Receptor
PDB id Resolution Class Description Source Keywords
5FP3 2.05 Å EC: 1.14.11.- CELL PENETRANT INHIBITORS OF THE JMJD2 (KDM4) AND JARID1 (KD FAMILIES OF HISTONE LYSINE DEMETHYLASES HOMO SAPIENS OXIDOREDUCTASE INHIBITOR JMJD3 KDM6B JUMONJI
Ref.: CELL PENETRANT INHIBITORS OF THE KDM4 AND KDM5 FAMI HISTONE LYSINE DEMETHYLASES. 1. 3-AMINO-4-PYRIDINE CARBOXYLATE DERIVATIVES. J.MED.CHEM. V. 59 1357 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BCN B:2640;
A:2640;
B:2641;
A:2641;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
163.172 C6 H13 N O4 C(CO)...
MG B:2639;
A:2642;
B:2642;
A:2639;
 Part of Protein;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
24.305 Mg [Mg+2...
CO A:3000;
B:3000;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
58.933 Co [Co+2...
ZN A:2000;
B:2000;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
65.409 Zn [Zn+2...
YC8 B:1;
A:1;
 Valid;
Valid;
 Atoms found LESS than expected: % Diff = 0.045;
Atoms found LESS than expected: % Diff = 0.045;
 ic50 = 1.259 uM
284.31 C16 H16 N2 O3 c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5FP3 2.05 Å EC: 1.14.11.- CELL PENETRANT INHIBITORS OF THE JMJD2 (KDM4) AND JARID1 (KD FAMILIES OF HISTONE LYSINE DEMETHYLASES HOMO SAPIENS OXIDOREDUCTASE INHIBITOR JMJD3 KDM6B JUMONJI
Ref.: CELL PENETRANT INHIBITORS OF THE KDM4 AND KDM5 FAMI HISTONE LYSINE DEMETHYLASES. 1. 3-AMINO-4-PYRIDINE CARBOXYLATE DERIVATIVES. J.MED.CHEM. V. 59 1357 2016
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 43 families.
1 4ASK - K0I C22 H23 N5 O2 c1ccc2c(c1....
2 5FP3 ic50 = 1.259 uM YC8 C16 H16 N2 O3 c1ccc(cc1)....
3 4EYU - OGA C4 H5 N O5 C(C(=O)O)N....
4 2XUE - AKG C5 H6 O5 C(CC(=O)O)....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 4ASK - K0I C22 H23 N5 O2 c1ccc2c(c1....
2 5FP3 ic50 = 1.259 uM YC8 C16 H16 N2 O3 c1ccc(cc1)....
3 4EYU - OGA C4 H5 N O5 C(C(=O)O)N....
4 2XUE - AKG C5 H6 O5 C(CC(=O)O)....
5 6FUK - 8XQ C10 H7 N O3 c1cc2c(ccc....
6 3AVS - OGA C4 H5 N O5 C(C(=O)O)N....
7 6G8F - K0I C22 H23 N5 O2 c1ccc2c(c1....
8 6FUL ic50 = 12 uM PG0 C5 H12 O3 COCCOCCO
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 28 families.
1 4ASK - K0I C22 H23 N5 O2 c1ccc2c(c1....
2 5FP3 ic50 = 1.259 uM YC8 C16 H16 N2 O3 c1ccc(cc1)....
3 4EYU - OGA C4 H5 N O5 C(C(=O)O)N....
4 2XUE - AKG C5 H6 O5 C(CC(=O)O)....
5 6FUK - 8XQ C10 H7 N O3 c1cc2c(ccc....
6 3AVS - OGA C4 H5 N O5 C(C(=O)O)N....
7 6G8F - K0I C22 H23 N5 O2 c1ccc2c(c1....
8 6FUL ic50 = 12 uM PG0 C5 H12 O3 COCCOCCO
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: YC8; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 YC8 1 1
2 6EO 0.507463 0.829787
Similar Ligands (3D)
Ligand no: 1; Ligand: YC8; Similar ligands found: 21
No: Ligand Similarity coefficient
1 0KG 0.9071
2 OA5 0.9049
3 9AW 0.8875
4 FZ8 0.8865
5 GYZ 0.8854
6 30Z 0.8826
7 1VG 0.8816
8 SAQ 0.8808
9 BBO 0.8770
10 5V3 0.8762
11 97Z 0.8700
12 PGI 0.8676
13 SNP 0.8660
14 9B2 0.8654
15 7GK 0.8635
16 Y09 0.8633
17 IDE 0.8619
18 Y03 0.8614
19 EXP 0.8592
20 2BE 0.8584
21 RC4 0.8532
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5FP3; Ligand: YC8; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 5fp3.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 6IP0 AKG 2.85714
Pocket No.: 2; Query (leader) PDB : 5FP3; Ligand: YC8; Similar sites found with APoc: 1
This union binding pocket(no: 2) in the query (biounit: 5fp3.bio2) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 6IP0 AKG 2.85714
APoc FAQ
Feedback