Receptor
PDB id Resolution Class Description Source Keywords
2Q8C 2.05 Å EC: 1.14.11.- CRYSTAL STRUCTURE OF JMJD2A IN TERNARY COMPLEX WITH AN HISTO PEPTIDE AND 2-OXOGLUTARATE HOMO SAPIENS HISTONE DEMETHYLASE HYDROXYLASE JUMONJI OXIDOREDUCTASE
Ref.: SPECIFICITY AND MECHANISM OF JMJD2A, A TRIMETHYLLYSINE-SPECIFIC HISTONE DEMETHYLASE. NAT.STRUCT.MOL.BIOL. V. 14 689 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AKG A:503;
B:504;
Valid;
Valid;
none;
none;
submit data
146.098 C5 H6 O5 C(CC(...
NI A:501;
B:502;
Part of Protein;
Part of Protein;
none;
none;
submit data
58.693 Ni [Ni+2...
ZN A:505;
B:506;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
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 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....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 19 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 17 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
Ligand no: 1; Ligand: AKG; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 AKG 1 1
2 SIN 0.526316 0.833333
3 OOG 0.5 0.947368
4 69O 0.458333 0.714286
5 2IT 0.423077 0.615385
6 SHF 0.416667 0.666667
7 3PY 0.409091 0.652174
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: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 6h8p.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
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