Receptor
PDB id Resolution Class Description Source Keywords
5A7O 2.15 Å EC: 1.14.11.- CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH COMPOUND 4 HOMO SAPIENS OXIDOREDUCTASE JMJD2A KDM4A
Ref.: DOCKING AND LINKING OF FRAGMENTS TO DISCOVER JUMONJ DEMETHYLASE INHIBITORS. J.MED.CHEM. V. 59 1580 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DMS A:1370;
B:1364;
Invalid;
Invalid;
none;
none;
submit data
78.133 C2 H6 O S CS(=O...
EDO A:1365;
A:1361;
B:1358;
B:1359;
A:1362;
A:1363;
A:1357;
B:1360;
A:1367;
A:1360;
B:1361;
A:1364;
A:1366;
A:1359;
B:1357;
A:1358;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
ZN B:1362;
A:1368;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
MN B:1363;
A:1369;
Part of Protein;
Part of Protein;
none;
none;
submit data
54.938 Mn [Mn+2...
SO4 A:1355;
B:1355;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
7WH B:1356;
A:1356;
Valid;
Valid;
none;
none;
submit data
302.282 C15 H14 N2 O5 COCC(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6H4R 2.14 Å EC: 1.14.11.- CRYSTAL STRUCTURE OF HUMAN KDM4A IN COMPLEX WITH COMPOUND 17 HOMO SAPIENS HISTONE DEMETHYLASE INHIBITOR TRANSCRIPTION OXIDOREDUCTAS
Ref.: C8-SUBSTITUTED PYRIDO[3,4-D]PYRIMIDIN-4(3H)-ONES: S TOWARDS THE IDENTIFICATION OF POTENT, CELL PENETRAN C DOMAIN CONTAINING HISTONE LYSINE DEMETHYLASE 4 SU (KDM4) INHIBITORS, COMPOUND PROFILING IN CELL-BASED ENGAGEMENT ASSAYS. EUR.J.MED.CHEM.
Members (38)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 43 families.
1 6H4T Ki = 0.004 uM FOW C25 H26 N6 O c1ccc2c(c1....
2 5A7P - 6Z1 C17 H13 N3 O5 Cc1cc(no1)....
3 5ANQ ic50 = 3.98 uM 5YQ C16 H13 N5 O2 c1cc(cnc1)....
4 6H4Q ic50 = 2.06 uM FO2 C16 H18 N6 O CN1CCC(CC1....
5 2OQ6 - OGA C4 H5 N O5 C(C(=O)O)N....
6 2OX0 - OGA C4 H5 N O5 C(C(=O)O)N....
7 6H4S Ki = 0.002 uM FQE C27 H33 N7 O CN(C)CCc1c....
8 5F3G ic50 = 0.126 uM 5UL C24 H25 Cl N6 O c1cc(ccc1C....
9 5A7Q - KCH C12 H10 N2 O3 c1cc(c(cc1....
10 6H4P Ki = 0.003 uM FQ5 C23 H23 Cl N6 O c1cc(cc(c1....
11 5A7N - VAO C13 H8 N2 O3 c1cc(c(cc1....
12 5F3E ic50 = 0.138 uM 5UO C23 H23 Cl N6 O c1cc(ccc1C....
13 2GP5 - AKG C5 H6 O5 C(CC(=O)O)....
14 6H4V ic50 = 0.613 uM FQN C20 H24 N6 O c1cnc(c2c1....
15 6H4O ic50 = 0.128 uM FQH C24 H23 F3 N6 O c1cc(cc(c1....
16 2OT7 - OGA C4 H5 N O5 C(C(=O)O)N....
17 6H4U - FO2 C16 H18 N6 O CN1CCC(CC1....
18 5A7S - S2X C14 H12 N2 O4 CC(=O)Nc1c....
19 6H4R Ki = 0.004 nM FQB C27 H33 N7 O CN(C)CCc1c....
20 4AI9 - DZA C6 H12 N2 O3 CN(C)NC(=O....
21 3U4S Ki = 114 nM ALA ARG M3L SER CYS GLY GLY LYS 08P n/a n/a
22 3PDQ ic50 = 0.18 uM KC6 C14 H14 N4 O3 c1cnc(cc1C....
23 5F3C ic50 = 0.9 uM 5U8 C20 H19 F N6 O CN(CCc1cnn....
24 5F32 ic50 = 11.5 uM 5V7 C10 H7 N5 O S c1cnc(c2c1....
25 4URA ic50 = 0.00000316 uM LEL C8 H6 N4 O2 c1cnc(cc1C....
26 5F2S ic50 = 0.2 uM 5TZ C9 H7 N3 O2 S c1cnc(cc1C....
27 2YBK ic50 = 24 uM 2HG C5 H8 O5 C(CC(=O)O)....
28 5TVR - AKG C5 H6 O5 C(CC(=O)O)....
29 5A80 - 9CJ C21 H18 N2 O5 COc1cccc(c....
30 6H4Y ic50 = 0.077 uM FO8 C29 H35 N7 O2 c1cc(ccc1C....
31 5A7O - 7WH C15 H14 N2 O5 COCC(=O)Nc....
32 6CG1 - QC1 C13 H11 F N2 O2 c1cc(ccc1C....
33 5F37 ic50 = 1.7 uM N5J C7 H5 N3 O c1cncc2c1C....
34 6H4X ic50 = 0.131 uM FNQ C28 H27 N7 O c1cc(cnc1)....
35 6CG2 - QC2 C15 H11 N3 O3 c1cc(cc(c1....
36 2OQ7 - OGA C4 H5 N O5 C(C(=O)O)N....
37 5FPV - MMK C15 H22 N4 O3 CCN(/C=C/N....
38 5F3I ic50 = 0.08 uM 5UJ C23 H22 Cl2 N6 O c1cnc(c2c1....
70% Homology Family (49)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 6H4T Ki = 0.004 uM FOW C25 H26 N6 O c1ccc2c(c1....
2 5A7P - 6Z1 C17 H13 N3 O5 Cc1cc(no1)....
3 5ANQ ic50 = 3.98 uM 5YQ C16 H13 N5 O2 c1cc(cnc1)....
4 6H4Q ic50 = 2.06 uM FO2 C16 H18 N6 O CN1CCC(CC1....
5 2OQ6 - OGA C4 H5 N O5 C(C(=O)O)N....
6 2OX0 - OGA C4 H5 N O5 C(C(=O)O)N....
7 6H4S Ki = 0.002 uM FQE C27 H33 N7 O CN(C)CCc1c....
8 5F3G ic50 = 0.126 uM 5UL C24 H25 Cl N6 O c1cc(ccc1C....
9 5A7Q - KCH C12 H10 N2 O3 c1cc(c(cc1....
10 6H4P Ki = 0.003 uM FQ5 C23 H23 Cl N6 O c1cc(cc(c1....
11 5A7N - VAO C13 H8 N2 O3 c1cc(c(cc1....
12 5F3E ic50 = 0.138 uM 5UO C23 H23 Cl N6 O c1cc(ccc1C....
13 2GP5 - AKG C5 H6 O5 C(CC(=O)O)....
14 6H4V ic50 = 0.613 uM FQN C20 H24 N6 O c1cnc(c2c1....
15 6H4O ic50 = 0.128 uM FQH C24 H23 F3 N6 O c1cc(cc(c1....
16 2OT7 - OGA C4 H5 N O5 C(C(=O)O)N....
17 6H4U - FO2 C16 H18 N6 O CN1CCC(CC1....
18 5A7S - S2X C14 H12 N2 O4 CC(=O)Nc1c....
19 6H4R Ki = 0.004 nM FQB C27 H33 N7 O CN(C)CCc1c....
20 4AI9 - DZA C6 H12 N2 O3 CN(C)NC(=O....
21 3U4S Ki = 114 nM ALA ARG M3L SER CYS GLY GLY LYS 08P n/a n/a
22 3PDQ ic50 = 0.18 uM KC6 C14 H14 N4 O3 c1cnc(cc1C....
23 5F3C ic50 = 0.9 uM 5U8 C20 H19 F N6 O CN(CCc1cnn....
24 5F32 ic50 = 11.5 uM 5V7 C10 H7 N5 O S c1cnc(c2c1....
25 4URA ic50 = 0.00000316 uM LEL C8 H6 N4 O2 c1cnc(cc1C....
26 5F2S ic50 = 0.2 uM 5TZ C9 H7 N3 O2 S c1cnc(cc1C....
27 2YBK ic50 = 24 uM 2HG C5 H8 O5 C(CC(=O)O)....
28 5TVR - AKG C5 H6 O5 C(CC(=O)O)....
29 5A80 - 9CJ C21 H18 N2 O5 COc1cccc(c....
30 6H4Y ic50 = 0.077 uM FO8 C29 H35 N7 O2 c1cc(ccc1C....
31 5A7O - 7WH C15 H14 N2 O5 COCC(=O)Nc....
32 6CG1 - QC1 C13 H11 F N2 O2 c1cc(ccc1C....
33 5F37 ic50 = 1.7 uM N5J C7 H5 N3 O c1cncc2c1C....
34 6H4X ic50 = 0.131 uM FNQ C28 H27 N7 O c1cc(cnc1)....
35 6CG2 - QC2 C15 H11 N3 O3 c1cc(cc(c1....
36 2OQ7 - OGA C4 H5 N O5 C(C(=O)O)N....
37 5FPV - MMK C15 H22 N4 O3 CCN(/C=C/N....
38 5F3I ic50 = 0.08 uM 5UJ C23 H22 Cl2 N6 O c1cnc(c2c1....
39 5KR7 ic50 = 2.88 uM 6X9 C11 H12 N4 O CCC1=C(Nc2....
40 4XDO ic50 = 84 uM OGA C4 H5 N O5 C(C(=O)O)N....
41 5FP4 ic50 = 0.251 uM YC8 C16 H16 N2 O3 c1ccc(cc1)....
42 5FP7 - YC8 C16 H16 N2 O3 c1ccc(cc1)....
43 5F5C - 5V3 C15 H14 N4 O c1ccc(cc1)....
44 5FP8 - AUY C12 H12 N2 O2 S Cc1cc(sc1)....
45 5F5A - 5V0 C12 H12 N2 O3 c1cc(oc1)C....
46 5FP9 ic50 = 1.585 uM 4SV C6 H6 N2 O2 c1cncc(c1C....
47 5FPA - N5J C7 H5 N3 O c1cncc2c1C....
48 5FPB - HA6 C10 H7 N5 O2 c1cncc2c1C....
49 4HON - THR ALA ARG M3L SER THR GLY GLY LYS ALA n/a n/a
50% Homology Family (50)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 28 families.
1 6H4T Ki = 0.004 uM FOW C25 H26 N6 O c1ccc2c(c1....
2 5A7P - 6Z1 C17 H13 N3 O5 Cc1cc(no1)....
3 5ANQ ic50 = 3.98 uM 5YQ C16 H13 N5 O2 c1cc(cnc1)....
4 6H4Q ic50 = 2.06 uM FO2 C16 H18 N6 O CN1CCC(CC1....
5 2OQ6 - OGA C4 H5 N O5 C(C(=O)O)N....
6 2OX0 - OGA C4 H5 N O5 C(C(=O)O)N....
7 6H4S Ki = 0.002 uM FQE C27 H33 N7 O CN(C)CCc1c....
8 5F3G ic50 = 0.126 uM 5UL C24 H25 Cl N6 O c1cc(ccc1C....
9 5A7Q - KCH C12 H10 N2 O3 c1cc(c(cc1....
10 6H4P Ki = 0.003 uM FQ5 C23 H23 Cl N6 O c1cc(cc(c1....
11 5A7N - VAO C13 H8 N2 O3 c1cc(c(cc1....
12 5F3E ic50 = 0.138 uM 5UO C23 H23 Cl N6 O c1cc(ccc1C....
13 2GP5 - AKG C5 H6 O5 C(CC(=O)O)....
14 6H4V ic50 = 0.613 uM FQN C20 H24 N6 O c1cnc(c2c1....
15 6H4O ic50 = 0.128 uM FQH C24 H23 F3 N6 O c1cc(cc(c1....
16 2OT7 - OGA C4 H5 N O5 C(C(=O)O)N....
17 6H4U - FO2 C16 H18 N6 O CN1CCC(CC1....
18 5A7S - S2X C14 H12 N2 O4 CC(=O)Nc1c....
19 6H4R Ki = 0.004 nM FQB C27 H33 N7 O CN(C)CCc1c....
20 4AI9 - DZA C6 H12 N2 O3 CN(C)NC(=O....
21 3U4S Ki = 114 nM ALA ARG M3L SER CYS GLY GLY LYS 08P n/a n/a
22 3PDQ ic50 = 0.18 uM KC6 C14 H14 N4 O3 c1cnc(cc1C....
23 5F3C ic50 = 0.9 uM 5U8 C20 H19 F N6 O CN(CCc1cnn....
24 5F32 ic50 = 11.5 uM 5V7 C10 H7 N5 O S c1cnc(c2c1....
25 4URA ic50 = 0.00000316 uM LEL C8 H6 N4 O2 c1cnc(cc1C....
26 5F2S ic50 = 0.2 uM 5TZ C9 H7 N3 O2 S c1cnc(cc1C....
27 2YBK ic50 = 24 uM 2HG C5 H8 O5 C(CC(=O)O)....
28 5TVR - AKG C5 H6 O5 C(CC(=O)O)....
29 5A80 - 9CJ C21 H18 N2 O5 COc1cccc(c....
30 6H4Y ic50 = 0.077 uM FO8 C29 H35 N7 O2 c1cc(ccc1C....
31 5A7O - 7WH C15 H14 N2 O5 COCC(=O)Nc....
32 6CG1 - QC1 C13 H11 F N2 O2 c1cc(ccc1C....
33 5F37 ic50 = 1.7 uM N5J C7 H5 N3 O c1cncc2c1C....
34 6H4X ic50 = 0.131 uM FNQ C28 H27 N7 O c1cc(cnc1)....
35 6CG2 - QC2 C15 H11 N3 O3 c1cc(cc(c1....
36 2OQ7 - OGA C4 H5 N O5 C(C(=O)O)N....
37 5FPV - MMK C15 H22 N4 O3 CCN(/C=C/N....
38 5F3I ic50 = 0.08 uM 5UJ C23 H22 Cl2 N6 O c1cnc(c2c1....
39 3OPT - AKG C5 H6 O5 C(CC(=O)O)....
40 5KR7 ic50 = 2.88 uM 6X9 C11 H12 N4 O CCC1=C(Nc2....
41 4XDO ic50 = 84 uM OGA C4 H5 N O5 C(C(=O)O)N....
42 5FP4 ic50 = 0.251 uM YC8 C16 H16 N2 O3 c1ccc(cc1)....
43 5FP7 - YC8 C16 H16 N2 O3 c1ccc(cc1)....
44 5F5C - 5V3 C15 H14 N4 O c1ccc(cc1)....
45 5FP8 - AUY C12 H12 N2 O2 S Cc1cc(sc1)....
46 5F5A - 5V0 C12 H12 N2 O3 c1cc(oc1)C....
47 5FP9 ic50 = 1.585 uM 4SV C6 H6 N2 O2 c1cncc(c1C....
48 5FPA - N5J C7 H5 N3 O c1cncc2c1C....
49 5FPB - HA6 C10 H7 N5 O2 c1cncc2c1C....
50 4HON - THR ALA ARG M3L SER THR GLY GLY LYS ALA n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 7WH; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 7WH 1 1
2 S2X 0.69697 0.75
3 6Z1 0.631579 0.645161
4 9CJ 0.626506 0.865385
5 35M 0.608108 0.730769
6 KCH 0.492958 0.622642
Similar Ligands (3D)
Ligand no: 1; Ligand: 7WH; Similar ligands found: 20
No: Ligand Similarity coefficient
1 E8B 0.9203
2 KC6 0.9096
3 T7O 0.9086
4 QIU 0.9077
5 M8Q 0.9076
6 2QO 0.8994
7 C9Q 0.8986
8 J57 0.8974
9 EFX 0.8856
10 WUL 0.8779
11 VAO 0.8736
12 A28 0.8703
13 35X 0.8685
14 43G 0.8672
15 61Y 0.8636
16 MLO 0.8608
17 76Z 0.8606
18 A07 0.8605
19 581 0.8584
20 GKW 0.8528
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6H4R; Ligand: FQB; 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: 6h4r.bio4) has 26 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6H4R; Ligand: FQB; Similar sites found with APoc: 2
This union binding pocket(no: 2) in the query (biounit: 6h4r.bio2) has 60 residues
No: Leader PDB Ligand Sequence Similarity
1 4IGQ OGA 41.3889
2 6IP0 AKG 43.3333
Pocket No.: 3; Query (leader) PDB : 6H4R; Ligand: FQB; Similar sites found with APoc: 1
This union binding pocket(no: 3) in the query (biounit: 6h4r.bio3) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 6IP0 AKG 43.3333
Pocket No.: 4; Query (leader) PDB : 6H4R; Ligand: FQB; Similar sites found with APoc: 3
This union binding pocket(no: 4) in the query (biounit: 6h4r.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
1 4IGQ OGA 41.3889
2 4IGQ THR M3L GLN 41.3889
3 6IP0 AKG 43.3333
APoc FAQ
Feedback