14 H18 N4 O CC1=Cc2ccn....
4 6S55 - KW5 C17 H21 Br N4 O5 S C[C@H]1CCC....
5 5A81 Kd = 2.9 uM 78J C21 H30 N4 O2 CC1=Cc2ccn....
6 5A5P ic50 = 0.1 mM JTF C14 H19 N3 O CC1=Cc2ccc....
7 4TU4 Kd = 175 uM 37N C18 H16 N2 O5 S Cc1c(c(on1....
8 4TZ8 Kd = 500 uM 39U C9 H13 N3 O S CC1(Cc2c(s....
9 5A5O - J5I C10 H9 N O CC1=Cc2ccc....
10 6HDN ic50 = 3.16 uM FZB C17 H22 N4 O CC1=Cc2ccn....
11 6S57 - KVT C20 H28 N4 O5 S Cc1ccc(cc1....
12 5A5N - 8WS C11 H21 N3 O3 CC(=O)NCCC....
13 4TTE Kd = 202 uM 36Z C13 H14 N2 O3 Cc1c(c(on1....
14 4TYL Kd = 600 uM 39O C10 H13 N3 O Cc1cc2c(cc....
15 4TZ2 Kd = 350 uM 39R C14 H12 N4 c1ccc(cc1)....
16 5A83 ic50 = 0.158 uM YD3 C27 H34 N4 O4 S Cc1cc(cnc1....
17 5LJ0 ic50 = 0.00000001 M 6XX C28 H35 F2 N5 O3 Cc1cc(cnc1....
18 6S56 - KVZ C22 H23 Cl N4 O5 S CN(C)S(=O)....
19 6VEO - YD4 C26 H33 N5 O4 S Cc1cc(cnc1....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: YEJ; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 YEJ 1 1
2 78J 0.8 0.789474
3 6XW 0.590909 0.962025
4 YD4 0.577982 0.962025
5 YD3 0.522523 0.936709
6 6XC 0.511628 0.684211
Similar Ligands (3D)
Ligand no: 1; Ligand: YEJ; 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 : 6HDN; Ligand: FZB; Similar sites found with APoc: 10
This union binding pocket(no: 1) in the query (biounit: 6hdn.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 4XUB 43D 27.3504
2 6HAZ FX5 27.6423
3 6HAZ FX5 27.6423
4 6DF7 G9V 30.7692
5 6DF7 G9V 30.7692
6 6J3O B4L 30.7692
7 6J3P B8O 39.2308
8 6J3P B8O 39.2308
9 5MG2 7M8 40
10 5IGL BMF 46.9231
11 5MLJ 9ST 50
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