Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 B:806;
B:803;
A:1004;
B:804;
A:1003;
A:1005;
A:1006;
B:805;
A:1007;
B:807;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
DAN A:1002;
B:802;
Valid;
Valid;
none;
none;
submit data
291.255 C11 H17 N O8 CC(=O...
GLC GAL SIA C:1;
D:1;
Valid;
Valid;
Atoms found LESS than expected: % Diff = 0.256;
Atoms found LESS than expected: % Diff = 0.256;
Kd = 1.48 mM
n/a n/a
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: DAN; Similar ligands found: 13
No: Ligand ECFP6 Tc MDL keys Tc
1 DAN 1 1
2 9AM 0.767857 0.913043
3 GC9 0.754386 0.933333
4 4AM 0.661017 0.913043
5 ZMR 0.615385 0.792453
6 KFN 0.542373 0.704545
7 49A 0.507692 0.87234
8 0HX 0.454545 0.75
9 RP6 0.452055 0.934783
10 LNV 0.434211 0.701754
11 FSI 0.408451 0.82
12 SLB 0.4 0.911111
13 SIA 0.4 0.911111
Ligand no: 2; Ligand: GLC GAL SIA; Similar ligands found: 0
No: Ligand ECFP6 Tc MDL keys Tc
Similar Ligands (3D)
Ligand no: 1; Ligand: DAN; Similar ligands found: 52
No: Ligand Similarity coefficient
1 DF4 0.9792
2 EQP 0.9783
3 E3M 0.9765
4 G28 0.9670
5 AXP 0.9657
6 NGE 0.9527
7 SFJ 0.9483
8 NGC 0.9350
9 2H8 0.9236
10 MNA 0.9230
11 9GW 0.9201
12 G39 0.9193
13 ST4 0.9184
14 42D 0.9176
15 ST5 0.9150
16 9GT 0.9105
17 SIA CMO 0.9051
18 18D 0.9030
19 MN0 0.9010
20 GOH 0.9001
21 9GQ 0.8971
22 9GN 0.8954
23 ST6 0.8953
24 SKD 0.8936
25 R2D 0.8931
26 9GZ 0.8929
27 5M8 0.8848
28 NIM 0.8848
29 NG1 0.8783
30 KDM 0.8755
31 KB8 0.8750
32 GYG 0.8720
33 FID 0.8714
34 FIR 0.8704
35 A0O 0.8700
36 CNP 0.8698
37 KDN 0.8670
38 3YW 0.8654
39 JT2 0.8647
40 3E2 0.8643
41 JUO 0.8627
42 ST1 0.8622
43 FIS 0.8610
44 G20 0.8608
45 U2P 0.8604
46 0L9 0.8587
47 53Q 0.8567
48 3N4 0.8564
49 GNT 0.8564
50 ET 0.8550
51 KLB 0.8543
52 SNG 0.8532
Ligand no: 2; Ligand: GLC GAL SIA; Similar ligands found: 9
No: Ligand Similarity coefficient
1 GLC GAL SIA 1.0000
2 BGC GAL SIA 0.9887
3 NAG GAL SIA 0.9303
4 NAG 2FG SIA 0.9284
5 GLC GAL NGC 0.9282
6 GAL BGC SIA 0.9156
7 NGA GAL SIA 0.8915
8 NAG GAL NGC 0.8628
9 A2G GAL SIA 0.8614
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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