Receptor
PDB id Resolution Class Description Source Keywords
4yw2 2 Å EC: 3.2.1.18 CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE NANC, COMPLEX STREPTOCOCCUS PNEUMONIAE SIALIDASE NEURAMINIDASE 6-prime SL CBM40 HYDROLASE
Ref.: STREPTOCOCCUS PNEUMONIAE NANC: STRUCTURAL INSIGHTS SPECIFICITY AND MECHANISM OF A SIALIDASE THAT PRODU SIALIDASE INHIBITOR. J.BIOL.CHEM. V. 290 27736 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:803;
B:802;
B:803;
A:802;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
PO4 A:801;
B:801;
 Invalid;
Invalid;
 none;
none;
 submit data
94.971 O4 P [O-]P...
GAL SIA C:1;
D:1;
 Valid;
Valid;
 none;
none;
 Kd = 1.6 mM
454.405 n/a O=C(N...
PEG A:804;
 Invalid;
 none;
 submit data
106.12 C4 H10 O3 C(COC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4YZ5 2.27 Å EC: 3.2.1.18 CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE NANC, IN COMPL SIALYLLACTOSE STREPTOCOCCUS PNEUMONIAE SIALIDASE NEURAMINIDASE BETA-PROPELLER CBM40 HYDROLASE
Ref.: STREPTOCOCCUS PNEUMONIAE NANC: STRUCTURAL INSIGHTS SPECIFICITY AND MECHANISM OF A SIALIDASE THAT PRODU SIALIDASE INHIBITOR. J.BIOL.CHEM. V. 290 27736 2015
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 30 families.
1 4YZ2 - DAN C11 H17 N O8 CC(=O)N[C@....
2 4YW5 - G39 C14 H24 N2 O4 CCC(CC)O[C....
3 4YW2 Kd = 1.6 mM GAL SIA n/a n/a
4 5F9T - SFJ C11 H17 F2 N O8 CC(=O)N[C@....
5 4YW3 - DAN C11 H17 N O8 CC(=O)N[C@....
6 4YW1 - SIA C11 H19 N O9 CC(=O)N[C@....
7 4YZ4 - SIA C11 H19 N O9 CC(=O)N[C@....
8 4YZ5 Kd = 1.48 mM GLC GAL SIA n/a n/a
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 24 families.
1 4YZ2 - DAN C11 H17 N O8 CC(=O)N[C@....
2 4YW5 - G39 C14 H24 N2 O4 CCC(CC)O[C....
3 4YW2 Kd = 1.6 mM GAL SIA n/a n/a
4 5F9T - SFJ C11 H17 F2 N O8 CC(=O)N[C@....
5 4YW3 - DAN C11 H17 N O8 CC(=O)N[C@....
6 4YW1 - SIA C11 H19 N O9 CC(=O)N[C@....
7 4YZ4 - SIA C11 H19 N O9 CC(=O)N[C@....
8 4YZ5 Kd = 1.48 mM GLC GAL SIA n/a n/a
50% Homology Family (25)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 2VK6 - DAN C11 H17 N O8 CC(=O)N[C@....
2 2JKB - SKD C11 H17 N O8 CC(=O)N[C@....
3 4FPF ic50 = 38.9 uM JKK C9 H12 Cl N O3 S c1cc(cc(c1....
4 4FOQ - TAU C2 H7 N O3 S C(CS(=O)(=....
5 4FPC - MFY C9 H12 Cl N O3 S c1cc(ccc1C....
6 4FOY - D53 C9 H13 N O3 S c1ccc(cc1)....
7 4FPL - 7HV C9 H11 Cl2 N O3 S c1cc(c(cc1....
8 4FOW - A20 C3 H9 N O3 S C(CN)CS(=O....
9 4FPJ - D8I C10 H15 N O4 S COc1cccc(c....
10 4FPK ic50 = 57.4 uM IJ1 C10 H15 N O3 S Cc1cccc(c1....
11 4FQ4 - IJ4 C10 H14 F N O3 S Cc1cc(ccc1....
12 4FPY - 0V8 C9 H12 Br N O3 S c1cc(cc(c1....
13 4X6K ic50 = 0.00487 mM 3XR C8 H15 N2 O5 CC(=O)N[C@....
14 4X47 ic50 = 1.41 mM DAN C11 H17 N O8 CC(=O)N[C@....
15 4X4A Ki = 2.37 mM SKD C11 H17 N O8 CC(=O)N[C@....
16 4YW5 - G39 C14 H24 N2 O4 CCC(CC)O[C....
17 4YW2 Kd = 1.6 mM GAL SIA n/a n/a
18 5F9T - SFJ C11 H17 F2 N O8 CC(=O)N[C@....
19 4YW3 - DAN C11 H17 N O8 CC(=O)N[C@....
20 4YW1 - SIA C11 H19 N O9 CC(=O)N[C@....
21 4YZ4 - SIA C11 H19 N O9 CC(=O)N[C@....
22 4YZ5 Kd = 1.48 mM GLC GAL SIA n/a n/a
23 4SLI - CNP C14 H23 N O8 CC(=O)N[C@....
24 3SLI - SKD C11 H17 N O8 CC(=O)N[C@....
25 2SLI - SKD C11 H17 N O8 CC(=O)N[C@....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GAL SIA; Similar ligands found: 60
No: Ligand ECFP6 Tc MDL keys Tc
1 GAL SIA 1 1
2 NAG SIA 0.710843 0.909091
3 SIA CMO 0.635135 0.867925
4 BGC GAL SIA 0.608247 0.980392
5 NDG GAL SIA SIA 0.592233 0.909091
6 GAL NAG GAL SIA 0.567308 0.943396
7 NAG GAL SIA SIA 0.561905 0.943396
8 MNA 0.558442 0.849057
9 2FG SIA 0.543478 0.890909
10 SIA SIA 0.516484 0.888889
11 NAG GAL NAG GAL SIA 0.513043 0.943396
12 SLB SIA SIA SIA 0.51087 0.888889
13 SLB SIA SIA SIA SIA 0.51087 0.888889
14 SLB SIA SIA 0.51087 0.888889
15 SIA SIA SIA SIA SIA SIA SIA 0.51087 0.888889
16 GAL SIA NGA GAL 0.509259 0.943396
17 BGC GAL NAG GAL SIA 0.508621 0.943396
18 NAG GAL 5N6 0.504587 0.925926
19 GAL SIA SIA 0.5 0.907407
20 A2G GAL SIA 0.495146 0.924528
21 NAG GAL SIA 0.490385 0.924528
22 GAL SIA NGA 0.485714 0.924528
23 SIA SIA SIA 0.484536 0.888889
24 GAL 5N6 0.474747 0.924528
25 NGS GAL SIA 0.473214 0.731343
26 SIA GAL NGA GAL 0.468468 0.924528
27 GAL NGA GAL SIA 0.468468 0.924528
28 GAL SIA NGA GAL SIA 0.468468 0.924528
29 NAG FUC GAL SIA 0.464912 0.924528
30 NAG 2FG SIA 0.462963 0.859649
31 SIA 0.4625 0.86
32 SLB 0.4625 0.86
33 MBG NGC 0.454545 0.90566
34 NGA GAL SIA 0.454545 0.90566
35 CNP 0.453488 0.796296
36 MAG FUC GAL SIA 0.452174 0.888889
37 NGS FUC GLA SIA 0.45082 0.731343
38 WIA SIA 0.44898 0.892857
39 MN0 0.447059 0.849057
40 NAG GAL NGC 0.446429 0.924528
41 GAL NAG FUC GAL SIA 0.441667 0.924528
42 BGC GAL SIA NAG 0.435897 0.924528
43 BGC GAL SIA NGA GAL SIA 0.433333 0.924528
44 BGC GAL SIA SIA 0.432203 0.907407
45 BGC GAL GLA NGA GAL SIA 0.429752 0.924528
46 BGC GAL SIA NGA GAL 0.429752 0.924528
47 SID 0.426966 0.781818
48 C5P SIA 0.425 0.662162
49 MUS 0.423077 0.793103
50 GAL SIA NGA GAL SIA SIA 0.419355 0.907407
51 NXD 0.417582 0.789474
52 GAL NGA GAL SIA SIA 0.416 0.907407
53 C4W NAG FUC BMA MAN NAG GAL SIA 0.414286 0.819672
54 423 0.407407 0.636364
55 6KL 0.406977 0.77193
56 GLY PRO ALA THR PRO ALA PRO A2G SIA 0.406897 0.724638
57 NGA POL GAL NGC AZI 0.406504 0.753846
58 GLC GAL NGC 0.401786 0.923077
59 PH5 0.4 0.888889
60 425 0.4 0.636364
Similar Ligands (3D)
Ligand no: 1; Ligand: GAL SIA; Similar ligands found: 1
No: Ligand Similarity coefficient
1 SIA GAL 0.9514
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4YZ5; Ligand: DAN; 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: 4yz5.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4YZ5; Ligand: GLC GAL SIA; Similar sites found with APoc: 1
This union binding pocket(no: 2) in the query (biounit: 4yz5.bio2) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 2V73 SIA 23.5602
Pocket No.: 3; Query (leader) PDB : 4YZ5; Ligand: DAN; 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: 4yz5.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
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