Receptor
PDB id Resolution Class Description Source Keywords
5M12 1.53 Å EC: 3.2.1.22 STRUCTURE OF GH36 ALPHA-GALACTOSIDASE FROM THERMOTOGA MARITI COMPLEX WITH INTACT CYCLOPROPYL-CARBASUGAR. THERMOTOGA MARITIMA ALPHA-GALACTOSIDASE GLYCOSIDE HYDROLASE HYDROLASE
Ref.: STRUCTURAL SNAPSHOTS FOR MECHANISM-BASED INACTIVATI GLYCOSIDE HYDROLASE BY CYCLOPROPYL CARBASUGARS. ANGEW.CHEM.INT.ED.ENGL. V. 55 14978 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:601;
A:602;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
7D0 A:604;
Valid;
none;
submit data
302.271 C14 H16 F2 O5 c1c(c...
MG A:603;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6GVD 1.22 Å EC: 3.2.1.22 ALPHA-GALACTOSIDASE FROM THERMOTOGA MARITIMA IN COMPLEX WITH CYCLOHEXENE-BASED CARBASUGAR MIMIC OF GALACTOSE THERMOTOGA MARITIMA (STRAIN ATCC 43589DSM 3109 / JCM 10099) GLYCOSIDE HYDROLASE GALACTOSIDASE CARBOHYDRATE PROCESSING INHIBITOR HYDROLASE
Ref.: REVEALING THE MECHANISM FOR COVALENT INHIBITION OF HYDROLASES BY CARBASUGARS AT AN ATOMIC LEVEL. NAT COMMUN V. 9 3243 2018
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 6GX8 - FH2 C7 H11 F O4 C1=C([C@@H....
2 5M16 - 7D2 C8 H14 O5 C1[C@H]2[C....
3 5M12 - 7D0 C14 H16 F2 O5 c1c(cc(cc1....
4 6GTA - F9W C13 H14 F2 O5 c1c(cc(cc1....
5 6GWF - FEQ C13 H13 F N2 O8 c1cc(c(cc1....
6 6GVD - FDK C7 H12 O5 C1=C([C@@H....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 6GX8 - FH2 C7 H11 F O4 C1=C([C@@H....
2 5M16 - 7D2 C8 H14 O5 C1[C@H]2[C....
3 5M12 - 7D0 C14 H16 F2 O5 c1c(cc(cc1....
4 6GTA - F9W C13 H14 F2 O5 c1c(cc(cc1....
5 6GWF - FEQ C13 H13 F N2 O8 c1cc(c(cc1....
6 6GVD - FDK C7 H12 O5 C1=C([C@@H....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 6GX8 - FH2 C7 H11 F O4 C1=C([C@@H....
2 5M16 - 7D2 C8 H14 O5 C1[C@H]2[C....
3 5M12 - 7D0 C14 H16 F2 O5 c1c(cc(cc1....
4 6GTA - F9W C13 H14 F2 O5 c1c(cc(cc1....
5 6GWF - FEQ C13 H13 F N2 O8 c1cc(c(cc1....
6 6GVD - FDK C7 H12 O5 C1=C([C@@H....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 7D0; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 7D0 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: 7D0; Similar ligands found: 41
No: Ligand Similarity coefficient
1 F9W 0.9359
2 GAT 0.9130
3 GAA 0.9093
4 GLA BEZ 0.9084
5 38E 0.8994
6 MBG GLA 0.8927
7 GAL GAL 0.8920
8 BQZ 0.8913
9 BGC BGC 0.8847
10 MHD GAL 0.8803
11 7NU 0.8792
12 5E1 0.8784
13 LI4 0.8766
14 GAL GLA 0.8765
15 GLC GAL 0.8752
16 HMD 0.8702
17 CZ0 0.8700
18 8HH 0.8700
19 NBZ GLA 0.8693
20 ZRL 0.8692
21 2QU 0.8690
22 GNG 0.8687
23 BGC GAL 0.8685
24 JRO 0.8674
25 553 0.8658
26 DXK 0.8654
27 5DN 0.8649
28 5NN 0.8647
29 MYG 0.8646
30 DS8 0.8646
31 MAN BMA 0.8639
32 NAB 0.8622
33 GWD 0.8614
34 3GX 0.8602
35 U19 0.8575
36 DNQ 0.8570
37 MAN GLC 0.8563
38 3WO 0.8552
39 3WN 0.8552
40 53X 0.8544
41 XMM 0.8540
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6GVD; Ligand: FDK; 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: 6gvd.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
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