Receptor
PDB id Resolution Class Description Source Keywords
4YZ4 2.15 Å EC: 3.2.1.18 CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE NANC, IN COMPL ACETYLNEURAMINIC ACID. 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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 B:1006;
B:1007;
A:1004;
B:1003;
A:1003;
B:1002;
A:1005;
A:1002;
A:1006;
A:1007;
B:1005;
B:1004;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
96.063 O4 S [O-]S...
SIA A:1001;
B:1001;
 Valid;
Valid;
 none;
none;
 submit data
309.27 C11 H19 N O9 CC(=O...
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: SIA; Similar ligands found: 38
No: Ligand ECFP6 Tc MDL keys Tc
1 SIA 1 1
2 SLB 1 1
3 42D 0.758621 0.875
4 18D 0.758621 0.955556
5 NGE 0.754386 0.933333
6 NGC 0.754386 0.933333
7 MNA 0.629032 0.895833
8 79J 0.615385 0.934783
9 SIA CMO 0.59375 0.877551
10 CNP 0.58209 0.875
11 KDM 0.568965 0.72093
12 KDN 0.568965 0.72093
13 SIA SIA 0.565789 0.826923
14 SLB SIA SIA SIA SIA 0.558442 0.826923
15 SLB SIA SIA SIA 0.558442 0.826923
16 SLB SIA SIA 0.558442 0.826923
17 SIA SIA SIA SIA SIA SIA SIA 0.558442 0.826923
18 FSI 0.515152 0.895833
19 SFJ 0.5 0.875
20 6KL 0.5 0.807692
21 MN0 0.485714 0.895833
22 EQP 0.470588 0.788462
23 AXP 0.470588 0.788462
24 GAL SIA 0.4625 0.86
25 SID 0.459459 0.82
26 SIA SIA SIA 0.453488 0.826923
27 MUS 0.449438 0.796296
28 NXD 0.447368 0.792453
29 WIA SIA 0.447059 0.767857
30 2FG SIA 0.447059 0.796296
31 KDO 0.435484 0.704545
32 NAG SIA 0.430233 0.781818
33 BND 0.416667 0.807692
34 SKD 0.414286 0.875
35 GAL SIA SIA 0.410526 0.811321
36 E3M 0.402778 0.606061
37 4AM 0.4 0.833333
38 DAN 0.4 0.911111
Similar Ligands (3D)
Ligand no: 1; Ligand: SIA; Similar ligands found: 27
No: Ligand Similarity coefficient
1 49A 0.9738
2 9AM 0.9671
3 DF4 0.9637
4 G28 0.9369
5 GC9 0.9014
6 G39 0.8962
7 9GW 0.8947
8 0HX 0.8920
9 ST5 0.8919
10 9GT 0.8895
11 K99 0.8872
12 ZMR 0.8860
13 2H8 0.8805
14 ST4 0.8777
15 R2D 0.8751
16 5M8 0.8749
17 9GN 0.8727
18 9GQ 0.8684
19 NG1 0.8662
20 KFN 0.8658
21 9GZ 0.8646
22 ST6 0.8636
23 LNV 0.8630
24 FID 0.8627
25 HBQ 0.8617
26 GYG 0.8600
27 RP6 0.8554
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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