Receptor
PDB id Resolution Class Description Source Keywords
6gta 2.2 Å EC: 3.2.1.22 ALPHA-GALACTOSIDASE MUTANT D378A FROM THERMOTOGA MARITIMA IN WITH INTACT CYCLOHEXENE-BASED CARBASUGAR MIMIC OF GALACTOSED IFLUOROPHENYL LEAVING GROUP 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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:604;
A:605;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
24.305 Mg [Mg+2...
F9W A:606;
 Valid;
 none;
 submit data
288.244 C13 H14 F2 O5 c1c(c...
SO4 A:603;
A:601;
A:602;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
96.063 O4 S [O-]S...
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: F9W; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 F9W 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: F9W; Similar ligands found: 54
No: Ligand Similarity coefficient
1 7D0 0.9359
2 GAL GAL 0.9134
3 BQZ 0.9130
4 GAT 0.9116
5 GAA 0.9097
6 MBG GLA 0.9086
7 GLA BEZ 0.9086
8 7NU 0.9051
9 56N 0.9029
10 XYP GCU 0.8992
11 GAL GLA 0.8991
12 GLA GLA 0.8956
13 TOP 0.8919
14 CJZ 0.8914
15 LI4 0.8874
16 MHD GAL 0.8854
17 12R 0.8850
18 KUP 0.8842
19 5AV 0.8823
20 DMB 0.8818
21 50Q 0.8815
22 B4L 0.8794
23 DSQ 0.8778
24 DS8 0.8767
25 3D8 0.8762
26 GA2 0.8756
27 SRE 0.8755
28 S7V 0.8751
29 C4F 0.8742
30 NAB 0.8737
31 B1T 0.8735
32 B2L 0.8733
33 LJ4 0.8725
34 5E4 0.8710
35 DGO Z61 0.8708
36 ON1 0.8686
37 TLF 0.8684
38 CMG 0.8661
39 BNY 0.8660
40 6J3 0.8660
41 GLC GLA 0.8659
42 BGC GLA 0.8645
43 BC3 0.8633
44 ID8 0.8622
45 MYG 0.8619
46 PU2 0.8618
47 9FN 0.8604
48 JMS 0.8591
49 NW1 0.8587
50 TWJ SDY 0.8580
51 MAN GLC 0.8579
52 P2L 0.8566
53 3AK 0.8555
54 GLA GAL 0.8552
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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