Receptor
PDB id Resolution Class Description Source Keywords
5IVE 1.78 Å EC: 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: 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 43 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 = 6.4 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 = 8.5 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 31 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 = 6.4 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 = 8.5 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 (44)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 28 families.
1 6H51 Ki = 0.016 uM FQK C20 H24 N6 O c1cnc(c2c1....
2 6H4Z Ki = 0.002 uM FQ5 C23 H23 Cl N6 O c1cc(cc(c1....
3 5A3N ic50 = 19 nM LQT C15 H25 N5 O2 CCN(CCN(C)....
4 6H52 ic50 = 0.068 uM FQN C20 H24 N6 O c1cnc(c2c1....
5 5A3W Ki = 0.39 uM PD2 C7 H5 N O4 c1cnc(cc1C....
6 6H50 ic50 = 0.156 uM FO2 C16 H18 N6 O CN1CCC(CC1....
7 5FPL - MN QAY n/a n/a
8 5FPU Ki = 0.14 uM K0I C22 H23 N5 O2 c1ccc2c(c1....
9 5FUP - AKG C5 H6 O5 C(CC(=O)O)....
10 5FV3 Ki = 6.32 uM OGA C4 H5 N O5 C(C(=O)O)N....
11 5A1F Ki = 6.32 uM OGA C4 H5 N O5 C(C(=O)O)N....
12 5FUN Ki = 0.01 uM GZA C17 H13 N5 O2 c1ccc(cc1)....
13 5A3T Ki = 0.001 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
14 5FWJ Ki = 0.0061 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
15 5IVE Kd = 0.027 uM 6E8 C11 H12 N4 O CC1=C(C(=O....
16 6DQA - H6V C22 H25 N3 O3 S c1cc(cc(c1....
17 6BGX Kd = 0.47 uM DKV C22 H21 Cl F2 N2 O3 c1ccc(c(c1....
18 6BGV Kd = 0.18 uM DQG C22 H24 Cl N3 O3 c1ccc(c(c1....
19 5IVY Kd = 0.36 uM 6EO C14 H11 Cl N2 O3 c1cc(ccc1C....
20 6DQ5 Kd = 6.4 uM H6G C20 H24 N6 O3 C=CC(=O)N1....
21 6DQ8 Kd = 0.26 uM H6S C22 H23 Cl N2 O3 S CN1CCC[C@H....
22 5IWF - LQT C15 H25 N5 O2 CCN(CCN(C)....
23 5IVC Kd = 1.2 uM 6E7 C20 H17 N3 O3 c1ccc(cc1)....
24 6BH2 Kd = 2.4 uM 90V C15 H22 N4 O2 CC(C)c1cc(....
25 5IVV Kd = 0.45 uM 6EN C14 H12 N4 O2 Cn1cc(c2c1....
26 5ISL Kd = 0.052 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
27 6BH5 Kd = 0.25 uM DNY C23 H26 Cl N3 O3 c1ccc(c(c1....
28 5E6H Kd = 79 uM AKG C5 H6 O5 C(CC(=O)O)....
29 6BGU Kd = 0.53 uM DKP C18 H17 Cl N2 O3 CCCO[C@H](....
30 6DQ6 Kd = 8.5 uM H6J C19 H24 N6 O4 S C=CS(=O)(=....
31 6BH1 Kd = 0.06 uM DQG C22 H24 Cl N3 O3 c1ccc(c(c1....
32 6DQ4 Kd = 12 uM K0I C22 H23 N5 O2 c1ccc2c(c1....
33 5IW0 Kd = 0.06 uM 6EP C17 H14 Cl N3 O3 Cc1cc(ccc1....
34 6BGY Kd = 0.15 uM DLJ C22 H24 Cl N3 O3 CN1CCC[C@@....
35 5IVJ Kd = 0.046 uM 6ED C20 H20 F3 N5 O2 c1cc2c(cc1....
36 6BH4 - DQS C17 H20 N6 O CC(C)C1=C(....
37 5IVB - AKG C5 H6 O5 C(CC(=O)O)....
38 5IVF - 6EB C15 H14 F3 N5 O2 Cn1cc(nc1)....
39 6BH0 Kd = 0.22 uM DO1 C22 H24 Cl N3 O3 c1ccc(c(c1....
40 6BGZ Kd = 0.41 uM DNV C21 H19 Cl N4 O3 Cn1ccnc1CC....
41 6BH3 - DQJ C15 H22 N4 O2 CC(C)c1cc(....
42 6BGW Kd = 0.21 uM DKS C22 H22 Cl F2 N3 O3 c1ccc(c(c1....
43 4IGQ - OGA C4 H5 N O5 C(C(=O)O)N....
44 4IGO - AKG C5 H6 O5 C(CC(=O)O)....
Polypharmacology
Similar Ligands (2D)
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 Ligands (3D)
Ligand no: 1; Ligand: 6E8; Similar ligands found: 241
No: Ligand Similarity coefficient
1 6X9 0.9490
2 NAG 0.9424
3 NDG 0.9383
4 HHR 0.9289
5 PH2 0.9282
6 N0Z 0.9149
7 68A 0.9081
8 3QV 0.9046
9 LTM 0.9037
10 LOG 0.9034
11 8MO 0.9034
12 CLZ 0.9030
13 GDL 0.9016
14 3R4 0.9012
15 PQ0 0.9002
16 2K8 0.9001
17 PRF 0.8995
18 NGA 0.8995
19 E1K 0.8983
20 44W 0.8982
21 MAG 0.8976
22 V1T 0.8957
23 9R5 0.8956
24 DNA 0.8953
25 UFO 0.8952
26 DQU 0.8943
27 N8Y 0.8935
28 ZZZ 0.8933
29 HHS 0.8931
30 8W9 0.8930
31 4RU 0.8928
32 5TY 0.8921
33 30G 0.8918
34 27B 0.8917
35 MVN 0.8916
36 4VS 0.8916
37 HBO 0.8910
38 OTW 0.8908
39 XHP 0.8907
40 GNY 0.8905
41 TIY 0.8905
42 GJP 0.8903
43 5NS 0.8898
44 1KP 0.8895
45 JU2 0.8895
46 B52 0.8894
47 28N 0.8892
48 1HN 0.8890
49 FDR 0.8888
50 EAE 0.8888
51 JXZ 0.8888
52 CFF 0.8887
53 0J4 0.8885
54 AJY 0.8880
55 B62 0.8880
56 A2G 0.8878
57 B56 0.8875
58 0FO 0.8875
59 2FQ 0.8873
60 GNV 0.8871
61 3Z8 0.8870
62 I6G 0.8870
63 K97 0.8863
64 GNM 0.8861
65 TOF 0.8854
66 6ME 0.8853
67 H5B 0.8851
68 549 0.8850
69 Y0V 0.8849
70 MNS 0.8846
71 39O 0.8846
72 5NE 0.8837
73 2HQ 0.8836
74 3N1 0.8836
75 9H2 0.8835
76 BGC 0.8830
77 QX4 0.8829
78 FLV 0.8825
79 BHQ 0.8822
80 5RO 0.8821
81 44V 0.8820
82 MS0 0.8820
83 BA5 0.8812
84 0FN 0.8810
85 SNG 0.8810
86 GXY 0.8805
87 HNT 0.8804
88 86J 0.8801
89 4YO 0.8800
90 BDP 0.8799
91 HKD 0.8797
92 WSD 0.8792
93 12T 0.8790
94 RH1 0.8790
95 344 0.8789
96 JTA 0.8788
97 K6X 0.8783
98 4JQ 0.8781
99 537 0.8773
100 PHH 0.8770
101 LZ2 0.8769
102 0TU 0.8769
103 428 0.8768
104 MQN 0.8767
105 EGR 0.8765
106 KJ5 0.8765
107 AJV 0.8764
108 0J5 0.8760
109 DPT 0.8755
110 E7S 0.8755
111 H4B 0.8753
112 94W 0.8752
113 CWS 0.8750
114 6FB 0.8747
115 WS7 0.8747
116 0FK 0.8746
117 4AB 0.8745
118 GF4 0.8744
119 CK2 0.8742
120 IV2 0.8742
121 H2B 0.8739
122 HBI 0.8739
123 AZ9 0.8738
124 0XT 0.8730
125 BIO 0.8729
126 8HC 0.8729
127 OCZ 0.8727
128 N2M 0.8727
129 K44 0.8727
130 AC2 0.8726
131 2KA 0.8721
132 MUA 0.8719
133 ZYR 0.8715
134 226 0.8709
135 VXX 0.8706
136 B5D 0.8705
137 8WO 0.8705
138 J6W 0.8704
139 KMY 0.8704
140 XM5 0.8703
141 RZH 0.8700
142 DX3 0.8700
143 7MX 0.8700
144 AP4 0.8696
145 4KL 0.8694
146 Q77 0.8693
147 2AK 0.8690
148 BGU 0.8690
149 15E 0.8690
150 JG8 0.8685
151 SJK 0.8684
152 APS 0.8684
153 3J8 0.8679
154 TGX 0.8677
155 4V6 0.8676
156 6QF 0.8673
157 HQD 0.8672
158 KUF 0.8671
159 BM3 0.8671
160 JXW 0.8670
161 APZ 0.8666
162 9KZ 0.8665
163 0P6 0.8663
164 1QP 0.8663
165 X0U 0.8663
166 F2W 0.8662
167 4TU 0.8660
168 7B3 0.8659
169 INE 0.8659
170 4AN 0.8658
171 ZEC 0.8658
172 MS9 0.8657
173 K68 0.8656
174 BPU 0.8656
175 6KT 0.8655
176 DPZ 0.8655
177 BSP 0.8655
178 0N7 0.8651
179 BZJ 0.8651
180 HRM 0.8646
181 AA 0.8645
182 2EC 0.8643
183 AMR 0.8640
184 0JD 0.8640
185 9AP 0.8639
186 VK3 0.8639
187 8CM 0.8634
188 LDR 0.8631
189 9LI 0.8631
190 XDE 0.8630
191 582 0.8630
192 ROI 0.8630
193 64C 0.8629
194 S60 0.8628
195 GSY 0.8628
196 EE8 0.8626
197 BHS 0.8624
198 2J1 0.8623
199 TT4 0.8620
200 PQK 0.8618
201 ZSP 0.8616
202 ANF 0.8611
203 KJY 0.8611
204 64E 0.8610
205 THA 0.8610
206 G12 0.8610
207 B60 0.8604
208 5GV 0.8604
209 21D 0.8604
210 PYQ 0.8602
211 BEA 0.8602
212 5XL 0.8600
213 TWO 0.8600
214 L1Q 0.8599
215 R9Y 0.8597
216 N2I 0.8590
217 ANC 0.8587
218 AN3 0.8586
219 4AA 0.8586
220 NQ 0.8585
221 AH9 0.8583
222 JYB 0.8583
223 7AP 0.8581
224 MAQ 0.8579
225 GTC 0.8574
226 7W1 0.8571
227 EZL 0.8570
228 M78 0.8560
229 FDB 0.8558
230 3VX 0.8556
231 LP8 0.8554
232 4BY 0.8550
233 ARP 0.8549
234 0FR 0.8546
235 RXA 0.8546
236 PEY 0.8544
237 GDE 0.8544
238 LT2 0.8537
239 4BL 0.8530
240 1U6 0.8529
241 BCU 0.8520
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: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5ive.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
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