Receptor
PDB id Resolution Class Description Source Keywords
2JKB 1.54 Å EC: 3.2.1.18 CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE NANB IN COMPLEX WITH 2,7-ANHYDRO-NEU5AC STREPTOCOCCUS PNEUMONIAE INTRAMOLECULAR TRANS-SIALIDASE LYASE GLYCOSIDASE NEURAMINIDASE
Ref.: STRUCTURAL AND FUNCTIONAL STUDIES OF STREPTOCOCCUS PNEUMONIAE NEURAMINIDASE B: AN INTRAMOLECULAR TRANS-SIALIDASE. FEBS LETT. V. 582 3348 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:1699;
A:1700;
A:1701;
A:1702;
A:1703;
A:1704;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
SKD A:1698;
 Valid;
 none;
 submit data
291.255 C11 H17 N O8 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2VW1 2.39 Å EC: 3.2.1.18 CRYSTAL STRUCTURE OF THE NANB SIALIDASE FROM STREPTOCOCCUS P STREPTOCOCCUS PNEUMONIAE HYDROLASE SIALIDASE NEURAMINIDASE VIRULENCE FACTOR DRUG
Ref.: CRYSTAL STRUCTURE OF THE NANB SIALIDASE FROM STREPT PNEUMONIAE J.MOL.BIOL. V. 384 436 2008
Members (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 30 families.
1 4FPE - 0H9 C10 H15 N O4 S COc1ccc(cc....
2 4FPH - 0V7 C9 H12 F N O3 S c1cc(cc(c1....
3 2JKB - SKD C11 H17 N O8 CC(=O)N[C@....
4 4FPF ic50 = 38.9 uM JKK C9 H12 Cl N O3 S c1cc(cc(c1....
5 4FOQ - TAU C2 H7 N O3 S C(CS(=O)(=....
6 4FPC - MFY C9 H12 Cl N O3 S c1cc(ccc1C....
7 4FOY - D53 C9 H13 N O3 S c1ccc(cc1)....
8 4FPL - 7HV C9 H11 Cl2 N O3 S c1cc(c(cc1....
9 4FOW - A20 C3 H9 N O3 S C(CN)CS(=O....
10 4FPJ - D8I C10 H15 N O4 S COc1cccc(c....
11 4FPK ic50 = 57.4 uM IJ1 C10 H15 N O3 S Cc1cccc(c1....
12 4FQ4 - IJ4 C10 H14 F N O3 S Cc1cc(ccc1....
13 4FPY - 0V8 C9 H12 Br N O3 S c1cc(cc(c1....
14 4FP2 - IJ6 C9 H19 N O3 S C1CCC(CC1)....
15 2VW1 Ki = 0.3 mM DAN C11 H17 N O8 CC(=O)N[C@....
70% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 24 families.
1 4FPE - 0H9 C10 H15 N O4 S COc1ccc(cc....
2 4FPH - 0V7 C9 H12 F N O3 S c1cc(cc(c1....
3 2JKB - SKD C11 H17 N O8 CC(=O)N[C@....
4 4FPF ic50 = 38.9 uM JKK C9 H12 Cl N O3 S c1cc(cc(c1....
5 4FOQ - TAU C2 H7 N O3 S C(CS(=O)(=....
6 4FPC - MFY C9 H12 Cl N O3 S c1cc(ccc1C....
7 4FOY - D53 C9 H13 N O3 S c1ccc(cc1)....
8 4FPL - 7HV C9 H11 Cl2 N O3 S c1cc(c(cc1....
9 4FOW - A20 C3 H9 N O3 S C(CN)CS(=O....
10 4FPJ - D8I C10 H15 N O4 S COc1cccc(c....
11 4FPK ic50 = 57.4 uM IJ1 C10 H15 N O3 S Cc1cccc(c1....
12 4FQ4 - IJ4 C10 H14 F N O3 S Cc1cc(ccc1....
13 4FPY - 0V8 C9 H12 Br N O3 S c1cc(cc(c1....
14 4FP2 - IJ6 C9 H19 N O3 S C1CCC(CC1)....
15 2VW1 Ki = 0.3 mM DAN C11 H17 N O8 CC(=O)N[C@....
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: SKD; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 SKD 1 1
2 SIA 0.414286 0.875
3 SLB 0.414286 0.875
4 CNP 0.407895 0.773585
Similar Ligands (3D)
Ligand no: 1; Ligand: SKD; Similar ligands found: 4
No: Ligand Similarity coefficient
1 DAN 0.8936
2 G39 0.8797
3 0HX 0.8679
4 372 0.8550
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2VW1; 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: 2vw1.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
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