Receptor
PDB id Resolution Class Description Source Keywords
5MKY 1.67 Å NON-ENZYME: OTHER BROMODOMAIN OF HUMAN BRD9 WITH 4-CHLORO-2-METHYL-5-((2-METHY TETRAHYDROISOQUINOLIN-5-YL)AMINO)PYRIDAZIN-3(2H)-ONE HOMO SAPIENS BRD9 INHIBITOR HISTONE EPIGENETIC READER BROMODOMAIN TRANSCRIPTION
Ref.: DISCOVERY OF A POTENT, CELL PENETRANT, AND SELECTIV P300/CBP-ASSOCIATED FACTOR (PCAF)/GENERAL CONTROL NONDEREPRESSIBLE 5 (GCN5) BROMODOMAIN CHEMICAL PROB J. MED. CHEM. V. 60 695 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
I0D A:202;
A:201;
 Valid;
Valid;
 none;
none;
 ic50 = 2 uM
304.775 C15 H17 Cl N4 O CN1CC...
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: I0D; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 I0D 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: I0D; Similar ligands found: 196
No: Ligand Similarity coefficient
1 XYP XIM 0.9404
2 LI4 0.9301
3 IWH 0.9241
4 7VF 0.9240
5 AX8 0.9222
6 LU2 0.9221
7 XZ1 0.9216
8 6XC 0.9185
9 3WK 0.9162
10 IMV 0.9146
11 XYP XYP 0.9125
12 ON1 0.9100
13 MQ1 0.9074
14 CIW 0.9062
15 DTQ 0.9052
16 EZB 0.9033
17 FL8 0.9026
18 FNA 0.9025
19 ELH 0.9022
20 QC1 0.9016
21 4K2 0.9011
22 7ZO 0.9009
23 5AV 0.9001
24 4P8 0.8997
25 12R 0.8995
26 2GE 0.8994
27 TCW 0.8991
28 XYS XYS 0.8989
29 NPZ 0.8984
30 4GU 0.8981
31 1Q4 0.8966
32 QRP 0.8965
33 3AK 0.8962
34 CDQ 0.8959
35 D5F 0.8953
36 CHV 0.8950
37 B4L 0.8950
38 DFL 0.8945
39 N1Y 0.8937
40 CBJ 0.8936
41 F0C 0.8931
42 BNY 0.8923
43 T34 0.8918
44 R75 0.8910
45 94M 0.8906
46 9ME 0.8905
47 21E 0.8901
48 NAR 0.8894
49 KTM 0.8888
50 48I 0.8876
51 M0Y 0.8875
52 Q2S 0.8874
53 LVB 0.8871
54 MHD GAL 0.8869
55 4L6 0.8863
56 T62 0.8862
57 7G1 0.8861
58 C4F 0.8859
59 DFV 0.8859
60 PU2 0.8858
61 NFG 0.8858
62 IM4 0.8858
63 AGI 0.8854
64 Y3J 0.8854
65 LM7 0.8853
66 6EN 0.8851
67 TAL 0.8850
68 6B5 0.8848
69 TH1 0.8845
70 AFX 0.8844
71 7Z9 0.8841
72 KMP 0.8839
73 C5Q 0.8836
74 8P3 0.8835
75 MTA 0.8834
76 CD9 0.8831
77 JNW 0.8830
78 4JV 0.8829
79 BC3 0.8829
80 O9Q 0.8828
81 MYC 0.8828
82 FZB 0.8823
83 DQH 0.8818
84 NOJ BGC 0.8817
85 D59 0.8817
86 5P7 0.8813
87 SAK 0.8812
88 CHJ 0.8812
89 IMK 0.8811
90 EP4 0.8809
91 D4X 0.8809
92 NOC 0.8807
93 ARJ 0.8807
94 KS5 0.8806
95 CJZ 0.8804
96 TOP 0.8803
97 VIB 0.8797
98 UI2 0.8796
99 P1Y 0.8794
100 DH2 0.8793
101 XDL XYP 0.8793
102 FT2 0.8791
103 JE7 0.8786
104 J47 0.8783
105 0HV 0.8782
106 1TD 0.8781
107 WL3 0.8774
108 VJJ 0.8772
109 DS8 0.8771
110 IRH 0.8771
111 IMH 0.8764
112 5TQ 0.8764
113 6QT 0.8760
114 JMS 0.8759
115 D4O 0.8755
116 536 0.8753
117 TLF 0.8752
118 40N 0.8751
119 XYP XDN 0.8751
120 7LU 0.8748
121 DSQ 0.8747
122 MQS 0.8745
123 Z15 0.8736
124 QS4 0.8736
125 KUP 0.8734
126 0QV 0.8733
127 15Q 0.8727
128 OAK 0.8726
129 J72 0.8725
130 M77 0.8724
131 MTH 0.8723
132 6J3 0.8721
133 EUN 0.8715
134 4KN 0.8714
135 AHR AHR 0.8707
136 UNM 0.8705
137 5CD 0.8703
138 DE7 0.8703
139 MTI 0.8696
140 OUA 0.8696
141 XDN XYP 0.8694
142 AJ4 0.8692
143 AD3 0.8687
144 NWL 0.8683
145 C0Y 0.8682
146 53X 0.8679
147 FT3 0.8677
148 BIE 0.8675
149 RK4 0.8672
150 TCL 0.8671
151 BXZ 0.8664
152 80R 0.8662
153 DTK 0.8661
154 MQR 0.8661
155 GCU BGC 0.8654
156 P2L 0.8653
157 6QX 0.8652
158 A0R 0.8643
159 2BI 0.8639
160 018 0.8634
161 ISX 0.8620
162 RB1 0.8619
163 VGG 0.8617
164 UX0 0.8616
165 2SY 0.8615
166 WDW 0.8615
167 FHI 0.8614
168 7O3 0.8611
169 JYM 0.8610
170 AMP 0.8609
171 A45 0.8604
172 CMG 0.8595
173 NQ7 0.8595
174 MXA 0.8595
175 LLG 0.8593
176 Z57 0.8592
177 7M9 0.8588
178 FMC 0.8585
179 5FD 0.8582
180 H35 0.8580
181 XIL 0.8577
182 BK1 0.8575
183 6KP 0.8572
184 50R 0.8572
185 NXY 0.8565
186 658 0.8563
187 100 0.8552
188 8KW 0.8545
189 HO4 0.8541
190 LFK 0.8534
191 6UW 0.8530
192 RGK 0.8529
193 H0V 0.8527
194 4L2 0.8514
195 SGV 0.8512
196 TBN 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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