Receptor
PDB id Resolution Class Description Source Keywords
2YBP 2.02 Å EC: 1.14.11.27 JMJD2A COMPLEXED WITH R-2-HYDROXYGLUTARATE AND HISTONE H3K36 PEPTIDE (30-41) HOMO SAPIENS OXIDOREDUCTASE-PEPTIDE COMPLEX NON-HEME IRON DIOXYGENASE STRANDED BETA HELIX DSBH FACIAL TRIAD METAL BINDING PROTEPIGENETIC AND TRANSCRIPTION REGULATION CHROMATIN REGULATOHYDROXYLATION
Ref.: THE ONCOMETABOLITE 2-HYDROXYGLUTARATE INHIBITS HIST LYSINE DEMETHYLASES. EMBO REP. V. 12 463 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
2HG A:1359;
B:1358;
Valid;
Valid;
none;
none;
submit data
148.114 C5 H8 O5 C(CC(...
GOL A:1358;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NI A:1356;
B:1356;
Part of Protein;
Part of Protein;
none;
none;
submit data
58.693 Ni [Ni+2...
ZN A:1357;
B:1357;
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
2YBP 2.02 Å EC: 1.14.11.27 JMJD2A COMPLEXED WITH R-2-HYDROXYGLUTARATE AND HISTONE H3K36 PEPTIDE (30-41) HOMO SAPIENS OXIDOREDUCTASE-PEPTIDE COMPLEX NON-HEME IRON DIOXYGENASE STRANDED BETA HELIX DSBH FACIAL TRIAD METAL BINDING PROTEPIGENETIC AND TRANSCRIPTION REGULATION CHROMATIN REGULATOHYDROXYLATION
Ref.: THE ONCOMETABOLITE 2-HYDROXYGLUTARATE INHIBITS HIST LYSINE DEMETHYLASES. EMBO REP. V. 12 463 2011
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 13 families.
1 2YBP - 2HG C5 H8 O5 C(CC(=O)O)....
2 2YBS - S2G C5 H8 O5 C(CC(=O)O)....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 2YBP - 2HG C5 H8 O5 C(CC(=O)O)....
2 2YBS - S2G C5 H8 O5 C(CC(=O)O)....
3 2OS2 - OGA C4 H5 N O5 C(C(=O)O)N....
4 2Q8E - OGA C4 H5 N O5 C(C(=O)O)N....
5 2Q8D - SIN C4 H6 O4 C(CC(=O)O)....
6 2PXJ - OGA C4 H5 N O5 C(C(=O)O)N....
7 2P5B - OGA C4 H5 N O5 C(C(=O)O)N....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 2YBP - 2HG C5 H8 O5 C(CC(=O)O)....
2 2YBS - S2G C5 H8 O5 C(CC(=O)O)....
3 2OS2 - OGA C4 H5 N O5 C(C(=O)O)N....
4 2Q8E - OGA C4 H5 N O5 C(C(=O)O)N....
5 2Q8D - SIN C4 H6 O4 C(CC(=O)O)....
6 2PXJ - OGA C4 H5 N O5 C(C(=O)O)N....
7 2P5B - OGA C4 H5 N O5 C(C(=O)O)N....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 2HG; Similar ligands found: 13
No: Ligand ECFP6 Tc MDL keys Tc
1 S2G 1 1
2 2HG 1 1
3 DMR 0.461538 0.809524
4 LMR 0.461538 0.809524
5 MLT 0.461538 0.809524
6 2RH 0.444444 0.652174
7 DGY 0.44 0.666667
8 9ON 0.433333 0.727273
9 DGL 0.433333 0.653846
10 GLU 0.433333 0.653846
11 GGL 0.433333 0.653846
12 HOC 0.411765 0.62963
13 HCT 0.40625 0.8
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2YBP; Ligand: 2HG; Similar sites found with APoc: 5
This union binding pocket(no: 1) in the query (biounit: 2ybp.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 6FUL E7Z 5.77428
2 5FP3 3JI 5.77428
3 4IGQ THR M3L GLN 41.3889
4 5A3T MMK 42.7822
5 5IVE 6E8 47.8788
Pocket No.: 2; Query (leader) PDB : 2YBP; Ligand: 2HG; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2ybp.bio2) has 13 residues
No: Leader PDB Ligand Sequence Similarity
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