Receptor
PDB id Resolution Class Description Source Keywords
5MEH 0.95 Å EC: 3.2.1.113 CRYSTAL STRUCTURE OF ALPHA-1,2-MANNOSIDASE FROM CAULOBACTER IN COMPLEX WITH 1-DEOXYMANNOJIRIMYCIN CAULOBACTER SP. GLYCOSIDE HYDROLASE MANNOSIDASE HYDROLASE
Ref.: CONFORMATIONAL BEHAVIOUR OF AZASUGARS BASED ON MANN ACID. CHEMBIOCHEM V. 18 1297 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:504;
A:503;
Part of Protein;
Part of Protein;
none;
none;
submit data
40.078 Ca [Ca+2...
GOL A:502;
A:501;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NA A:505;
Part of Protein;
none;
submit data
22.99 Na [Na+]
DMJ A:506;
Valid;
Atoms found LESS than expected: % Diff = 0;
Kd = 481 nM
163.172 C6 H13 N O4 C1[C@...
ACT A:507;
Invalid;
none;
submit data
59.044 C2 H3 O2 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5NE5 1.05 Å EC: 3.2.1.113 CRYSTAL STRUCTURE OF FAMILY 47 ALPHA-1,2-MANNOSIDASE FROM CA K31 STRAIN IN COMPLEX WITH KIFUNENSINE CAULOBACTER SP. MANNOSIDASE GLYCOSIDASE HYDROLYSIS INHIBITOR HYDROLASE
Ref.: CONFORMATIONAL ANALYSIS OF THE MANNOSIDASE INHIBITO KIFUNENSINE: A QUANTUM MECHANICAL AND STRUCTURAL AP CHEMBIOCHEM V. 18 1496 2017
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 4AYR Kd = 99 nM IFL C6 H11 N O4 C1[C@@H]([....
2 5NE5 Kd = 39 nM KIF C8 H12 N2 O6 C([C@@H]1[....
3 4AYP Kd = 755 nM SMD C13 H24 O10 S CO[C@@H]1[....
4 5MEH Kd = 481 nM DMJ C6 H13 N O4 C1[C@H]([C....
5 4AYQ Kd = 47 nM MVL C8 H12 N2 O4 c1cn2c(n1)....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4AYR Kd = 99 nM IFL C6 H11 N O4 C1[C@@H]([....
2 5NE5 Kd = 39 nM KIF C8 H12 N2 O6 C([C@@H]1[....
3 4AYP Kd = 755 nM SMD C13 H24 O10 S CO[C@@H]1[....
4 5MEH Kd = 481 nM DMJ C6 H13 N O4 C1[C@H]([C....
5 4AYQ Kd = 47 nM MVL C8 H12 N2 O4 c1cn2c(n1)....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4AYR Kd = 99 nM IFL C6 H11 N O4 C1[C@@H]([....
2 5NE5 Kd = 39 nM KIF C8 H12 N2 O6 C([C@@H]1[....
3 4AYP Kd = 755 nM SMD C13 H24 O10 S CO[C@@H]1[....
4 5MEH Kd = 481 nM DMJ C6 H13 N O4 C1[C@H]([C....
5 4AYQ Kd = 47 nM MVL C8 H12 N2 O4 c1cn2c(n1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DMJ; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 NOJ 1 1
2 DGJ 1 1
3 DMJ 1 1
4 IMR 0.703704 0.853659
5 EDG 0.703704 0.853659
6 1AB 0.703704 0.853659
7 LDU 0.703704 0.853659
8 HQ6 0.454545 0.765957
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5NE5; Ligand: KIF; 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: 5ne5.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
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