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
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
Members (25)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 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 5DY7 - 5GT C9 H7 F3 N2 O c1cc2c(cc1....
8 5T4V ic50 = 60 nM N48 C19 H17 N3 O4 S CC1=CC(=O)....
9 5DYC - 5GU C8 H7 Br N2 O c1cc2c(cc1....
10 5EQ1 Kd = 21 uM BEA C9 H8 N3 S Cc1cccc2c1....
11 5G4S ic50 = 1 uM 8VI C24 H31 N5 O3 CCN(c1cc2c....
12 5EWC - 5SJ C12 H14 N2 O3 CCOC(=O)c1....
13 5EPR Kd = 91 uM 5QY C9 H10 N2 O C[C@H]1C(=....
14 5EVA - 5S9 C11 H9 F2 N3 O Cn1c(ccn1)....
15 5ETD - 5RN C10 H9 N O CC(=O)c1c[....
16 5DYA - 5GV C11 H12 N2 O3 CC[C@@H]1C....
17 5EV9 - 5SB C14 H12 N4 O CC(=O)Nc1c....
18 5MYG Kd = 31 nM LS8 C19 H17 N3 O4 S CC1=Cc2cc(....
19 5G4R ic50 = 7.943 nM LF1 C22 H27 N5 O3 C[C@@H]1CN....
20 5EM3 - 5Q0 C9 H7 N O c1cc2c(ccc....
21 5ETB Kd = 29 uM 5RO C11 H11 N O Cc1cccc2c1....
22 4UYE ic50 = 79.4 nM 9F9 C22 H26 N4 O3 CN1c2cc(c(....
23 5C7N Kd = 0.27 uM BMF C17 H20 N6 O4 S CCOC(=O)Nc....
24 5EPS Kd = 38 uM 5QX C9 H10 N2 O CN1c2ccccc....
25 5D7X Kd = 15 uM XZ8 C14 H13 N3 O2 CC1=C(C(=O....
70% Homology Family (26)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 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 5DY7 - 5GT C9 H7 F3 N2 O c1cc2c(cc1....
8 5T4V ic50 = 60 nM N48 C19 H17 N3 O4 S CC1=CC(=O)....
9 5DYC - 5GU C8 H7 Br N2 O c1cc2c(cc1....
10 5EQ1 Kd = 21 uM BEA C9 H8 N3 S Cc1cccc2c1....
11 5G4S ic50 = 1 uM 8VI C24 H31 N5 O3 CCN(c1cc2c....
12 5EWC - 5SJ C12 H14 N2 O3 CCOC(=O)c1....
13 5EPR Kd = 91 uM 5QY C9 H10 N2 O C[C@H]1C(=....
14 5EVA - 5S9 C11 H9 F2 N3 O Cn1c(ccn1)....
15 5ETD - 5RN C10 H9 N O CC(=O)c1c[....
16 5DYA - 5GV C11 H12 N2 O3 CC[C@@H]1C....
17 5EV9 - 5SB C14 H12 N4 O CC(=O)Nc1c....
18 5MYG Kd = 31 nM LS8 C19 H17 N3 O4 S CC1=Cc2cc(....
19 5G4R ic50 = 7.943 nM LF1 C22 H27 N5 O3 C[C@@H]1CN....
20 5EM3 - 5Q0 C9 H7 N O c1cc2c(ccc....
21 5ETB Kd = 29 uM 5RO C11 H11 N O Cc1cccc2c1....
22 4UYE ic50 = 79.4 nM 9F9 C22 H26 N4 O3 CN1c2cc(c(....
23 5C7N Kd = 0.27 uM BMF C17 H20 N6 O4 S CCOC(=O)Nc....
24 5EPS Kd = 38 uM 5QX C9 H10 N2 O CN1c2ccccc....
25 5D7X Kd = 15 uM XZ8 C14 H13 N3 O2 CC1=C(C(=O....
26 3RCW - MB3 C5 H9 N O CN1CCCC1=O
50% Homology Family (28)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 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 4UIU ic50 = 125.89 uM TVU C22 H24 N2 O6 S2 CN1C=C(c2c....
6 4UIT ic50 = 19.95 uM N1D C22 H25 N3 O6 S2 CN1C=C(c2c....
7 5I40 ic50 = 13.7 uM 67N C8 H8 N2 O CN1C=Cc2cc....
8 5I7X ic50 = 0.23 uM 67B C17 H17 N3 O2 CN1C=C(c2c....
9 4XY8 ic50 = 3.5 uM 43U C12 H10 Br N5 O COc1ccc(cc....
10 5IGM Kd = 41.7 nM BMF C17 H20 N6 O4 S CCOC(=O)Nc....
11 4Z6H Kd = 612 nM 4L2 C16 H18 N2 O2 CC1=CC(=O)....
12 5F1H Kd = 14.1 nM 5U6 C20 H23 N3 O3 CN1C=C(c2c....
13 5F1L ic50 = 21 nM 5U2 C19 H24 N2 O4 CC1=CC(=CN....
14 5F25 Kd = 9.1 uM 5TU C14 H14 N2 O2 CC1=CC(=CN....
15 4Z6I - 4L3 C27 H31 N3 O4 CC1=CC(=O)....
16 5EU1 Kd = 15.4 nM 5SW C20 H23 N3 O3 CN1C=C(c2c....
17 5F2P Kd = 37.5 uM 5TY C10 H12 N4 O CN1C=Cc2c(....
18 5DY7 - 5GT C9 H7 F3 N2 O c1cc2c(cc1....
19 5T4V ic50 = 60 nM N48 C19 H17 N3 O4 S CC1=CC(=O)....
20 5DYC - 5GU C8 H7 Br N2 O c1cc2c(cc1....
21 5G4R ic50 = 7.943 nM LF1 C22 H27 N5 O3 C[C@@H]1CN....
22 5EM3 - 5Q0 C9 H7 N O c1cc2c(ccc....
23 5ETB Kd = 29 uM 5RO C11 H11 N O Cc1cccc2c1....
24 4UYE ic50 = 79.4 nM 9F9 C22 H26 N4 O3 CN1c2cc(c(....
25 5C7N Kd = 0.27 uM BMF C17 H20 N6 O4 S CCOC(=O)Nc....
26 5EPS Kd = 38 uM 5QX C9 H10 N2 O CN1c2ccccc....
27 5D7X Kd = 15 uM XZ8 C14 H13 N3 O2 CC1=C(C(=O....
28 3RCW - MB3 C5 H9 N O CN1CCCC1=O
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 : 5G4R; Ligand: LF1; Similar sites found: 20
This union binding pocket(no: 1) in the query (biounit: 5g4r.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4LZB URA 0.01536 0.40847 None
2 4YGM URA 0.02712 0.40528 None
3 4UY1 TJM 0.008227 0.40565 2.54237
4 1UH4 GLC GLC GLC GLC GLC GLC 0.006345 0.41596 4.23729
5 3B9Q MLI 0.0105 0.42215 5.08475
6 2Z9I GLY ALA THR VAL 0.01697 0.40598 8.47458
7 3B2Q AES 0.007469 0.43974 11.0169
8 5H6S HDH 0.01354 0.40658 11.8644
9 3PE2 E1B 0.03713 0.40402 11.8644
10 2QZZ EMF 0.02243 0.41068 13.5593
11 2QZZ NAP 0.02145 0.41068 13.5593
12 5IGL BMF 0.000000241 0.65212 33.8983
13 5MG2 7M8 0.0000002447 0.63411 33.8983
14 4YC9 4C1 0.0000000009811 0.69832 35.5932
15 5FDZ 5X0 0.00000001151 0.68676 38.1356
16 5TPX 7H7 0.000000008024 0.72789 38.9831
17 3UVD MB3 0.000005161 0.44905 38.9831
18 5I8G 69E 0.000001034 0.60373 40.678
19 5I89 69B 0.000002099 0.57985 40.678
20 5LJ0 6XX 0.00000002262 0.67842 45.7627
Pocket No.: 2; Query (leader) PDB : 5G4R; Ligand: LF1; Similar sites found: 9
This union binding pocket(no: 2) in the query (biounit: 5g4r.bio3) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4IP7 FBP 0.01253 0.40325 2.54237
2 5N2I NAP 0.02004 0.40063 2.54237
3 5AHS SIN 0.01686 0.40325 3.38983
4 3RFV NAI 0.0457 0.41562 5.08475
5 1U1F 183 0.03625 0.41204 5.08475
6 3FW3 GLC 0.009233 0.40429 5.08475
7 1HFE CYS 0.006503 0.42088 6.77966
8 4XP7 FNR 0.01174 0.4085 7.62712
9 1YKI NFZ 0.03658 0.4028 12.7119
Pocket No.: 3; Query (leader) PDB : 5G4R; Ligand: LF1; Similar sites found: 5
This union binding pocket(no: 3) in the query (biounit: 5g4r.bio2) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2OFW ADX 0.04118 0.41048 2.54237
2 3KFL ME8 0.03717 0.40067 5.08475
3 4BQH 9VU 0.01774 0.40634 12.7119
4 4S3R 7SA 0.02123 0.42104 20.339
5 3SI2 PBD 0.01685 0.40131 27.1186
Pocket No.: 4; Query (leader) PDB : 5G4R; Ligand: LF1; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5g4r.bio4) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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