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Receptor
PDB id Resolution Class Description Source Keywords
5G4R 1.96 Å NON-ENZYME: OTHER BROMODOMAIN OF HUMAN BRPF1 WITH N-1,3-DIMETHYL-6-2R-2- METHYLPIPERAZIN-1-YL-2-OXO-2,3-DIHYDRO-1H-1,3-BENZODIAZOL- 5 -YL-2-METHOXYBENZAMIDE HOMO SAPIENS TRANSCRIPTION
Ref.: GSK6853, A CHEMICAL PROBE FOR INHIBITION OF THE BRP BROMODOMAIN. ACS MED.CHEM.LETT. V. 7 552 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
LF1 D:1739;
A:1739;
B:1739;
C:1739;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
ic50 = 7.943 nM
409.481 C22 H27 N5 O3 C[C@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4UYE 1.65 Å NON-ENZYME: OTHER BROMODOMAIN OF HUMAN BRPF1 WITH N-1,3-DIMETHYL-2-OXO-6-( PIPERIDIN-1-YL)-2,3-DIHYDRO-1H-1,3-BENZODIAZOL-5-YL-2- M ETHOXYBENZAMIDE HOMO SAPIENS TRANSCRIPTION INHIBITOR HISTONE EPIGENETIC READER ANTAGO
Ref.: 1,3-DIMETHYL BENZIMIDAZOLONES ARE POTENT, SELECTIVE INHIBITORS OF THE BRPF1 BROMODOMAIN. ACS MED.CHEM.LETT. V. 5 1190 2014
Members (37)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 5E3G - 5JQ C5 H4 N4 O2 S C12=C(NC(=....
2 5T4U ic50 = 4800 nM 12Q C10 H9 N O CN1c2ccccc....
3 5EWH Kd = 170 uM 5SG C9 H7 N O c1cc2cnccc....
4 5C85 Kd = 105 uM 4YO C8 H7 Br N2 O c1cc2c(cc1....
5 5E3D Kd = 95 uM 5JL C5 H4 N4 O S2 C12=C(NC(=....
6 5C87 - 4YS C9 H7 N O c1ccc2c(c1....
7 5O4T - 9KT C10 H10 N2 O2 CN1c2ccccc....
8 5OV8 ic50 = 11 uM AXN C24 H30 N4 O4 S CC(C)Cc1cc....
9 5O4S ic50 = 3.4 uM 9KW C24 H28 N4 O5 S CN1c2cc(c(....
10 5MWH ic50 = 1.9 uM UWX C24 H30 N4 O5 S CC(C)Cc1cc....
11 5DY7 - 5GT C9 H7 F3 N2 O c1cc2c(cc1....
12 5T4V ic50 = 60 nM N48 C19 H17 N3 O4 S CC1=CC(=O)....
13 5DYC - 5GU C8 H7 Br N2 O c1cc2c(cc1....
14 5O55 - 9L5 C19 H23 N5 O2 CCN1c2ccc(....
15 5EQ1 Kd = 21 uM BEA C9 H8 N3 S Cc1cccc2c1....
16 5G4S ic50 = 1 uM 8VI C24 H31 N5 O3 CCN(c1cc2c....
17 5EWC - 5SJ C12 H14 N2 O3 CCOC(=O)c1....
18 5EPR Kd = 91 uM 5QY C9 H10 N2 O C[C@H]1C(=....
19 5EVA - 5S9 C11 H9 F2 N3 O Cn1c(ccn1)....
20 5ETD - 5RN C10 H9 N O CC(=O)c1c[....
21 5DYA - 5GV C11 H12 N2 O3 CC[C@@H]1C....
22 5EV9 - 5SB C14 H12 N4 O CC(=O)Nc1c....
23 5MYG Kd = 31 nM LS8 C19 H17 N3 O4 S CC1=Cc2cc(....
24 5MWZ ic50 = 16 uM KGU C24 H36 N6 O3 CCN1c2cc(c....
25 5G4R ic50 = 7.943 nM LF1 C22 H27 N5 O3 C[C@@H]1CN....
26 5OWA ic50 = 30.6 uM B0H C17 H24 N4 O2 S Cc1c(oc(n1....
27 5EM3 - 5Q0 C9 H7 N O c1cc2c(ccc....
28 5ETB Kd = 29 uM 5RO C11 H11 N O Cc1cccc2c1....
29 4UYE ic50 = 79.4 nM 9F9 C22 H26 N4 O3 CN1c2cc(c(....
30 5O5F - 9LT C22 H20 F N5 O3 CCN1c2ccc(....
31 5O5A - 9LN C22 H21 N5 O3 CCN1c2ccc(....
32 5O5H - 9LK C17 H14 Cl N3 O3 Cc1c(oc(n1....
33 5C7N Kd = 0.27 uM BMF C17 H20 N6 O4 S CCOC(=O)Nc....
34 5EPS Kd = 38 uM 5QX C9 H10 N2 O CN1c2ccccc....
35 5MWG ic50 = 1.7 uM WGX C25 H30 N4 O4 S CN1c2cc(c(....
36 5D7X Kd = 15 uM XZ8 C14 H13 N3 O2 CC1=C(C(=O....
37 6EKQ ic50 = 30.6 uM B0H C17 H24 N4 O2 S Cc1c(oc(n1....
70% Homology Family (39)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 5E3G - 5JQ C5 H4 N4 O2 S C12=C(NC(=....
2 5T4U ic50 = 4800 nM 12Q C10 H9 N O CN1c2ccccc....
3 5EWH Kd = 170 uM 5SG C9 H7 N O c1cc2cnccc....
4 5C85 Kd = 105 uM 4YO C8 H7 Br N2 O c1cc2c(cc1....
5 5E3D Kd = 95 uM 5JL C5 H4 N4 O S2 C12=C(NC(=....
6 5C87 - 4YS C9 H7 N O c1ccc2c(c1....
7 5O4T - 9KT C10 H10 N2 O2 CN1c2ccccc....
8 5OV8 ic50 = 11 uM AXN C24 H30 N4 O4 S CC(C)Cc1cc....
9 5O4S ic50 = 3.4 uM 9KW C24 H28 N4 O5 S CN1c2cc(c(....
10 5MWH ic50 = 1.9 uM UWX C24 H30 N4 O5 S CC(C)Cc1cc....
11 5DY7 - 5GT C9 H7 F3 N2 O c1cc2c(cc1....
12 5T4V ic50 = 60 nM N48 C19 H17 N3 O4 S CC1=CC(=O)....
13 5DYC - 5GU C8 H7 Br N2 O c1cc2c(cc1....
14 5O55 - 9L5 C19 H23 N5 O2 CCN1c2ccc(....
15 5EQ1 Kd = 21 uM BEA C9 H8 N3 S Cc1cccc2c1....
16 5G4S ic50 = 1 uM 8VI C24 H31 N5 O3 CCN(c1cc2c....
17 5EWC - 5SJ C12 H14 N2 O3 CCOC(=O)c1....
18 5EPR Kd = 91 uM 5QY C9 H10 N2 O C[C@H]1C(=....
19 5EVA - 5S9 C11 H9 F2 N3 O Cn1c(ccn1)....
20 5ETD - 5RN C10 H9 N O CC(=O)c1c[....
21 5DYA - 5GV C11 H12 N2 O3 CC[C@@H]1C....
22 5EV9 - 5SB C14 H12 N4 O CC(=O)Nc1c....
23 5MYG Kd = 31 nM LS8 C19 H17 N3 O4 S CC1=Cc2cc(....
24 5MWZ ic50 = 16 uM KGU C24 H36 N6 O3 CCN1c2cc(c....
25 5G4R ic50 = 7.943 nM LF1 C22 H27 N5 O3 C[C@@H]1CN....
26 5OWA ic50 = 30.6 uM B0H C17 H24 N4 O2 S Cc1c(oc(n1....
27 5EM3 - 5Q0 C9 H7 N O c1cc2c(ccc....
28 5ETB Kd = 29 uM 5RO C11 H11 N O Cc1cccc2c1....
29 4UYE ic50 = 79.4 nM 9F9 C22 H26 N4 O3 CN1c2cc(c(....
30 5O5F - 9LT C22 H20 F N5 O3 CCN1c2ccc(....
31 5O5A - 9LN C22 H21 N5 O3 CCN1c2ccc(....
32 5O5H - 9LK C17 H14 Cl N3 O3 Cc1c(oc(n1....
33 5C7N Kd = 0.27 uM BMF C17 H20 N6 O4 S CCOC(=O)Nc....
34 5EPS Kd = 38 uM 5QX C9 H10 N2 O CN1c2ccccc....
35 5MWG ic50 = 1.7 uM WGX C25 H30 N4 O4 S CN1c2cc(c(....
36 5D7X Kd = 15 uM XZ8 C14 H13 N3 O2 CC1=C(C(=O....
37 6EKQ ic50 = 30.6 uM B0H C17 H24 N4 O2 S Cc1c(oc(n1....
38 3RCW - MB3 C5 H9 N O CN1CCCC1=O
39 5N49 ic50 = 60 nM 8LW C22 H17 N3 O3 Cc1cc2c(cc....
50% Homology Family (41)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 5I7Y ic50 = 0.16 uM 69G C20 H21 N3 O2 C/C=C/CN1C....
2 4UIW ic50 = 501.187 uM H1B C22 H22 F3 N3 O3 S2 CCN1C=C(c2....
3 4UIV ic50 = 158.489 uM XZB C21 H20 F3 N3 O3 S2 CN1C=C(c2c....
4 5JI8 Kd = 23.4 uM 6KT C8 H7 N3 O S c1cc2c(cc1....
5 5MKY ic50 = 2 uM I0D C15 H17 Cl N4 O CN1CCc2c(c....
6 4UIU ic50 = 125.89 uM TVU C22 H24 N2 O6 S2 CN1C=C(c2c....
7 4UIT ic50 = 19.95 uM N1D C22 H25 N3 O6 S2 CN1C=C(c2c....
8 5I40 ic50 = 13.7 uM 67N C8 H8 N2 O CN1C=Cc2cc....
9 5I7X ic50 = 0.23 uM 67B C17 H17 N3 O2 CN1C=C(c2c....
10 4XY8 ic50 = 3.5 uM 43U C12 H10 Br N5 O COc1ccc(cc....
11 5IGM Kd = 41.7 nM BMF C17 H20 N6 O4 S CCOC(=O)Nc....
12 4Z6H Kd = 612 nM 4L2 C16 H18 N2 O2 CC1=CC(=O)....
13 5F1H Kd = 14.1 nM 5U6 C20 H23 N3 O3 CN1C=C(c2c....
14 5F1L ic50 = 21 nM 5U2 C19 H24 N2 O4 CC1=CC(=CN....
15 5F25 Kd = 9.1 uM 5TU C14 H14 N2 O2 CC1=CC(=CN....
16 4Z6I - 4L3 C27 H31 N3 O4 CC1=CC(=O)....
17 5EU1 Kd = 15.4 nM 5SW C20 H23 N3 O3 CN1C=C(c2c....
18 5F2P Kd = 37.5 uM 5TY C10 H12 N4 O CN1C=Cc2c(....
19 5G4S ic50 = 1 uM 8VI C24 H31 N5 O3 CCN(c1cc2c....
20 5EWC - 5SJ C12 H14 N2 O3 CCOC(=O)c1....
21 5EPR Kd = 91 uM 5QY C9 H10 N2 O C[C@H]1C(=....
22 5EVA - 5S9 C11 H9 F2 N3 O Cn1c(ccn1)....
23 5ETD - 5RN C10 H9 N O CC(=O)c1c[....
24 5DYA - 5GV C11 H12 N2 O3 CC[C@@H]1C....
25 5EV9 - 5SB C14 H12 N4 O CC(=O)Nc1c....
26 5MYG Kd = 31 nM LS8 C19 H17 N3 O4 S CC1=Cc2cc(....
27 5MWZ ic50 = 16 uM KGU C24 H36 N6 O3 CCN1c2cc(c....
28 5G4R ic50 = 7.943 nM LF1 C22 H27 N5 O3 C[C@@H]1CN....
29 5OWA ic50 = 30.6 uM B0H C17 H24 N4 O2 S Cc1c(oc(n1....
30 5EM3 - 5Q0 C9 H7 N O c1cc2c(ccc....
31 5ETB Kd = 29 uM 5RO C11 H11 N O Cc1cccc2c1....
32 4UYE ic50 = 79.4 nM 9F9 C22 H26 N4 O3 CN1c2cc(c(....
33 5O5F - 9LT C22 H20 F N5 O3 CCN1c2ccc(....
34 5O5A - 9LN C22 H21 N5 O3 CCN1c2ccc(....
35 5O5H - 9LK C17 H14 Cl N3 O3 Cc1c(oc(n1....
36 5C7N Kd = 0.27 uM BMF C17 H20 N6 O4 S CCOC(=O)Nc....
37 5EPS Kd = 38 uM 5QX C9 H10 N2 O CN1c2ccccc....
38 5MWG ic50 = 1.7 uM WGX C25 H30 N4 O4 S CN1c2cc(c(....
39 5D7X Kd = 15 uM XZ8 C14 H13 N3 O2 CC1=C(C(=O....
40 6EKQ ic50 = 30.6 uM B0H C17 H24 N4 O2 S Cc1c(oc(n1....
41 5N49 ic50 = 60 nM 8LW C22 H17 N3 O3 Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: LF1; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 LF1 1 1
2 9F9 0.609195 0.9
3 8VI 0.57732 0.957747
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4UYE; Ligand: 9F9; Similar sites found with APoc: 43
This union binding pocket(no: 1) in the query (biounit: 4uye.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 4LZB URA None
2 6F5W KG1 None
3 2AK3 AMP None
4 3P7G MAN None
5 4OOE NDP 1.69492
6 4OOE FOM 1.69492
7 1Q0H NDP 2.54237
8 1Q0H FOM 2.54237
9 4URG C2E 3.38983
10 1FUR MLT 5.08475
11 3AB1 FAD 5.08475
12 3RUV ANP 5.08475
13 3FW3 GLC 5.08475
14 6C0B MLI 5.9322
15 3B9Z CO2 5.9322
16 3WFD AXO 5.9322
17 3UA1 08Y 5.9322
18 1OFZ FUC 6.77966
19 1HFE CYS 6.77966
20 3BJE URA 8.47458
21 4M3P HCS 11.0169
22 2UXR ICT 11.0169
23 4OB6 S2T 11.8644
24 6AC9 ANP 14.4068
25 5TWB FAD 15.2542
26 4URS C2E 16.1017
27 2H7C SIA 16.9492
28 2GAG FOA 26.2626
29 5MG2 7M8 33.8983
30 5IGL BMF 33.8983
31 6DF7 G9V 33.8983
32 4YC9 4C1 35.5932
33 5FDZ 5X0 38.1356
34 5TPX 7H7 38.9831
35 3UVD MB3 38.9831
36 5MLJ 9ST 40.1786
37 5I8G 69E 40.678
38 5XXH E0D 40.678
39 5W0E 9U4 40.678
40 6GYT GLY LEU GLY ALY GLY GLY ALA ALY ALA 40.678
41 6AY3 C3J 41.7391
42 5ML0 P2L 45.4545
43 5LJ0 6XX 45.7627
Pocket No.: 2; Query (leader) PDB : 4UYE; Ligand: 9F9; Similar sites found with APoc: 20
This union binding pocket(no: 2) in the query (biounit: 4uye.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 3JQG AX6 None
2 5Y02 MXN None
3 5OWC AYZ None
4 4XDZ NDP 2.54237
5 5AHS SIN 3.38983
6 4TXI FAD 3.38983
7 5UI2 SUC 4.23729
8 3KP6 SAL 5.08475
9 2P4Y C03 5.08475
10 3G9E RO7 5.08475
11 2VCN ISZ 8.47458
12 5MY8 RXZ 8.47458
13 3WDM ADN 9.32203
14 3B2Q AES 11.0169
15 4TXJ THM 11.0169
16 2F2H XTG 11.0169
17 2QZZ EMF 13.5593
18 2QZZ NAP 13.5593
19 4S3R 7SA 20.339
20 3QCJ NX4 22.8814
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