Receptor
PDB id Resolution Class Description Source Keywords
5a7w 2.27 Å EC: 1.14.11.- CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH COMPOUND 3 HOMO SAPIENS OXIDOREDUCTASE 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
35M A:1355;
B:1355;
 Valid;
Valid;
 none;
none;
 submit data
350.325 C19 H14 N2 O5 c1cc(...
EDO B:1360;
B:1358;
B:1359;
A:1359;
A:1358;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
MN B:1356;
A:1356;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
54.938 Mn [Mn+2...
SO4 A:1354;
B:1354;
 Invalid;
Invalid;
 none;
none;
 submit data
96.063 O4 S [O-]S...
ZN A:1357;
B:1357;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
65.409 Zn [Zn+2...
DMS B:1361;
A:1360;
 Invalid;
Invalid;
 none;
none;
 submit data
78.133 C2 H6 O S CS(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6H8P 1.98 Å EC: 1.14.11.- JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND HISTONE H1.4(18 PEPTIDE (15-MER) HOMO SAPIENS JMJD2A KDM4A OXIDOREDUCTASE NON-HEME IRON 2-OXOGLUTARATDIOXYGENASE OXYGENASE DOUBLE-STRANDED BETA HELIX DSBH FTRIAD DEMETHYLASE HISTONE JMJC DOMAIN METAL BINDING PROEPIGENETIC AND TRANSCRIPTION REGULATION CHROMATIN REGULATOHYDROXYLATION
Ref.: MECHANISTIC AND STRUCTURAL STUDIES OF KDM-CATALYSED DEMETHYLATION OF HISTONE 1 ISOTYPE 4 AT LYSINE 26. FEBS LETT. V. 592 3264 2018
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 43 families.
1 2Q8C - AKG C5 H6 O5 C(CC(=O)O)....
2 5A7W - 35M C19 H14 N2 O5 c1cc(ccc1C....
3 6H8P - OGA C4 H5 N O5 C(C(=O)O)N....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 2Q8C - AKG C5 H6 O5 C(CC(=O)O)....
2 5A7W - 35M C19 H14 N2 O5 c1cc(ccc1C....
3 6H8P - OGA C4 H5 N O5 C(C(=O)O)N....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 28 families.
1 2Q8C - AKG C5 H6 O5 C(CC(=O)O)....
2 5A7W - 35M C19 H14 N2 O5 c1cc(ccc1C....
3 6H8P - OGA C4 H5 N O5 C(C(=O)O)N....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 35M; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 35M 1 1
2 S2X 0.681818 0.974359
3 6Z1 0.64 0.76
4 7WH 0.608108 0.730769
5 9CJ 0.505618 0.844444
6 KCH 0.5 0.846154
7 VAO 0.486111 0.725
Similar Ligands (3D)
Ligand no: 1; Ligand: 35M; Similar ligands found: 4
No: Ligand Similarity coefficient
1 QSJ 0.8747
2 WI2 0.8589
3 DN6 0.8576
4 G9L 0.8549
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6H8P; Ligand: OGA; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 6h8p.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 6IP0 AKG 40.9449
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