Receptor
PDB id Resolution Class Description Source Keywords
5I7X 1.18 Å NON-ENZYME: OTHER BRD9 IN COMPLEX WITH CPD2 (N,N-DIMETHYL-3-(6-METHYL-7-OXO-6, 1H-PYRROLO[2,3-C]PYRIDIN-4-YL)BENZAMIDE) HOMO SAPIENS BROMODOMAIN INHIBITOR EPIGENETICS STRUCTURE-BASED DRUG DESIGBINDING PROTEIN
Ref.: DIVING INTO THE WATER: INDUCIBLE BINDING CONFORMATI BRD4, TAF1(2), BRD9, AND CECR2 BROMODOMAINS. J.MED.CHEM. V. 59 5391 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
67B A:201;
Valid;
none;
Kd = 53 nM
295.336 C17 H17 N3 O2 CN1C=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5I7Y 1.45 Å NON-ENZYME: OTHER BRD9 IN COMPLEX WITH CPD4 ((E)-3-(6-(BUT-2-EN-1-YL)-7-OXO-6, 1H-PYRROLO[2,3-C]PYRIDIN-4-YL)-N,N-DIMETHYLBENZAMIDE) HOMO SAPIENS BRD9 BROMODOMAIN EPIGENETICS STRUCTURE-BASED DESIGN TRAN
Ref.: DIVING INTO THE WATER: INDUCIBLE BINDING CONFORMATI BRD4, TAF1(2), BRD9, AND CECR2 BROMODOMAINS. J.MED.CHEM. V. 59 5391 2016
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 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....
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: 67B; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 67B 1 1
2 69G 0.623377 0.907407
3 67C 0.615385 0.859649
Similar Ligands (3D)
Ligand no: 1; Ligand: 67B; Similar ligands found: 77
No: Ligand Similarity coefficient
1 25V 0.9362
2 581 0.9340
3 FLF 0.9163
4 HGH 0.9067
5 QNI 0.9040
6 H6D 0.8995
7 NFL 0.8958
8 FO2 0.8941
9 TCW 0.8900
10 8WW 0.8858
11 LM7 0.8832
12 KOT 0.8805
13 BNY 0.8803
14 BFS 0.8801
15 QMG 0.8797
16 69W 0.8796
17 QLH 0.8790
18 4BE 0.8785
19 ZW2 0.8779
20 15I 0.8776
21 FX5 0.8775
22 2BE 0.8766
23 CMZ 0.8765
24 U98 0.8753
25 E44 0.8752
26 ZY5 0.8745
27 0KG 0.8734
28 Q2R 0.8730
29 M0Y 0.8719
30 MT6 0.8718
31 OQR 0.8717
32 SIJ 0.8715
33 AV4 0.8709
34 0KC 0.8706
35 TMP 0.8699
36 SNP 0.8684
37 FUL PK6 0.8684
38 2GE 0.8681
39 3BE 0.8670
40 GLA BEZ 0.8666
41 T7O 0.8664
42 MBP 0.8662
43 VM7 0.8661
44 6PB 0.8660
45 ZJB 0.8659
46 8GP 0.8656
47 ARJ 0.8656
48 IQP 0.8654
49 EXP 0.8654
50 M0S 0.8654
51 6F3 0.8645
52 43H 0.8636
53 ZYW 0.8636
54 E2N 0.8634
55 ELH 0.8634
56 NOC 0.8630
57 IXG 0.8626
58 ON1 0.8624
59 7GP 0.8623
60 E3Y 0.8622
61 GAL PHB 0.8612
62 S2X 0.8601
63 XEV 0.8595
64 G9Y 0.8591
65 145 0.8588
66 5XK 0.8584
67 G30 0.8576
68 53X 0.8574
69 6EN 0.8568
70 F9B 0.8565
71 T21 0.8561
72 KCH 0.8553
73 0HV 0.8532
74 YI5 0.8529
75 CAU 0.8524
76 5PK 0.8524
77 LKS 0.8511
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5I7Y; Ligand: 69G; Similar sites found with APoc: 7
This union binding pocket(no: 1) in the query (biounit: 5i7y.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 6J3O B4L 41.5842
2 5FDZ 5X0 41.5842
3 5FDZ 5X0 41.5842
4 6J3P B8O 42.5743
5 6J3P B8O 42.5743
6 5MLJ 9ST 42.5743
7 5TPX 7H7 43.5644
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