Receptor
PDB id Resolution Class Description Source Keywords
3I3M 1.5 Å EC: 1.14.11.- CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH MN(II), 2-OXOGLUTA METHYLATED TRINUCLEOTIDE T-MEC-T ESCHERICHIA COLI BETA JELLYROLL PROTEIN-DNA COMPLEX DIOXYGENASE DNA DAMAGEREPAIR IRON METAL-BINDING OXIDOREDUCTASE OXIDOREDUCTASECOMPLEX
Ref.: ENZYMOLOGICAL AND STRUCTURAL STUDIES OF THE MECHANI PROMISCUOUS SUBSTRATE RECOGNITION BY THE OXIDATIVE REPAIR ENZYME ALKB. PROC.NATL.ACAD.SCI.USA V. 106 14315 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AKG A:400;
Valid;
none;
submit data
146.098 C5 H6 O5 C(CC(...
DT ME6 DT B:501;
Valid;
none;
submit data
925.584 n/a P(=O)...
MN A:300;
Part of Protein;
none;
submit data
54.938 Mn [Mn+2...
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 (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 33 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 3T3Y ic50 = 3.4 uM MD6 C8 H8 N2 O4 c1cc(c(nc1....
5 3I3Q - AKG C5 H6 O5 C(CC(=O)O)....
6 2FDF - DT MA7 DT n/a n/a
7 2FDH - DT MA7 DT n/a n/a
8 3I2O - DT MA7 DT n/a n/a
9 2FDK - DT MA7 DT n/a n/a
10 2FDG - SIN C4 H6 O4 C(CC(=O)O)....
11 3I49 - DT ME6 DT n/a n/a
12 2FDJ - SIN C4 H6 O4 C(CC(=O)O)....
13 3I3M - DT ME6 DT n/a n/a
14 2FDI - DT MA7 DT n/a n/a
15 4RFR Kd = 0.29 uM RHN C15 H8 O6 c1cc2c(c(c....
70% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 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 3T3Y ic50 = 3.4 uM MD6 C8 H8 N2 O4 c1cc(c(nc1....
5 3I3Q - AKG C5 H6 O5 C(CC(=O)O)....
6 2FDF - DT MA7 DT n/a n/a
7 2FDH - DT MA7 DT n/a n/a
8 3I2O - DT MA7 DT n/a n/a
9 2FDK - DT MA7 DT n/a n/a
10 2FDG - SIN C4 H6 O4 C(CC(=O)O)....
11 3I49 - DT ME6 DT n/a n/a
12 2FDJ - SIN C4 H6 O4 C(CC(=O)O)....
13 3I3M - DT ME6 DT n/a n/a
14 2FDI - DT MA7 DT n/a n/a
15 4RFR Kd = 0.29 uM RHN C15 H8 O6 c1cc2c(c(c....
50% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 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 3T3Y ic50 = 3.4 uM MD6 C8 H8 N2 O4 c1cc(c(nc1....
5 3I3Q - AKG C5 H6 O5 C(CC(=O)O)....
6 2FDF - DT MA7 DT n/a n/a
7 2FDH - DT MA7 DT n/a n/a
8 3I2O - DT MA7 DT n/a n/a
9 2FDK - DT MA7 DT n/a n/a
10 2FDG - SIN C4 H6 O4 C(CC(=O)O)....
11 3I49 - DT ME6 DT n/a n/a
12 2FDJ - SIN C4 H6 O4 C(CC(=O)O)....
13 3I3M - DT ME6 DT n/a n/a
14 2FDI - DT MA7 DT n/a n/a
15 4RFR Kd = 0.29 uM RHN C15 H8 O6 c1cc2c(c(c....
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
Ligand no: 2; Ligand: DT ME6 DT; Similar ligands found: 48
No: Ligand ECFP6 Tc MDL keys Tc
1 DT ME6 DT 1 1
2 DT DT DT 0.791667 0.945946
3 DT DT PST 0.721154 0.897436
4 DT DT DT DT DT 0.685714 0.921053
5 DT MA7 DT 0.606061 0.91358
6 DC DC DT DG 0.582609 0.92
7 TTP MG 0.53271 0.918919
8 DU DU DU DU BRU DU DU 0.520325 0.848101
9 TMP 0.509804 0.881579
10 TYD 0.5 0.87013
11 DA DT DA DA 0.485714 0.843373
12 9RC 0.478632 0.833333
13 THP 0.471698 0.868421
14 DWN 0.471074 0.8625
15 TTP 0.468468 0.87013
16 3R2 0.454545 0.873418
17 TBD 0.45045 0.860759
18 DT DA DC DG 0.447853 0.837209
19 3YN 0.447154 0.884615
20 DC DG DT DA 0.445122 0.837209
21 0N2 0.443548 0.851852
22 DT DC 0.442748 0.909091
23 0FX 0.44 0.8625
24 T3F 0.435484 0.8625
25 T3Q 0.435484 0.8625
26 TLO 0.433333 0.871795
27 T46 0.432 0.884615
28 1JB 0.430894 0.884615
29 TDX 0.430894 0.871795
30 TRH 0.430894 0.884615
31 18T 0.430894 0.884615
32 JHZ 0.429688 0.841463
33 T3P 0.428571 0.844156
34 MMF 0.428571 0.886076
35 DAU 0.427419 0.860759
36 DT 64T DT DT 0.423313 0.888889
37 ADS THS THS THS 0.422535 0.804598
38 ATY 0.422414 0.848101
39 FNF 0.418605 0.873418
40 1YF 0.418605 0.873418
41 AKM 0.418605 0.821429
42 LLT 0.415842 0.802632
43 THM 0.415842 0.802632
44 QDM 0.410853 0.875
45 DU DU DU DU BRU DA DU 0.410256 0.781609
46 0DN 0.407767 0.789474
47 4TG 0.40458 0.873418
48 4TA 0.404255 0.833333
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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