Receptor
PDB id Resolution Class Description Source Keywords
3GVK 1.84 Å EC: 3.2.1.129 CRYSTAL STRUCTURE OF ENDO-NEURAMINIDASE NF MUTANT ENTEROBACTERIA PHAGE K1F ENDO NEURAMINIDASE POLYSIALIC ACID TRIPLE-BETA HELIX GLYCHYDROLASE
Ref.: STRUCTURAL BASIS FOR THE RECOGNITION AND CLEAVAGE O POLYSIALIC ACID BY THE BACTERIOPHAGE K1F TAILSPIKE ENDONF. J.MOL.BIOL. V. 397 341 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NA A:916;
B:916;
C:916;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
22.99 Na [Na+]
SLB SIA A:914;
B:914;
C:914;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
598.511 n/a O=C([...
SLB SIA SIA A:1;
A:911;
B:1;
B:911;
C:1;
C:911;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
submit data
888.759 n/a O=C([...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3GVL 1.41 Å EC: 3.2.1.129 CRYSTAL STRUCTURE OF ENDO-NEURAMINIDASENF ENTEROBACTERIA PHAGE K1F ENDO-NEURAMINIDASE POLYSIALIC ACID TRIPLE-BETA HELIX GLYCHYDROLASE
Ref.: STRUCTURAL BASIS FOR THE RECOGNITION AND CLEAVAGE O POLYSIALIC ACID BY THE BACTERIOPHAGE K1F TAILSPIKE ENDONF. J.MOL.BIOL. V. 397 341 2010
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3JU4 - SLB C11 H19 N O9 CC(=O)N[C@....
2 3GVJ - SLB SIA SIA SIA SIA n/a n/a
3 3GVL - SLB SIA n/a n/a
4 3GVK - SLB SIA n/a n/a
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3JU4 - SLB C11 H19 N O9 CC(=O)N[C@....
2 3GVJ - SLB SIA SIA SIA SIA n/a n/a
3 3GVL - SLB SIA n/a n/a
4 3GVK - SLB SIA n/a n/a
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3JU4 - SLB C11 H19 N O9 CC(=O)N[C@....
2 3GVJ - SLB SIA SIA SIA SIA n/a n/a
3 3GVL - SLB SIA n/a n/a
4 3GVK - SLB SIA n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SLB SIA; Similar ligands found: 70
No: Ligand ECFP6 Tc MDL keys Tc
1 SLB SIA 1 1
2 SIA SIA 1 1
3 SIA SIA SIA SIA SIA SIA SIA 0.985915 1
4 SLB SIA SIA 0.985915 1
5 SLB SIA SIA SIA SIA 0.985915 1
6 SIA SIA SIA SLB 0.985915 1
7 SIA SIA SIA 0.717647 1
8 SIA SIA GAL 0.648936 0.981132
9 SIA CMO 0.64 0.87037
10 SLB 0.565789 0.826923
11 SIA 0.565789 0.826923
12 SIA SIA GLA BGC 0.554545 0.981132
13 BGC SIA SIA GAL 0.554545 0.981132
14 MNA 0.544304 0.851852
15 GAL SIA 0.521739 0.907407
16 SIA SIA GAL NGA GAL SIA 0.521368 0.981132
17 SIA SIA GAL NGA GAL 0.516949 0.981132
18 SIA GAL 0.516129 0.924528
19 SIA 2FG 0.5 0.859649
20 SIA GAL SIA BGC NGA 0.495935 0.981132
21 SIA GAL SIA GLC NGA 0.495935 0.981132
22 SIA NAG 0.484536 0.910714
23 18D 0.464286 0.796296
24 42D 0.464286 0.8
25 CNP 0.45977 0.767857
26 MUS 0.456311 0.79661
27 SIA GAL NGA 0.449541 0.962264
28 SIA GAL SIA BGC NGA CEQ 0.448529 0.8
29 BGC GAL CEQ SLB NGA GAL SIA SIA 0.445255 0.866667
30 NGA GAL SIA 0.444444 0.962264
31 SIA GAL A2G 0.444444 0.962264
32 NGC 0.440476 0.811321
33 SIA BGC GAL 0.440367 0.924528
34 BGC GAL SIA 0.440367 0.924528
35 SIA GAL BGC 0.440367 0.924528
36 NAG SIA GAL 0.440367 0.962264
37 SIA GAL NAG 0.440367 0.962264
38 SIA GAL GLC 0.440367 0.924528
39 GLA GLC SIA 0.440367 0.924528
40 BGC SIA GAL 0.440367 0.924528
41 GAL BGC SIA 0.440367 0.924528
42 MN0 0.436782 0.818182
43 NAG GAL SIA 0.432432 0.944444
44 SIA NAG GAL 0.428571 0.910714
45 SIA 2FG NAG 0.428571 0.894737
46 5N6 GAL 0.423077 0.925926
47 GAL SIA NGA GAL SIA 0.422414 0.962264
48 GAL SIA NGA GAL 0.422414 0.962264
49 GAL TNR SIA 0.422414 0.927273
50 NDG FUC SIA GAL 0.420168 0.962264
51 FUC NDG GAL SIA 0.420168 0.962264
52 SIA GAL MAG FUC 0.420168 0.962264
53 SIA GLA NAG FUC 0.420168 0.962264
54 NAG FUC SIA GAL 0.420168 0.962264
55 SIA GAL NAG FUC 0.420168 0.962264
56 SIA GAL NDG FUC 0.420168 0.962264
57 SID 0.417582 0.785714
58 NGC MBG 0.417476 0.907407
59 SIA WIA 0.411765 0.862069
60 GAL NGA GAL SIA 0.410256 0.962264
61 SIA GAL NGA GAL 0.410256 0.962264
62 SIA NAG GAL GAL 0.410256 0.944444
63 NXD 0.408602 0.793103
64 SIA GAL NDG SIA 0.40678 0.910714
65 SIA GAL NAG SIA 0.40678 0.944444
66 C5P SIA 0.406504 0.666667
67 425 0.405405 0.662338
68 SIA GAL NGS 0.403361 0.784615
69 NAG GAL NGC 0.401709 0.925926
70 79J 0.4 0.849057
Ligand no: 2; Ligand: SLB SIA SIA; Similar ligands found: 68
No: Ligand ECFP6 Tc MDL keys Tc
1 SIA SIA SIA SLB 1 1
2 SIA SIA SIA SIA SIA SIA SIA 1 1
3 SLB SIA SIA SIA SIA 1 1
4 SLB SIA SIA 1 1
5 SIA SIA 0.985915 1
6 SLB SIA 0.985915 1
7 SIA SIA SIA 0.729412 1
8 SIA SIA GAL 0.659574 0.981132
9 SIA CMO 0.631579 0.87037
10 BGC SIA SIA GAL 0.563636 0.981132
11 SIA SIA GLA BGC 0.563636 0.981132
12 SLB 0.558442 0.826923
13 SIA 0.558442 0.826923
14 MNA 0.5375 0.851852
15 SIA SIA GAL NGA GAL SIA 0.529915 0.981132
16 SIA SIA GAL NGA GAL 0.525424 0.981132
17 GAL SIA 0.516129 0.907407
18 SIA GAL 0.510638 0.924528
19 SIA GAL SIA GLC NGA 0.504065 0.981132
20 SIA GAL SIA BGC NGA 0.504065 0.981132
21 SIA 2FG 0.494845 0.859649
22 SIA NAG 0.479592 0.910714
23 18D 0.458824 0.796296
24 42D 0.458824 0.8
25 SIA GAL SIA BGC NGA CEQ 0.455882 0.8
26 CNP 0.454545 0.767857
27 BGC GAL CEQ SLB NGA GAL SIA SIA 0.452555 0.866667
28 MUS 0.451923 0.79661
29 SIA GAL NGA 0.445455 0.962264
30 SIA GAL A2G 0.440367 0.962264
31 NGA GAL SIA 0.440367 0.962264
32 SIA BGC GAL 0.436364 0.924528
33 BGC GAL SIA 0.436364 0.924528
34 NAG SIA GAL 0.436364 0.962264
35 SIA GAL NAG 0.436364 0.962264
36 SIA GAL BGC 0.436364 0.924528
37 SIA GAL GLC 0.436364 0.924528
38 GLA GLC SIA 0.436364 0.924528
39 BGC SIA GAL 0.436364 0.924528
40 GAL BGC SIA 0.436364 0.924528
41 NGC 0.435294 0.811321
42 MN0 0.431818 0.818182
43 NAG GAL SIA 0.428571 0.944444
44 SIA 2FG NAG 0.424779 0.894737
45 SIA NAG GAL 0.424779 0.910714
46 5N6 GAL 0.419048 0.925926
47 GAL TNR SIA 0.418803 0.927273
48 GAL SIA NGA GAL 0.418803 0.962264
49 GAL SIA NGA GAL SIA 0.418803 0.962264
50 SIA GLA NAG FUC 0.416667 0.962264
51 FUC NDG GAL SIA 0.416667 0.962264
52 NDG FUC SIA GAL 0.416667 0.962264
53 SIA GAL NAG FUC 0.416667 0.962264
54 SIA GAL NDG FUC 0.416667 0.962264
55 SIA GAL MAG FUC 0.416667 0.962264
56 NAG FUC SIA GAL 0.416667 0.962264
57 NGC MBG 0.413462 0.907407
58 SID 0.413043 0.785714
59 SIA WIA 0.407767 0.862069
60 SIA NAG GAL GAL 0.40678 0.944444
61 SIA GAL NGA GAL 0.40678 0.962264
62 GAL NGA GAL SIA 0.40678 0.962264
63 NXD 0.404255 0.793103
64 SIA GAL NDG SIA 0.403361 0.910714
65 SIA GAL NAG SIA 0.403361 0.944444
66 C5P SIA 0.403226 0.666667
67 425 0.401786 0.662338
68 SIA GAL NGS 0.4 0.784615
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3GVL; Ligand: SLB; Similar sites found: 15
This union binding pocket(no: 1) in the query (biounit: 3gvl.bio1) has 43 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4RJK PYR 0.01948 0.41728 2.10158
2 4LTN FMN 0.002046 0.41311 3.5533
3 4LTN NAI 0.002825 0.41203 3.5533
4 1RZM E4P 0.007469 0.43111 4.14201
5 3VHZ SOG 0.005601 0.41083 4.77612
6 2EB5 OXL 0.02027 0.40518 4.86891
7 2ZO9 MLI 0.0005971 0.44584 5.10949
8 1V7R CIT 0.04688 0.41047 6.98925
9 1ZJ6 G3D 0.00211 0.42189 7.48663
10 4COQ SAN 0.0006831 0.47228 8.50202
11 2JGS BTN 0.01702 0.40123 9.23077
12 4F8L GAL 0.002722 0.48734 9.65517
13 1T0S BML 0.01757 0.4195 11.6279
14 1BTN I3P 0.005084 0.47384 14.1509
15 3KPE TM3 0.01113 0.4171 23.5294
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