Receptor
PDB id Resolution Class Description Source Keywords
4RDN 2.1 Å NON-ENZYME: OTHER STRUCTURE OF YTH-YTHDF2 IN COMPLEX WITH M6A HOMO SAPIENS M6A METHYLATED RNA BINDING ATYPICAL BETA-PROPELLER RNA BINMETHYLATED RNA RNA BINDING PROTEIN
Ref.: STRUCTURE OF THE YTH DOMAIN OF HUMAN YTHDF2 IN COMP AN M(6)A MONONUCLEOTIDE REVEALS AN AROMATIC CAGE FO RECOGNITION. CELL RES. V. 24 1490 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 B:602;
B:603;
A:602;
A:603;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
6MD B:601;
A:601;
Valid;
Valid;
none;
none;
submit data
281.268 C11 H15 N5 O4 CNc1c...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4RDN 2.1 Å NON-ENZYME: OTHER STRUCTURE OF YTH-YTHDF2 IN COMPLEX WITH M6A HOMO SAPIENS M6A METHYLATED RNA BINDING ATYPICAL BETA-PROPELLER RNA BINMETHYLATED RNA RNA BINDING PROTEIN
Ref.: STRUCTURE OF THE YTH DOMAIN OF HUMAN YTHDF2 IN COMP AN M(6)A MONONUCLEOTIDE REVEALS AN AROMATIC CAGE FO RECOGNITION. CELL RES. V. 24 1490 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 4RDN - 6MD C11 H15 N5 O4 CNc1c2c(nc....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 4RDN - 6MD C11 H15 N5 O4 CNc1c2c(nc....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 4RDN - 6MD C11 H15 N5 O4 CNc1c2c(nc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 6MD; Similar ligands found: 44
No: Ligand ECFP6 Tc MDL keys Tc
1 6MD 1 1
2 TT8 0.5875 0.830986
3 RAB 0.580645 0.952381
4 ADN 0.580645 0.952381
5 XYA 0.580645 0.952381
6 MTP 0.578125 0.895522
7 26A 0.569231 0.938462
8 6IA 0.518519 0.759494
9 1DA 0.5 0.952381
10 6C6 0.487805 0.753247
11 3DH 0.479452 0.865672
12 MTA 0.472222 0.893939
13 5N5 0.470588 0.921875
14 2SA 0.470588 0.776316
15 6CR 0.464789 0.869565
16 EP4 0.464789 0.867647
17 5CD 0.463768 0.876923
18 A4D 0.463768 0.921875
19 M2T 0.458333 0.842857
20 2FA 0.457143 0.882353
21 6K6 0.449438 0.819444
22 DTA 0.438356 0.826087
23 5AS 0.432099 0.705882
24 ABM 0.43038 0.833333
25 AMP 0.428571 0.805556
26 LMS 0.428571 0.707317
27 A 0.428571 0.805556
28 6RE 0.423077 0.794521
29 MHZ 0.421687 0.769231
30 IVH 0.414634 0.824324
31 IMO 0.4125 0.767123
32 A3N 0.4125 0.880597
33 J7C 0.4125 0.805556
34 ZAS 0.410256 0.802817
35 GJV 0.407407 0.783784
36 S4M 0.407407 0.779221
37 SRA 0.405063 0.763158
38 M33 0.404762 0.847222
39 MAO 0.402439 0.769231
40 NEC 0.4 0.863636
41 TBN 0.4 0.936508
42 AOC 0.4 0.865672
43 S7M 0.4 0.763158
44 DSH 0.4 0.805556
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4RDN; Ligand: 6MD; 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: 4rdn.bio2) has 13 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4RDN; Ligand: 6MD; 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: 4rdn.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
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