Receptor
PDB id Resolution Class Description Source Keywords
5IVY 1.45 Å EC: 1.14.11.- LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N16 [3-(2-(4- CHLOROPHENYL)ACETAMIDO)ISONICOTINIC ACID] 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
6EO A:601;
 Valid;
 none;
 Kd = 0.36 uM
290.702 C14 H11 Cl N2 O3 c1cc(...
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: 6EO; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 6EO 1 1
2 YC8 0.507463 0.829787
3 QC1 0.426471 0.723404
Similar Ligands (3D)
Ligand no: 1; Ligand: 6EO; Similar ligands found: 46
No: Ligand Similarity coefficient
1 8WW 0.9194
2 A0R 0.9045
3 ZW2 0.9036
4 4VC 0.9036
5 EMU 0.8936
6 RE2 0.8919
7 BC3 0.8918
8 12R 0.8892
9 AX5 0.8889
10 AX6 0.8876
11 5AV 0.8872
12 9X0 0.8863
13 C3G 0.8844
14 RE4 0.8843
15 1BD 0.8841
16 SCE 0.8837
17 HI6 0.8825
18 J90 0.8816
19 1XF 0.8812
20 4JV 0.8809
21 D5F 0.8805
22 4KN 0.8804
23 0RU 0.8801
24 DE7 0.8787
25 TCW 0.8785
26 GJW 0.8783
27 21X 0.8774
28 8KW 0.8766
29 SIJ 0.8759
30 F91 0.8740
31 QNI 0.8726
32 15I 0.8715
33 EXP 0.8712
34 STL 0.8710
35 1A6 0.8668
36 KUP 0.8665
37 3RC 0.8663
38 0HV 0.8659
39 OA5 0.8656
40 7ZO 0.8650
41 0OP 0.8633
42 137 0.8622
43 OAK 0.8615
44 GVI 0.8605
45 0RB 0.8575
46 Q5M 0.8555
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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