Receptor
PDB id Resolution Class Description Source Keywords
5X1L 1.9 Å EC: 7.-.-.- VANILLATE/3-O-METHYLGALLATE O-DEMETHYLASE, LIGM, TETRAHYDROF COMPLEX FORM SPHINGOBIUM SP. SYK-6 LIGNIN SPHINGOBIUM SP. SYK-6 OXIDOREDUCTASE
Ref.: THE CRYSTAL STRUCTURE OF A NEW O-DEMETHYLASE FROM SPHINGOBIUM SP. STRAIN SYK-6 FEBS J. V. 284 1855 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO C:502;
A:503;
B:502;
A:502;
B:503;
A:501;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
THG C:501;
B:501;
 Valid;
Valid;
 none;
none;
 submit data
445.429 C19 H23 N7 O6 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5X1M 1.9 Å EC: 7.-.-.- VANILLATE/3-O-METHYLGALLATE O-DEMETHYLASE, LIGM, PROTOCATECH TETRAHYDROFOLATE COMPLEX FORM SPHINGOBIUM SP. SYK-6 LIGNIN SPHINGOBIUM SP. SYK-6 OXIDOREDUCTASE
Ref.: THE CRYSTAL STRUCTURE OF A NEW O-DEMETHYLASE FROM SPHINGOBIUM SP. STRAIN SYK-6 FEBS J. V. 284 1855 2017
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 319 families.
1 5X1L - THG C19 H23 N7 O6 c1cc(ccc1C....
2 5X1J - VNL C8 H7 O4 COc1cc(ccc....
3 5X1K - 7WR C8 H8 O5 COc1cc(cc(....
4 5X1N - DHB C7 H6 O4 c1cc(c(cc1....
5 5X1M - DHB C7 H6 O4 c1cc(c(cc1....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 271 families.
1 5X1L - THG C19 H23 N7 O6 c1cc(ccc1C....
2 5X1J - VNL C8 H7 O4 COc1cc(ccc....
3 5X1K - 7WR C8 H8 O5 COc1cc(cc(....
4 5X1N - DHB C7 H6 O4 c1cc(c(cc1....
5 5X1M - DHB C7 H6 O4 c1cc(c(cc1....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 223 families.
1 5X1L - THG C19 H23 N7 O6 c1cc(ccc1C....
2 5X1J - VNL C8 H7 O4 COc1cc(ccc....
3 5X1K - 7WR C8 H8 O5 COc1cc(cc(....
4 5X1N - DHB C7 H6 O4 c1cc(c(cc1....
5 5X1M - DHB C7 H6 O4 c1cc(c(cc1....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: THG; Similar ligands found: 28
No: Ligand ECFP6 Tc MDL keys Tc
1 THG 1 1
2 1YJ 1 1
3 1YA 0.66 0.954545
4 C2F 0.623762 0.887324
5 FFO 0.617647 0.926471
6 FON 0.518182 0.926471
7 THF 0.490909 0.873239
8 9L9 0.484848 0.892308
9 TLL 0.478632 0.863014
10 FGD 0.471698 0.846154
11 MEF 0.469027 0.84
12 DHF 0.462963 1
13 THH 0.455357 0.733333
14 GHC 0.454545 0.684211
15 29C 0.452174 0.838235
16 28Z 0.452174 0.838235
17 3TZ 0.452174 0.774648
18 29D 0.452174 0.838235
19 83A 0.45045 0.826087
20 GHW 0.449541 0.693333
21 GUE 0.431034 0.875
22 FOL 0.428571 0.863636
23 DZF 0.428571 0.848485
24 LYA 0.422018 0.782609
25 DXZ 0.401786 0.777778
26 DXY 0.401786 0.777778
27 DDF 0.4 0.910448
28 21V 0.4 0.910448
Similar Ligands (3D)
Ligand no: 1; Ligand: THG; Similar ligands found: 3
No: Ligand Similarity coefficient
1 MTX 0.9330
2 GPB 0.8987
3 LY3 0.8631
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5X1M; Ligand: DHB; 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: 5x1m.bio2) has 31 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5X1M; Ligand: THG; 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: 5x1m.bio2) has 32 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5X1M; Ligand: THG; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5x1m.bio2) has 31 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5X1M; Ligand: DHB; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5x1m.bio2) has 30 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5X1M; Ligand: DHB; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 5x1m.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 5X1M; Ligand: DHB; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5x1m.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 5X1M; Ligand: DHB; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 5x1m.bio1) has 6 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 5X1M; Ligand: DHB; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 5x1m.bio1) has 6 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback