Receptor
PDB id Resolution Class Description Source Keywords
4XY8 1.7 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE BROMODOMAIN OF BRD9 IN COMPLEX WITH AMINE-9H-PURINE LIGAND HOMO SAPIENS BROMODOMAIN LIGAND COMPLEX STRUCTURAL GENOMICS CONSORTIUMTRANSCRIPTION
Ref.: 9H-PURINE SCAFFOLD REVEALS INDUCED-FIT POCKET PLAST THE BRD9 BROMODOMAIN. J.MED.CHEM. V. 58 2718 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
43U A:201;
 Valid;
 none;
 Kd = 397 nM
320.145 C12 H10 Br N5 O COc1c...
BR A:202;
 Invalid;
 none;
 submit data
79.904 Br [Br-]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5F1H 1.82 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE BRD9 BROMODAMIAN IN COMPLEX WITH BI HOMO SAPIENS BROMODOMAIN INHIBITOR TRANSCRIPTION
Ref.: STRUCTURE-BASED DESIGN OF AN IN VIVO ACTIVE SELECTI INHIBITOR. J.MED.CHEM. V. 59 4462 2016
Members (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 6V1B Kd = 37 nM H1B C22 H22 F3 N3 O3 S2 CCN1C=C(c2....
2 6V0X Kd = 277 uM B49 C22 H27 F N4 O2 CCN(CC)CCN....
3 4XY8 Kd = 397 nM 43U C12 H10 Br N5 O COc1ccc(cc....
4 5IGM Kd = 41.7 nM BMF C17 H20 N6 O4 S CCOC(=O)Nc....
5 4Z6H Kd = 612 nM 4L2 C16 H18 N2 O2 CC1=CC(=O)....
6 6HM0 Kd = 73 nM GBW C50 H64 N8 O9 S Cc1c(scn1)....
7 5F1H Kd = 14.1 nM 5U6 C20 H23 N3 O3 CN1C=C(c2c....
8 5F1L ic50 = 21 nM 5U2 C19 H24 N2 O4 CC1=CC(=CN....
9 5F25 Kd = 9.1 uM 5TU C14 H14 N2 O2 CC1=CC(=CN....
10 4Z6I - 4L3 C27 H31 N3 O4 CC1=CC(=O)....
11 6V0S Kd = 16000 nM EAE C13 H15 N O2 S CCN1c2cc(c....
12 5EU1 Kd = 15.4 nM 5SW C20 H23 N3 O3 CN1C=C(c2c....
13 6V14 Kd = 82 nM QMG C20 H19 N3 O2 Cc1ccc(cc1....
14 5F2P Kd = 37.5 uM 5TY C10 H12 N4 O CN1C=Cc2c(....
70% Homology Family (29)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 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 6V1E Kd = 121 nM 5SW C20 H23 N3 O3 CN1C=C(c2c....
25 6V17 Kd = 148 nM H1B C22 H22 F3 N3 O3 S2 CCN1C=C(c2....
26 6V0Q Kd = 4200 nM EAE C13 H15 N O2 S CCN1c2cc(c....
27 6V1H Kd = 114 nM BMF C17 H20 N6 O4 S CCOC(=O)Nc....
28 6V16 Kd = 556 nM QMG C20 H19 N3 O2 Cc1ccc(cc1....
29 6V1F Kd = 418 nM 5U6 C20 H23 N3 O3 CN1C=C(c2c....
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: 43U; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 43U 1 1
2 43S 0.474359 0.823529
Similar Ligands (3D)
Ligand no: 1; Ligand: 43U; Similar ligands found: 98
No: Ligand Similarity coefficient
1 6PB 0.9402
2 WOE 0.9261
3 17C 0.9208
4 ZYV 0.9202
5 5JT 0.9113
6 B2T 0.9110
7 XZ8 0.9095
8 EAJ 0.9063
9 QZ8 0.9057
10 ELH 0.9036
11 25O 0.9023
12 52B 0.9018
13 JMS 0.9013
14 3RP 0.9013
15 W8G 0.8992
16 636 0.8980
17 3RQ 0.8980
18 TLF 0.8970
19 DBQ 0.8960
20 683 0.8959
21 ID8 0.8950
22 DIF 0.8949
23 PBQ 0.8943
24 H70 0.8937
25 5E4 0.8926
26 Z16 0.8922
27 145 0.8921
28 2GD 0.8917
29 6J3 0.8915
30 ZYW 0.8898
31 X11 0.8884
32 GO0 0.8874
33 ABJ 0.8870
34 SOV 0.8866
35 BQ5 0.8856
36 6J9 0.8846
37 ZME 0.8835
38 AUV 0.8834
39 A3K 0.8831
40 38B 0.8823
41 KCH 0.8822
42 VAO 0.8814
43 MEX 0.8811
44 A3Q 0.8809
45 3RR 0.8801
46 36Z 0.8792
47 BGC OXZ 0.8775
48 Q2R 0.8769
49 8WZ 0.8763
50 5VL 0.8758
51 T28 0.8755
52 K3Y 0.8752
53 0RY 0.8750
54 ACE TRP 0.8747
55 1Z8 0.8743
56 ONZ 0.8739
57 HMD 0.8737
58 IA2 0.8735
59 HO4 0.8735
60 P9I 0.8730
61 FC3 0.8727
62 WUB 0.8721
63 CK1 0.8720
64 B4O 0.8712
65 43P 0.8710
66 BZE 0.8710
67 2KU 0.8707
68 3Y7 0.8702
69 JR2 0.8698
70 EVO 0.8681
71 R9G 0.8680
72 XFE 0.8680
73 9X5 0.8675
74 BNY 0.8673
75 GLC GAL 0.8667
76 5I5 0.8666
77 9CE 0.8663
78 5UD 0.8658
79 5V7 0.8654
80 6EN 0.8649
81 C9E 0.8647
82 HDU 0.8639
83 4GU 0.8631
84 B21 0.8631
85 IKY 0.8624
86 H7S 0.8620
87 BPY 0.8606
88 RPP 0.8605
89 96R 0.8599
90 CJZ 0.8593
91 K6B 0.8587
92 LL1 0.8581
93 4A1 0.8577
94 X29 0.8572
95 3CA 0.8560
96 1ZC 0.8543
97 W29 0.8535
98 54X 0.8524
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5F1H; Ligand: 5U6; Similar sites found with APoc: 4
This union binding pocket(no: 1) in the query (biounit: 5f1h.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 6J3P B8O 34.9594
2 6J3O B4L 35
3 6J3O B4L 35
4 5TPX 7H7 35.7724
Pocket No.: 2; Query (leader) PDB : 5F1H; Ligand: 5U6; Similar sites found with APoc: 9
This union binding pocket(no: 2) in the query (biounit: 5f1h.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 6J3P B8O 34.9594
2 6J3P B8O 34.9594
3 6J3O B4L 35
4 5TPX 7H7 35.7724
5 5MLJ 9ST 38.3929
6 5MLJ 9ST 38.3929
7 5ML0 P2L 39.0909
8 5FDZ 5X0 41.1765
9 5FDZ 5X0 41.1765
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