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Receptor
PDB id Resolution Class Description Source Keywords
5IVE 1.78 Å EC: 2.1.14.11 LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N8 ( 5-METHYL (PROPAN-2-YL)-4,7-DIHYDROPYRAZOLO[1,5-A]PYRIMIDINE-3-CARBON HOMO SAPIENS DEMETHYLASE INHIBITION OXIDOREDUCTASE-OXIDOREDUCTASE INHIBICOMPLEX
Ref.: STRUCTURAL BASIS FOR KDM5A HISTONE LYSINE DEMETHYLA INHIBITION BY DIVERSE COMPOUNDS. CELL CHEM BIOL V. 23 769 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
6E8 A:601;
 Valid;
 none;
 Kd = 0.027 uM
216.239 C11 H12 N4 O CC1=C...
MN A:602;
 Invalid;
 none;
 submit data
54.938 Mn [Mn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5IVE 1.78 Å EC: 2.1.14.11 LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N8 ( 5-METHYL (PROPAN-2-YL)-4,7-DIHYDROPYRAZOLO[1,5-A]PYRIMIDINE-3-CARBON HOMO SAPIENS DEMETHYLASE INHIBITION OXIDOREDUCTASE-OXIDOREDUCTASE INHIBICOMPLEX
Ref.: STRUCTURAL BASIS FOR KDM5A HISTONE LYSINE DEMETHYLA INHIBITION BY DIVERSE COMPOUNDS. CELL CHEM BIOL V. 23 769 2016
Members (28)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5IVE Kd = 0.027 uM 6E8 C11 H12 N4 O CC1=C(C(=O....
2 6DQA - H6V C22 H25 N3 O3 S c1cc(cc(c1....
3 6BGX Kd = 0.47 uM DKV C22 H21 Cl F2 N2 O3 c1ccc(c(c1....
4 6BGV Kd = 0.18 uM DQG C22 H24 Cl N3 O3 c1ccc(c(c1....
5 5IVY Kd = 0.36 uM 6EO C14 H11 Cl N2 O3 c1cc(ccc1C....
6 6DQ5 Kd = 6 uM H6G C20 H24 N6 O3 C=CC(=O)N1....
7 6DQ8 Kd = 0.26 uM H6S C22 H23 Cl N2 O3 S CN1CCC[C@H....
8 5IWF - LQT C15 H25 N5 O2 CCN(CCN(C)....
9 5IVC Kd = 1.2 uM 6E7 C20 H17 N3 O3 c1ccc(cc1)....
10 6BH2 Kd = 2.4 uM 90V C15 H22 N4 O2 CC(C)c1cc(....
11 5IVV Kd = 0.45 uM 6EN C14 H12 N4 O2 Cn1cc(c2c1....
12 5ISL Kd = 0.052 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
13 6BH5 Kd = 0.25 uM DNY C23 H26 Cl N3 O3 c1ccc(c(c1....
14 5E6H Kd = 79 uM AKG C5 H6 O5 C(CC(=O)O)....
15 6BGU Kd = 0.53 uM DKP C18 H17 Cl N2 O3 CCCO[C@H](....
16 6DQ6 Kd = 9 uM H6J C19 H24 N6 O4 S C=CS(=O)(=....
17 6BH1 Kd = 0.06 uM DQG C22 H24 Cl N3 O3 c1ccc(c(c1....
18 6DQ4 Kd = 12 uM K0I C22 H23 N5 O2 c1ccc2c(c1....
19 5IW0 Kd = 0.06 uM 6EP C17 H14 Cl N3 O3 Cc1cc(ccc1....
20 6BGY Kd = 0.15 uM DLJ C22 H24 Cl N3 O3 CN1CCC[C@@....
21 5IVJ Kd = 0.046 uM 6ED C20 H20 F3 N5 O2 c1cc2c(cc1....
22 6BH4 - DQS C17 H20 N6 O CC(C)C1=C(....
23 5IVB - AKG C5 H6 O5 C(CC(=O)O)....
24 5IVF - 6EB C15 H14 F3 N5 O2 Cn1cc(nc1)....
25 6BH0 Kd = 0.22 uM DO1 C22 H24 Cl N3 O3 c1ccc(c(c1....
26 6BGZ Kd = 0.41 uM DNV C21 H19 Cl N4 O3 Cn1ccnc1CC....
27 6BH3 - DQJ C15 H22 N4 O2 CC(C)c1cc(....
28 6BGW Kd = 0.21 uM DKS C22 H22 Cl F2 N3 O3 c1ccc(c(c1....
70% Homology Family (28)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5IVE Kd = 0.027 uM 6E8 C11 H12 N4 O CC1=C(C(=O....
2 6DQA - H6V C22 H25 N3 O3 S c1cc(cc(c1....
3 6BGX Kd = 0.47 uM DKV C22 H21 Cl F2 N2 O3 c1ccc(c(c1....
4 6BGV Kd = 0.18 uM DQG C22 H24 Cl N3 O3 c1ccc(c(c1....
5 5IVY Kd = 0.36 uM 6EO C14 H11 Cl N2 O3 c1cc(ccc1C....
6 6DQ5 Kd = 6 uM H6G C20 H24 N6 O3 C=CC(=O)N1....
7 6DQ8 Kd = 0.26 uM H6S C22 H23 Cl N2 O3 S CN1CCC[C@H....
8 5IWF - LQT C15 H25 N5 O2 CCN(CCN(C)....
9 5IVC Kd = 1.2 uM 6E7 C20 H17 N3 O3 c1ccc(cc1)....
10 6BH2 Kd = 2.4 uM 90V C15 H22 N4 O2 CC(C)c1cc(....
11 5IVV Kd = 0.45 uM 6EN C14 H12 N4 O2 Cn1cc(c2c1....
12 5ISL Kd = 0.052 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
13 6BH5 Kd = 0.25 uM DNY C23 H26 Cl N3 O3 c1ccc(c(c1....
14 5E6H Kd = 79 uM AKG C5 H6 O5 C(CC(=O)O)....
15 6BGU Kd = 0.53 uM DKP C18 H17 Cl N2 O3 CCCO[C@H](....
16 6DQ6 Kd = 9 uM H6J C19 H24 N6 O4 S C=CS(=O)(=....
17 6BH1 Kd = 0.06 uM DQG C22 H24 Cl N3 O3 c1ccc(c(c1....
18 6DQ4 Kd = 12 uM K0I C22 H23 N5 O2 c1ccc2c(c1....
19 5IW0 Kd = 0.06 uM 6EP C17 H14 Cl N3 O3 Cc1cc(ccc1....
20 6BGY Kd = 0.15 uM DLJ C22 H24 Cl N3 O3 CN1CCC[C@@....
21 5IVJ Kd = 0.046 uM 6ED C20 H20 F3 N5 O2 c1cc2c(cc1....
22 6BH4 - DQS C17 H20 N6 O CC(C)C1=C(....
23 5IVB - AKG C5 H6 O5 C(CC(=O)O)....
24 5IVF - 6EB C15 H14 F3 N5 O2 Cn1cc(nc1)....
25 6BH0 Kd = 0.22 uM DO1 C22 H24 Cl N3 O3 c1ccc(c(c1....
26 6BGZ Kd = 0.41 uM DNV C21 H19 Cl N4 O3 Cn1ccnc1CC....
27 6BH3 - DQJ C15 H22 N4 O2 CC(C)c1cc(....
28 6BGW Kd = 0.21 uM DKS C22 H22 Cl F2 N3 O3 c1ccc(c(c1....
50% Homology Family (40)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5FWJ Ki = 0.0061 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
2 5IVE Kd = 0.027 uM 6E8 C11 H12 N4 O CC1=C(C(=O....
3 6DQA - H6V C22 H25 N3 O3 S c1cc(cc(c1....
4 6BGX Kd = 0.47 uM DKV C22 H21 Cl F2 N2 O3 c1ccc(c(c1....
5 6BGV Kd = 0.18 uM DQG C22 H24 Cl N3 O3 c1ccc(c(c1....
6 5IVY Kd = 0.36 uM 6EO C14 H11 Cl N2 O3 c1cc(ccc1C....
7 6DQ5 Kd = 6 uM H6G C20 H24 N6 O3 C=CC(=O)N1....
8 6DQ8 Kd = 0.26 uM H6S C22 H23 Cl N2 O3 S CN1CCC[C@H....
9 5IWF - LQT C15 H25 N5 O2 CCN(CCN(C)....
10 5IVC Kd = 1.2 uM 6E7 C20 H17 N3 O3 c1ccc(cc1)....
11 6BH2 Kd = 2.4 uM 90V C15 H22 N4 O2 CC(C)c1cc(....
12 5IVV Kd = 0.45 uM 6EN C14 H12 N4 O2 Cn1cc(c2c1....
13 5ISL Kd = 0.052 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
14 6BH5 Kd = 0.25 uM DNY C23 H26 Cl N3 O3 c1ccc(c(c1....
15 5E6H Kd = 79 uM AKG C5 H6 O5 C(CC(=O)O)....
16 6BGU Kd = 0.53 uM DKP C18 H17 Cl N2 O3 CCCO[C@H](....
17 6DQ6 Kd = 9 uM H6J C19 H24 N6 O4 S C=CS(=O)(=....
18 6BH1 Kd = 0.06 uM DQG C22 H24 Cl N3 O3 c1ccc(c(c1....
19 6DQ4 Kd = 12 uM K0I C22 H23 N5 O2 c1ccc2c(c1....
20 5IW0 Kd = 0.06 uM 6EP C17 H14 Cl N3 O3 Cc1cc(ccc1....
21 6BGY Kd = 0.15 uM DLJ C22 H24 Cl N3 O3 CN1CCC[C@@....
22 5IVJ Kd = 0.046 uM 6ED C20 H20 F3 N5 O2 c1cc2c(cc1....
23 6BH4 - DQS C17 H20 N6 O CC(C)C1=C(....
24 5IVB - AKG C5 H6 O5 C(CC(=O)O)....
25 5IVF - 6EB C15 H14 F3 N5 O2 Cn1cc(nc1)....
26 6BH0 Kd = 0.22 uM DO1 C22 H24 Cl N3 O3 c1ccc(c(c1....
27 6BGZ Kd = 0.41 uM DNV C21 H19 Cl N4 O3 Cn1ccnc1CC....
28 6BH3 - DQJ C15 H22 N4 O2 CC(C)c1cc(....
29 6BGW Kd = 0.21 uM DKS C22 H22 Cl F2 N3 O3 c1ccc(c(c1....
30 5A3N ic50 = 19 nM LQT C15 H25 N5 O2 CCN(CCN(C)....
31 5A3W Ki = 0.39 uM PD2 C7 H5 N O4 c1cnc(cc1C....
32 5FPL - MN QAY n/a n/a
33 5FPU Ki = 0.14 uM K0I C22 H23 N5 O2 c1ccc2c(c1....
34 5FUP - AKG C5 H6 O5 C(CC(=O)O)....
35 5FV3 Ki = 6.32 uM OGA C4 H5 N O5 C(C(=O)O)N....
36 5A1F Ki = 6.32 uM OGA C4 H5 N O5 C(C(=O)O)N....
37 5FUN Ki = 0.01 uM GZA C17 H13 N5 O2 c1ccc(cc1)....
38 5A3T Ki = 0.001 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
39 4IGQ - OGA C4 H5 N O5 C(C(=O)O)N....
40 4IGO - AKG C5 H6 O5 C(CC(=O)O)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 6E8; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 6E8 1 1
2 DQS 0.523077 0.909091
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5IVE; Ligand: 6E8; Similar sites found with APoc: 295
This union binding pocket(no: 1) in the query (biounit: 5ive.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
1 6GNO XDI None
2 1RV1 IMZ None
3 3HCH RSM None
4 1DRY AAG 1.23457
5 1DRY AKG 1.23457
6 4NZ6 DLY 1.27796
7 6GVZ CHO 1.31148
8 1GZW GAL BGC 1.49254
9 5O9W AKG 1.51515
10 1Q11 TYE 1.51515
11 1F9V ADP 1.51515
12 3C0G 3AM 1.51515
13 3WW2 SF6 1.5625
14 3WW2 LPK 1.5625
15 5C3R AKG 1.81818
16 5C3R HMU 1.81818
17 6G33 5ID 1.81818
18 4JZR 4JR 1.85185
19 6BT6 3GK 1.90114
20 4XCB AKG 1.91571
21 4XCB HY0 1.91571
22 4RDL FUC GAL NDG FUC 1.94805
23 5TPV TYD 1.96078
24 1ZY5 ANP 1.9802
25 5L9V OGA 1.98413
26 5L9B AKG 1.98413
27 3HQR OGA 2.03252
28 5Z5I XYP 2.12121
29 5LUN OGA 2.12121
30 4FFG 0U8 2.12121
31 2WBP ZZU 2.12121
32 2WBP SIN 2.12121
33 4WOE ADP 2.12121
34 2HBL AMP 2.12121
35 4MOB ADP 2.12121
36 3JU6 ANP 2.12121
37 2OHH FMN 2.12121
38 2POC UD1 2.12121
39 3JRX S1A 2.12121
40 6FRN FMN 2.12121
41 4L4J NAG NAG BMA MAN NAG 2.26244
42 4QM9 CYS 2.31214
43 1OIK AKG 2.32558
44 1OIJ AKG 2.32558
45 1OIK C26 2.32558
46 1KGI T4A 2.3622
47 4OJ8 AKG 2.38908
48 4OJ8 2TQ 2.38908
49 1ZNY GDP 2.41546
50 5X7Q GLC GLC 2.42424
51 5L2R MLA 2.42424
52 4ZNO SUC 2.42424
53 1VEM GLC GLC 2.42424
54 3TXO 07U 2.42424
55 3H9A PPY 2.46914
56 4D4U FUC NDG GAL FUC 2.53968
57 5F6U 5VK 2.54777
58 1NX4 AKG 2.5641
59 1UNB AKG 2.57235
60 1Y9Q MED 2.60417
61 3SJK LYS PRO VAL LEU ARG THR ALA 2.63158
62 1WLJ U5P 2.6455
63 2G30 ALA ALA PHE 2.71318
64 3PUA OGA 2.72727
65 1LSH PLD 2.72727
66 4ZWP M44 2.72727
67 5OF1 SAL 2.85714
68 4GK9 MAN BMA MAN MAN MAN 2.86738
69 3KV4 OGA 3.0303
70 5N0F 7K2 3.0303
71 5Y4K AKR 3.0303
72 6F5W KG1 3.0303
73 4B74 1LH 3.0303
74 2GC0 PAN 3.19149
75 4IAW LIZ 3.19149
76 4RYV ZEA 3.22581
77 6GW4 CHO 3.25733
78 4GC1 MAN MAN 3.26087
79 4ZXA H8N 3.33333
80 2OVW CBI 3.33333
81 4YVN EBS 3.33333
82 3HQP OXL 3.33333
83 4BG1 IVL 3.33333
84 4BG1 OGA 3.33333
85 1GP6 DH2 3.33333
86 1GP6 SIN 3.33333
87 4OUC 5ID 3.33333
88 1GP6 QUE 3.33333
89 5HX1 UMP 3.33333
90 1W96 S1A 3.33333
91 2J3M PRI 3.33333
92 4J0M BLD 3.33333
93 2V7O DRN 3.33333
94 2J3M ATP 3.33333
95 3WG3 A2G GAL NAG FUC 3.37079
96 3A76 SPD 3.40909
97 5C5T AKG 3.50877
98 5GLT BGC GAL NAG GAL 3.52113
99 6BHQ NAG NAG FUL BMA MAN MAN NAG GAL 3.57143
100 5ACM MBT 3.6036
101 2VL1 GLY GLY 3.63636
102 2J5B TYE 3.63636
103 5F7U GLC GLC 3.63636
104 1ELI PYC 3.63636
105 4QCK ASD 3.63636
106 5HV0 AKG 3.68664
107 5V1B 8UY 3.75
108 5FLJ QUE 3.76344
109 4Z7X 3CX 3.78151
110 1QGQ UDP 3.92157
111 5OQW A4E 3.93701
112 4LIT AKG 3.93939
113 4YRD 3IT 3.93939
114 3JQ3 ADP 3.93939
115 5YJS SAL 3.93939
116 6F6J CUW 3.93939
117 6F6J SIN 3.93939
118 2VQ5 HBA 3.9801
119 4Z1D PEP 3.98551
120 5OO5 UUA 4.03226
121 4WUJ FMN 4.08163
122 5YW0 SIN 4.08805
123 4CC6 L5Y 4.08805
124 4H69 10Y 4.12371
125 1B4P GPS 4.14747
126 2OFD NGA 4.22535
127 4IE6 UN9 4.24242
128 3FW9 SLX 4.24242
129 2TOH HBI 4.24242
130 2ARC ARA 4.26829
131 4NAO AKG 4.29448
132 2AGC DAO 4.32099
133 4I94 ANP 4.33333
134 4J25 OGA 4.36681
135 2JIG PD2 4.46429
136 4NS0 PIO 4.51128
137 4RF7 ARG 4.54545
138 3ZW2 NAG GAL FUC 4.5977
139 6DW2 HD4 4.64135
140 3KYF 5GP 5GP 4.7619
141 4GQP B40 4.81928
142 5UQD AKG 4.84848
143 5KWW 6YA 4.84848
144 1A5Z FBP 5.01567
145 2HIM ASP 5.02793
146 3QRC SCR 5.09554
147 6D61 4AA 5.12821
148 4H6B 10Y 5.12821
149 1PIG BGC 5.15152
150 3ZDS HMQ 5.15152
151 3ZDS OMD 5.15152
152 3ZDS M8O 5.15152
153 1U6R ADP 5.15152
154 4W9F 3JU 5.15464
155 5XEG AKG 5.19481
156 4NPL AKG 5.2
157 5EPA AKG 5.37634
158 4OCT AKG 5.40541
159 4CCK OGA 5.45455
160 4Y3O OGA 5.45455
161 4CCN OGA 5.45455
162 2IUW AKG 5.46218
163 2A1X AKG 5.51948
164 1LRH NLA 5.52147
165 2BS5 BGC GAL FUC 5.55556
166 3QXV MTX 5.55556
167 1KQR MNA 5.58659
168 4R38 RBF 5.71429
169 4HSJ 6PC 5.74713
170 1QY1 PRZ 5.74713
171 1ODM ASV 5.75758
172 1J3R 6PG 5.78947
173 2YG2 S1P 5.81395
174 1VKF CIT 5.85106
175 2ET1 GLV 5.97015
176 5HVJ ANP 6.03175
177 3U6W KIV 6.06061
178 2UYN 2KT 6.20155
179 2P3I MNA 6.21118
180 3SAO NKN 6.25
181 3SAO DBH 6.25
182 2HRL SIA GAL SIA BGC NGA CEQ 6.29921
183 4LOC OXM 6.36364
184 4M26 AKG 6.36364
185 1DZK PRZ 6.36943
186 3E2M E2M 6.48649
187 4Y24 TD2 6.49351
188 3H7J PPY 6.58436
189 3ACL 3F1 6.75676
190 5FUI APY 6.81818
191 2RDQ AKG 6.94444
192 4JX1 CAH 6.9697
193 3T4L ZEA 7.03704
194 1QKQ MAN 7.04225
195 4Z2S NDG 7.04225
196 4Z2S NAG 7.04225
197 5T7I LAT NAG GAL 7.09677
198 3ACC 5GP 7.18232
199 3GJB AKG 7.21003
200 6FXR AKG 7.27273
201 2HYQ MAN MAN 7.37705
202 3W9R A8S 7.40741
203 5UGW GSH 7.42857
204 6F4T OGA 7.45098
205 3ZXE PGZ 7.5188
206 2RDE C2E 7.56972
207 1H2M OGA 7.57576
208 3P3N AKG 7.57576
209 1H2K OGA 7.57576
210 2WA4 069 7.57576
211 1Y7P RIP 7.87879
212 2YIP YIO 7.97101
213 5TZO 7V7 7.97872
214 5TFZ 7BC 8
215 3WUD GLC GAL 8.08823
216 3CF6 SP1 8.18182
217 5JWP AKG 8.23864
218 5JSP DQY 8.45771
219 5LDQ NAP 8.47458
220 6GR0 F8W 8.62069
221 2FCU AKG 8.6262
222 5WHT SIA 8.69565
223 5WHT SIA GAL 8.69565
224 1F5F DHT 8.78049
225 3N9P OGA 8.78788
226 3N9O OGA 8.78788
227 3PUR 2HG 8.78788
228 3N9Q OGA 8.78788
229 5NW7 9C2 8.78788
230 5KEW 6SB 9.02778
231 4MPO AMP 9.15033
232 1Y2W NAG 9.15493
233 1OS7 AKG 9.18728
234 1OS7 TAU 9.18728
235 5IQT 6CU 9.20635
236 5IQT AKG 9.20635
237 1ZZ7 S0H 9.59596
238 3SCH TB6 9.59596
239 6EWZ APC 9.70464
240 4WCX MET 10
241 5NIU 8YZ 10.1562
242 5D9G GLU ASN LEU TYR PHE GLN 10.1626
243 4B9K TG0 10.3093
244 5NVX 4YY 10.3093
245 4BKS X6C 10.3093
246 4W9H 3JF 10.3093
247 5WHU SIA GAL 10.7383
248 4YEE 4CQ 11.1111
249 3H0L ADP 11.2121
250 2QL9 CIT 11.3402
251 1EXF GLY 11.5702
252 6F6D AKG 12.1212
253 5FP3 3JI 12.1212
254 6CZI 38E 12.5
255 5OM2 DXT 12.5
256 4WVW SLT 12.5
257 6EOZ AKG 12.987
258 6EOZ 58K 12.987
259 3SRV S19 12.9964
260 1RZX ACE VAL LYS GLU SER LEU VAL 13.2653
261 1SQL GUN 14.3836
262 5N2D 8J8 14.5833
263 1SDW IYT 14.6497
264 5SVV FMN 15.3285
265 5M6N 7H9 16.1017
266 2IGA XX3 16.6667
267 4QXB OGA 17.6471
268 5ODY 9SK 18.1159
269 4LO2 GAL BGC 18.2432
270 4UF0 MMK 18.4848
271 3KV5 OGA 18.7879
272 3AVR OGA 19.0909
273 6FUL E7Z 19.0909
274 1N5S ADL 19.6429
275 3WUC GLC GAL 22.6277
276 4M1U A2G MBG 22.8571
277 5H9P TD2 23.4177
278 4K55 H6P 24.1935
279 1I06 TZL 24.4444
280 4BXF AKG 26.3158
281 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU 26.3158
282 5FPX GLY SER SER HIS HIS HIS HIS HIS 26.5487
283 4CCO OGA 35
284 5FP4 YC8 45.7576
285 3OPT AKG 46.9697
286 5KR7 6X9 47.5758
287 5FWE OGA 47.8788
288 2Q8E OGA 47.8788
289 2YBP 2HG 47.8788
290 2P5B OGA 47.8788
291 6H8P OGA 47.8788
292 5LY1 PPI 47.8788
293 5F3I 5UJ 47.8788
294 2OS2 OGA 47.8788
295 5LY2 OGA 47.8788
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