Receptor
PDB id Resolution Class Description Source Keywords
5M7Y 1.55 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF GH125 1,6-ALPHA-MANNOSIDASE MUTANT FROM CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH 1,6-ALPHA-MANNOTRIO CLOSTRIDIUM PERFRINGENS (STRAIN 13 / TORGANISM_TAXID: 195102 GLYCOSIDE HYDROLASE MANNOSIDASE CARBOHYDRATE HYDROLASE
Ref.: COMPUTATIONAL DESIGN OF EXPERIMENT UNVEILS THE CONFORMATIONAL REACTION COORDINATE OF GH125 ALPHA-MANNOSIDASES. J. AM. CHEM. SOC. V. 139 1085 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:505;
A:504;
 Invalid;
Part of Protein;
 none;
none;
 submit data
24.305 Mg [Mg+2...
MAN MAN MAN B:1;
 Valid;
 none;
 submit data
502.422 n/a O(CC1...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6RQK 1.85 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF GH125 1,6-ALPHA-MANNOSIDASE FROM CLOSTR PERFRINGENS IN COMPLEX WITH MANNOIMIDAZOLE CLOSTRIDIUM PERFRINGENS STR. 13 CARBOHYDRATE INHIBITOR GLYCOSIDE HYDROLASE COMPLEX HYDRO
Ref.: DISTORTION OF MANNOIMIDAZOLE SUPPORTS A B2,5BOAT TR STATE FOR THE FAMILY GH125 ALPHA-1,6-MANNOSIDASE FR CLOSTRIDIUM PERFRINGENS. ORG.BIOMOL.CHEM. V. 17 7863 2019
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 5M7Y - MAN MAN MAN n/a n/a
2 3QT9 - Z4Y MAN n/a n/a
3 5M7I - BMA MAN n/a n/a
4 6RQK Kd = 1.6 mM MVL C8 H12 N2 O4 c1cn2c(n1)....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 5M7Y - MAN MAN MAN n/a n/a
2 3QT9 - Z4Y MAN n/a n/a
3 5M7I - BMA MAN n/a n/a
4 6RQK Kd = 1.6 mM MVL C8 H12 N2 O4 c1cn2c(n1)....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 3QSP - BMA MAN n/a n/a
2 3QRY - DMJ C6 H13 N O4 C1[C@H]([C....
3 5M7Y - MAN MAN MAN n/a n/a
4 3QT9 - Z4Y MAN n/a n/a
5 5M7I - BMA MAN n/a n/a
6 6RQK Kd = 1.6 mM MVL C8 H12 N2 O4 c1cn2c(n1)....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: MAN MAN MAN; Similar ligands found: 59
No: Ligand ECFP6 Tc MDL keys Tc
1 MAN MAN MAN 1 1
2 BMA MAN MAN 0.777778 0.970588
3 BGC BGC BGC BGC 0.621622 0.970588
4 MAN MAN MAN MAN MAN MAN MAN 0.6125 0.970588
5 GAL SO4 GAL 0.583333 0.68
6 GAL GLA 0.578125 0.970588
7 MMA MAN MAN 0.540541 0.916667
8 BGC BGC BGC BGC BGC 0.536232 0.970588
9 BGC BGC BGC 0.536232 0.970588
10 BGC BGC BGC BGC BGC BGC BGC 0.536232 0.970588
11 BGC BGC BGC BGC BGC BGC 0.536232 0.970588
12 GLC BGC BGC BGC 0.536232 0.970588
13 BGC GLC GLC GLC GLC 0.529412 0.970588
14 BGC GLC GLC GLC GLC GLC 0.529412 0.970588
15 BGC GLC GLC 0.5 0.970588
16 GLC GLC GLC GLC GLC 0.493671 0.970588
17 BGC GLC GLC GLC 0.493671 0.970588
18 MAN MAN MAN MAN MAN MAN MAN MAN 0.483871 0.871795
19 MAN MAN BMA 0.480519 0.916667
20 MAN BMA MAN MAN MAN MAN MAN 0.472527 0.916667
21 BMA MAN MAN MAN 0.46988 0.891892
22 BMA BMA BMA BMA GLA 0.469136 0.970588
23 MAN MAN M6P 0.469136 0.809524
24 NAG BMA MAN MAN MAN MAN MAN 0.465909 0.846154
25 BMA MAN MAN MAN MAN 0.465116 0.916667
26 GLC GLC GLC 0.4625 0.916667
27 BMA MAN MAN NAG GAL NAG 0.46 0.673469
28 GCU BGC 0.453333 0.942857
29 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.451219 0.970588
30 AHR AHR AHR AHR AHR AHR 0.449275 0.833333
31 AHR AHR AHR AHR 0.449275 0.833333
32 AHR AHR AHR AHR AHR 0.449275 0.833333
33 AHR AHR 0.447761 0.833333
34 H1M MAN MAN 0.445783 0.846154
35 BQZ 0.439394 0.882353
36 MAN MAN MAN NAG NAG 0.430108 0.673469
37 BGC GAL GLA 0.428571 0.970588
38 BGC BGC BGC BGC BGC BGC BGC BGC 0.425 0.970588
39 GLC BGC FUC GAL 0.425 0.942857
40 BGC FUC GAL 0.425 0.942857
41 NAG NAG MAN MAN MAN 0.424242 0.673469
42 NAG BMA MAN MAN MAN MAN 0.42268 0.717391
43 MAN BMA BMA BMA BMA BMA BMA 0.418919 0.970588
44 GLC GLC GLC GLC BGC GLC GLC 0.418919 0.970588
45 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.418919 0.970588
46 BMA NGT MAN MAN 0.416667 0.647059
47 GAL NAG GAL 0.413793 0.717391
48 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.411765 0.717391
49 A2G GAL NAG 0.411111 0.673469
50 BGC BGC BGC XYS BGC XYS 0.411111 0.916667
51 MMA MAN 0.410959 0.916667
52 MBG GAL 0.410959 0.916667
53 MAN AML MAN MAN MAN MAN MAN MAN MAN 0.408163 0.804878
54 1GN ACY GAL 1GN BGC ACY GAL BGC 0.408163 0.673469
55 MAN MAN MAN GLC 0.402439 0.970588
56 BGC BGC BGC XYS BGC XYS BGC XYS BGC 0.402174 0.916667
57 BGC BGC BGC BGC XYS BGC XYS BGC BGC 0.402174 0.916667
58 BGC BGC BGC BGC BGC XYS 0.402174 0.916667
59 NAG GAL BGC GAL 0.4 0.717391
Similar Ligands (3D)
Ligand no: 1; Ligand: MAN MAN MAN; Similar ligands found: 1
No: Ligand Similarity coefficient
1 YZ0 MAN Z4Y 0.9447
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6RQK; Ligand: MVL; 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: 6rqk.bio2) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6RQK; Ligand: MVL; 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: 6rqk.bio2) has 10 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 6RQK; Ligand: MVL; 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: 6rqk.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 6RQK; Ligand: MVL; 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: 6rqk.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
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