Receptor
PDB id Resolution Class Description Source Keywords
3T4V 1.73 Å EC: 1.14.11.- CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH FE(III) AND N-OXAL NAPTHALENEMETHYL)-L-CYSTEINE ESCHERICHIA COLI DOUBLE-STRANDED BETA-HELIX NUCLEIC ACID DEMETHYLASE OXIDOROXIDOREDUCTASE INHIBITOR COMPLEX
Ref.: DYNAMIC COMBINATORIAL MASS SPECTROMETRY LEADS TO IN OF A 2-OXOGLUTARATE-DEPENDENT NUCLEIC ACID DEMETHYL J.MED.CHEM. V. 55 2173 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FE A:300;
 Part of Protein;
 none;
 submit data
55.845 Fe [Fe+3...
GOL A:2000;
 Invalid;
 none;
 submit data
92.094 C3 H8 O3 C(C(C...
MD3 A:401;
 Valid;
 none;
 ic50 = 0.5 uM
333.359 C16 H15 N O5 S c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4RFR 1.5 Å EC: 1.14.11.- COMPLEX STRUCTURE OF ALKB/RHEIN ESCHERICHIA COLI PROTEIN-INHIBITOR COMPLEX DEMETHYLATION ALKB FAMILY JELLYFOLD DEMETHYLASE NUCLEIC ACID BINDING NUCLEUS OXIDOREDUINHIBITOR COMPLEX
Ref.: RHEIN INHIBITS ALKB REPAIR ENZYMES AND SENSITIZES C METHYLATED DNA DAMAGE. J.BIOL.CHEM. V. 291 11083 2016
Members (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 43 families.
1 3T4V ic50 = 0.5 uM MD3 C16 H15 N O5 S c1ccc2cc(c....
2 3T4H ic50 = 5.2 uM MD5 C12 H12 N2 O7 S c1cc(cc(c1....
3 2FD8 - DT MA7 DT n/a n/a
4 6YPV - AKG C5 H6 O5 C(CC(=O)O)....
5 3T3Y ic50 = 3.4 uM MD6 C8 H8 N2 O4 c1cc(c(nc1....
6 3I3Q - AKG C5 H6 O5 C(CC(=O)O)....
7 2FDF - DT MA7 DT n/a n/a
8 2FDH - DT MA7 DT n/a n/a
9 3I2O - DT MA7 DT n/a n/a
10 2FDK - DT MA7 DT n/a n/a
11 2FDG - SIN C4 H6 O4 C(CC(=O)O)....
12 3I49 - DT ME6 DT n/a n/a
13 2FDJ - SIN C4 H6 O4 C(CC(=O)O)....
14 3I3M - DT ME6 DT n/a n/a
15 6Y0Q - AKG C5 H6 O5 C(CC(=O)O)....
16 2FDI - DT MA7 DT n/a n/a
17 4RFR Kd = 0.29 uM RHN C15 H8 O6 c1cc2c(c(c....
70% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 3T4V ic50 = 0.5 uM MD3 C16 H15 N O5 S c1ccc2cc(c....
2 3T4H ic50 = 5.2 uM MD5 C12 H12 N2 O7 S c1cc(cc(c1....
3 2FD8 - DT MA7 DT n/a n/a
4 6YPV - AKG C5 H6 O5 C(CC(=O)O)....
5 3T3Y ic50 = 3.4 uM MD6 C8 H8 N2 O4 c1cc(c(nc1....
6 3I3Q - AKG C5 H6 O5 C(CC(=O)O)....
7 2FDF - DT MA7 DT n/a n/a
8 2FDH - DT MA7 DT n/a n/a
9 3I2O - DT MA7 DT n/a n/a
10 2FDK - DT MA7 DT n/a n/a
11 2FDG - SIN C4 H6 O4 C(CC(=O)O)....
12 3I49 - DT ME6 DT n/a n/a
13 2FDJ - SIN C4 H6 O4 C(CC(=O)O)....
14 3I3M - DT ME6 DT n/a n/a
15 6Y0Q - AKG C5 H6 O5 C(CC(=O)O)....
16 2FDI - DT MA7 DT n/a n/a
17 4RFR Kd = 0.29 uM RHN C15 H8 O6 c1cc2c(c(c....
50% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 28 families.
1 3T4V ic50 = 0.5 uM MD3 C16 H15 N O5 S c1ccc2cc(c....
2 3T4H ic50 = 5.2 uM MD5 C12 H12 N2 O7 S c1cc(cc(c1....
3 2FD8 - DT MA7 DT n/a n/a
4 6YPV - AKG C5 H6 O5 C(CC(=O)O)....
5 3T3Y ic50 = 3.4 uM MD6 C8 H8 N2 O4 c1cc(c(nc1....
6 3I3Q - AKG C5 H6 O5 C(CC(=O)O)....
7 2FDF - DT MA7 DT n/a n/a
8 2FDH - DT MA7 DT n/a n/a
9 3I2O - DT MA7 DT n/a n/a
10 2FDK - DT MA7 DT n/a n/a
11 2FDG - SIN C4 H6 O4 C(CC(=O)O)....
12 3I49 - DT ME6 DT n/a n/a
13 2FDJ - SIN C4 H6 O4 C(CC(=O)O)....
14 3I3M - DT ME6 DT n/a n/a
15 6Y0Q - AKG C5 H6 O5 C(CC(=O)O)....
16 2FDI - DT MA7 DT n/a n/a
17 4RFR Kd = 0.29 uM RHN C15 H8 O6 c1cc2c(c(c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: MD3; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 MD3 1 1
2 MD5 0.550725 0.641509
3 NAL 0.41791 0.657895
Similar Ligands (3D)
Ligand no: 1; Ligand: MD3; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4RFR; Ligand: RHN; 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: 4rfr.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
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