Receptor
PDB id Resolution Class Description Source Keywords
6VEO 2.4 Å EC: 7.-.-.- ATAD2B BROMODOMAIN IN COMPLEX WITH 4-({[(3R,4R)-4-{[3-METHYL METHYLPYRIDIN-3-YL)-2-OXO-1,2-DIHYDRO-1,7-NAPHTHYRIDIN-8- Y L]AMINO}PIPERIDIN-3-YL]OXY}METHYL)-1LAMBDA~6~-THIANE-1,1-D(C OMPOUND 38) HOMO SAPIENS BROMODOMAIN EPIGENETICS NUCLEAR PROTEIN
Ref.: STRUCTURAL INSIGHTS INTO THE RECOGNITION OF MONO- A DIACETYLATED HISTONES BY THE ATAD2B BROMODOMAIN. J.MED.CHEM. V. 63 12799 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:1102;
A:1101;
 Invalid;
Invalid;
 none;
none;
 submit data
96.063 O4 S [O-]S...
YD4 A:1103;
 Valid;
 none;
 submit data
511.636 C26 H33 N5 O4 S Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6VEO 2.4 Å EC: 7.-.-.- ATAD2B BROMODOMAIN IN COMPLEX WITH 4-({[(3R,4R)-4-{[3-METHYL METHYLPYRIDIN-3-YL)-2-OXO-1,2-DIHYDRO-1,7-NAPHTHYRIDIN-8- Y L]AMINO}PIPERIDIN-3-YL]OXY}METHYL)-1LAMBDA~6~-THIANE-1,1-D(C OMPOUND 38) HOMO SAPIENS BROMODOMAIN EPIGENETICS NUCLEAR PROTEIN
Ref.: STRUCTURAL INSIGHTS INTO THE RECOGNITION OF MONO- A DIACETYLATED HISTONES BY THE ATAD2B BROMODOMAIN. J.MED.CHEM. V. 63 12799 2020
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 319 families.
1 6VEO - YD4 C26 H33 N5 O4 S Cc1cc(cnc1....
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: YD4; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 YD4 1 1
2 6XW 0.838095 0.975
3 YD3 0.715596 0.974684
4 YEJ 0.577982 0.962025
5 6XX 0.557377 0.732558
6 FZE 0.476562 0.616279
7 78J 0.461538 0.759494
8 NP8 0.452174 0.740741
Similar Ligands (3D)
Ligand no: 1; Ligand: YD4; 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 : 6VEO; Ligand: YD4; 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: 6veo.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
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