Receptor
PDB id Resolution Class Description Source Keywords
5D7X 1.35 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE HUMAN BRPF1 BROMODOMAIN IN COMPLEX HOMO SAPIENS BROMODOMAIN AND PHD FINGER-CONTAINING PROTEIN 1(BRPF1) MONOLEUKEMIA ZINC-FINGER (MOZ) INHIBITOR DNA BINDING PROTEIN
Ref.: THE "GATEKEEPER" RESIDUE INFLUENCES THE MODE OF BIN ACETYL INDOLES TO BROMODOMAINS. J.MED.CHEM. V. 59 3087 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
XZ8 A:802;
Valid;
none;
Kd = 15 uM
255.272 C14 H13 N3 O2 CC1=C...
NO3 A:801;
Invalid;
none;
submit data
62.005 N O3 [N+](...
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 1610 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 Kd = 18 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 Kd = 1.8 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 Kd = 7.1 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 Kd = 3.5 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 Kd = 9.54 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 Kd = 10.9 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 1331 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 Kd = 18 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 Kd = 1.8 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 Kd = 7.1 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 Kd = 3.5 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 Kd = 9.54 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 Kd = 10.9 uM B0H C17 H24 N4 O2 S Cc1c(oc(n1....
38 3RCW - MB3 C5 H9 N O CN1CCCC1=O
39 5N49 ic50 = 450 nM 8LW C22 H17 N3 O3 Cc1cc2c(cc....
50% Homology Family (64)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 5I7Y Kd = 52 nM 69G C20 H21 N3 O2 C/C=C/CN1C....
2 4UIW ic50 = 0.00000001 M H1B C22 H22 F3 N3 O3 S2 CCN1C=C(c2....
3 4UIV ic50 = 0.00000001 M 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 = 0.00000001 M TVU C22 H24 N2 O6 S2 CN1C=C(c2c....
7 4UIT ic50 = 0.00000001 M N1D C22 H25 N3 O6 S2 CN1C=C(c2c....
8 5I40 ic50 = 13.7 uM 67N C8 H8 N2 O CN1C=Cc2cc....
9 5I7X Kd = 53 nM 67B C17 H17 N3 O2 CN1C=C(c2c....
10 6V1B Kd = 37 nM H1B C22 H22 F3 N3 O3 S2 CCN1C=C(c2....
11 6V0X Kd = 277 uM B49 C22 H27 F N4 O2 CCN(CC)CCN....
12 4XY8 Kd = 397 nM 43U C12 H10 Br N5 O COc1ccc(cc....
13 5IGM Kd = 41.7 nM BMF C17 H20 N6 O4 S CCOC(=O)Nc....
14 4Z6H Kd = 612 nM 4L2 C16 H18 N2 O2 CC1=CC(=O)....
15 6HM0 Kd = 73 nM GBW C50 H64 N8 O9 S Cc1c(scn1)....
16 5F1H Kd = 14.1 nM 5U6 C20 H23 N3 O3 CN1C=C(c2c....
17 5F1L ic50 = 21 nM 5U2 C19 H24 N2 O4 CC1=CC(=CN....
18 5F25 Kd = 9.1 uM 5TU C14 H14 N2 O2 CC1=CC(=CN....
19 4Z6I - 4L3 C27 H31 N3 O4 CC1=CC(=O)....
20 6V0S Kd = 16000 nM EAE C13 H15 N O2 S CCN1c2cc(c....
21 5EU1 Kd = 15.4 nM 5SW C20 H23 N3 O3 CN1C=C(c2c....
22 6V14 Kd = 82 nM QMG C20 H19 N3 O2 Cc1ccc(cc1....
23 5F2P Kd = 37.5 uM 5TY C10 H12 N4 O CN1C=Cc2c(....
24 5E3D Kd = 95 uM 5JL C5 H4 N4 O S2 C12=C(NC(=....
25 5C87 - 4YS C9 H7 N O c1ccc2c(c1....
26 5O4T - 9KT C10 H10 N2 O2 CN1c2ccccc....
27 5OV8 Kd = 18 uM AXN C24 H30 N4 O4 S CC(C)Cc1cc....
28 5O4S ic50 = 3.4 uM 9KW C24 H28 N4 O5 S CN1c2cc(c(....
29 5MWH Kd = 1.8 uM UWX C24 H30 N4 O5 S CC(C)Cc1cc....
30 5DY7 - 5GT C9 H7 F3 N2 O c1cc2c(cc1....
31 5T4V ic50 = 60 nM N48 C19 H17 N3 O4 S CC1=CC(=O)....
32 5DYC - 5GU C8 H7 Br N2 O c1cc2c(cc1....
33 5O55 - 9L5 C19 H23 N5 O2 CCN1c2ccc(....
34 5EQ1 Kd = 21 uM BEA C9 H8 N3 S Cc1cccc2c1....
35 5G4S ic50 = 1 uM 8VI C24 H31 N5 O3 CCN(c1cc2c....
36 5EWC - 5SJ C12 H14 N2 O3 CCOC(=O)c1....
37 5EPR Kd = 91 uM 5QY C9 H10 N2 O C[C@H]1C(=....
38 5EVA - 5S9 C11 H9 F2 N3 O Cn1c(ccn1)....
39 5ETD - 5RN C10 H9 N O CC(=O)c1c[....
40 5DYA - 5GV C11 H12 N2 O3 CC[C@@H]1C....
41 5EV9 - 5SB C14 H12 N4 O CC(=O)Nc1c....
42 5MYG Kd = 31 nM LS8 C19 H17 N3 O4 S CC1=Cc2cc(....
43 5MWZ Kd = 7.1 uM KGU C24 H36 N6 O3 CCN1c2cc(c....
44 5G4R ic50 = 7.943 nM LF1 C22 H27 N5 O3 C[C@@H]1CN....
45 5OWA Kd = 3.5 uM B0H C17 H24 N4 O2 S Cc1c(oc(n1....
46 5EM3 - 5Q0 C9 H7 N O c1cc2c(ccc....
47 5ETB Kd = 29 uM 5RO C11 H11 N O Cc1cccc2c1....
48 4UYE Kd = 9.54 nM 9F9 C22 H26 N4 O3 CN1c2cc(c(....
49 5O5F - 9LT C22 H20 F N5 O3 CCN1c2ccc(....
50 5O5A - 9LN C22 H21 N5 O3 CCN1c2ccc(....
51 5O5H - 9LK C17 H14 Cl N3 O3 Cc1c(oc(n1....
52 5C7N Kd = 0.27 uM BMF C17 H20 N6 O4 S CCOC(=O)Nc....
53 5EPS Kd = 38 uM 5QX C9 H10 N2 O CN1c2ccccc....
54 5MWG ic50 = 1.7 uM WGX C25 H30 N4 O4 S CN1c2cc(c(....
55 5D7X Kd = 15 uM XZ8 C14 H13 N3 O2 CC1=C(C(=O....
56 6EKQ Kd = 10.9 uM B0H C17 H24 N4 O2 S Cc1c(oc(n1....
57 6V1E Kd = 121 nM 5SW C20 H23 N3 O3 CN1C=C(c2c....
58 6V17 Kd = 148 nM H1B C22 H22 F3 N3 O3 S2 CCN1C=C(c2....
59 6V0Q Kd = 4200 nM EAE C13 H15 N O2 S CCN1c2cc(c....
60 6V1H Kd = 114 nM BMF C17 H20 N6 O4 S CCOC(=O)Nc....
61 6V16 Kd = 556 nM QMG C20 H19 N3 O2 Cc1ccc(cc1....
62 6V1F Kd = 418 nM 5U6 C20 H23 N3 O3 CN1C=C(c2c....
63 3RCW - MB3 C5 H9 N O CN1CCCC1=O
64 5N49 ic50 = 450 nM 8LW C22 H17 N3 O3 Cc1cc2c(cc....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: XZ8; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 XZ8 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: XZ8; Similar ligands found: 106
No: Ligand Similarity coefficient
1 36Z 0.9450
2 QZ8 0.9357
3 P9I 0.9340
4 BQ5 0.9304
5 DIF 0.9293
6 25O 0.9225
7 ABJ 0.9212
8 AB3 0.9197
9 B2T 0.9176
10 ID8 0.9174
11 2GD 0.9106
12 TLF 0.9105
13 43U 0.9095
14 JMS 0.9091
15 8WZ 0.9052
16 43S 0.9042
17 6PB 0.9028
18 17C 0.9014
19 96R 0.9013
20 6J3 0.8975
21 SGV 0.8974
22 3Y7 0.8972
23 M4B 0.8955
24 5P3 0.8937
25 89J 0.8926
26 FHI 0.8903
27 2LX 0.8899
28 5E4 0.8897
29 AUV 0.8886
30 MUR 0.8879
31 K3Y 0.8879
32 DXK 0.8877
33 LUR 0.8872
34 WVV 0.8869
35 636 0.8868
36 SOV 0.8864
37 A3K 0.8861
38 6J9 0.8857
39 KB8 0.8854
40 B4O 0.8853
41 AJD 0.8847
42 ELH 0.8841
43 5SB 0.8832
44 TQU 0.8830
45 AKD 0.8821
46 A3Q 0.8808
47 MEX 0.8801
48 WOE 0.8790
49 11G 0.8786
50 683 0.8783
51 X6P 0.8782
52 WUB 0.8757
53 5I5 0.8757
54 LWS 0.8749
55 5F8 0.8744
56 NIR 0.8743
57 JR2 0.8742
58 78P 0.8741
59 HO4 0.8741
60 IQQ 0.8741
61 145 0.8722
62 4E5 0.8722
63 KCH 0.8716
64 3RH 0.8706
65 AVA 0.8703
66 KFN 0.8700
67 7ZL 0.8700
68 2GE 0.8696
69 ZME 0.8696
70 Q2R 0.8694
71 4GP 0.8693
72 5FL 0.8691
73 EAJ 0.8679
74 Q4G 0.8678
75 7NU 0.8670
76 L5D 0.8667
77 RVE 0.8662
78 3WJ 0.8658
79 NYJ 0.8653
80 61O 0.8652
81 OX2 0.8650
82 1Z8 0.8643
83 7L4 0.8640
84 SA0 0.8638
85 692 0.8636
86 Z16 0.8634
87 56N 0.8632
88 1ER 0.8627
89 XFE 0.8623
90 3GX 0.8612
91 EVO 0.8612
92 VM1 0.8606
93 AYS 0.8605
94 52B 0.8602
95 LP8 0.8595
96 PBQ 0.8594
97 YJD 0.8592
98 1SF 0.8591
99 3CA 0.8589
100 H70 0.8580
101 LFQ 0.8575
102 RPP 0.8574
103 A1Y 0.8567
104 1FF 0.8553
105 3YQ 0.8547
106 I46 0.8514
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: 4
This union binding pocket(no: 1) in the query (biounit: 4uye.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 4YC9 4C1 35.5932
2 6J3O B4L 38.1356
3 5MLJ 9ST 40.1786
4 5ML0 P2L 45.4545
Pocket No.: 2; Query (leader) PDB : 4UYE; Ligand: 9F9; Similar sites found with APoc: 7
This union binding pocket(no: 2) in the query (biounit: 4uye.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 6J3P B8O 38.1356
2 6J3O B4L 38.1356
3 6J3P B8O 38.1356
4 5TPX 7H7 38.9831
5 5MLJ 9ST 40.1786
6 5MLJ 9ST 40.1786
7 5ML0 P2L 45.4545
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