Receptor
PDB id Resolution Class Description Source Keywords
6EZC 2 Å EC: 1.3.1.- CRYSTAL STRUCTURE OF HUMAN TRNA-DIHYDROURIDINE(20) SYNTHASE DOMAIN E294K Q305K DOUBLE MUTANT HOMO SAPIENS RNA BINDING PROTEIN TRNA PROCESSING FLAVOPROTEIN OXIDORED
Ref.: ELECTROSTATIC POTENTIAL IN THE TRNA BINDING EVOLUTI DIHYDROURIDINE SYNTHASES. BIOCHEMISTRY V. 57 5407 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:406;
A:407;
 Invalid;
Invalid;
 none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
SO4 A:403;
A:404;
A:402;
A:410;
A:409;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
96.063 O4 S [O-]S...
PGE A:408;
 Invalid;
 none;
 submit data
150.173 C6 H14 O4 C(COC...
CL A:405;
 Invalid;
 none;
 submit data
35.453 Cl [Cl-]
FMN A:401;
 Valid;
 none;
 submit data
456.344 C17 H21 N4 O9 P Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4XP7 1.9 Å EC: 1.3.1.- CRYSTAL STRUCTURE OF HUMAN TRNA DIHYDROURIDINE SYNTHASE 2 HOMO SAPIENS TRNA DUS OXIDOREDUCTASE
Ref.: FROM BACTERIAL TO HUMAN DIHYDROURIDINE SYNTHASE: AU STRUCTURE DETERMINATION. ACTA CRYSTALLOGR.,SECT.D V. 71 1564 2015
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 6EZA - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 6EZB - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 6EZC - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
4 4XP7 - FNR C17 H23 N4 O9 P Cc1cc2c(cc....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 6EZA - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 6EZB - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 6EZC - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
4 4XP7 - FNR C17 H23 N4 O9 P Cc1cc2c(cc....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 6EZA - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 6EZB - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 6EZC - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
4 4XP7 - FNR C17 H23 N4 O9 P Cc1cc2c(cc....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: FMN; Similar ligands found: 18
No: Ligand ECFP6 Tc MDL keys Tc
1 FMN 1 1
2 RBF 0.75641 0.876712
3 9O9 0.574468 0.934211
4 RS3 0.571429 0.831169
5 FAD 0.543307 0.876543
6 FAS 0.543307 0.876543
7 FAE 0.539062 0.865854
8 UBG 0.534351 0.888889
9 5DD 0.475248 0.972603
10 LFN 0.475 0.643836
11 C3F 0.473684 0.74359
12 CF4 0.463918 0.734177
13 FAY 0.446043 0.864198
14 FNR 0.444444 0.909091
15 RFL 0.442857 0.845238
16 4LS 0.411215 0.875
17 1VY 0.406593 0.769231
18 DLZ 0.404494 0.782051
Similar Ligands (3D)
Ligand no: 1; Ligand: FMN; Similar ligands found: 10
No: Ligand Similarity coefficient
1 7O6 0.9670
2 4X4 0.8996
3 4LU 0.8884
4 E2U 0.8865
5 HDF 0.8834
6 AFQ 0.8817
7 E2X 0.8805
8 E89 0.8698
9 1WJ 0.8673
10 FZZ 0.8606
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4XP7; Ligand: FNR; Similar sites found with APoc: 7
This union binding pocket(no: 1) in the query (biounit: 4xp7.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 1Z44 FMN 1.77515
2 1Z44 FMN 1.77515
3 1Z42 FMN 1.77515
4 3B0P FMN 23.1214
5 3B0P FMN 23.1214
6 1VHN FMN 32.0755
7 3W9Z FMN 36.9565
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