Receptor
PDB id Resolution Class Description Source Keywords
5eq3 2 Å NON-ENZYME: BINDING CRYSTAL STRUCTURE OF THE SRPA ADHESIN FROM STREPTOCOCCUS SAN WITH A SIALYL GALACTOSE DISACCHARIDE BOUND STREPTOCOCCUS SANGUINIS BACTERIAL ADHESIN LECTIN IMMUNOGLOBULIN FOLD SERINE-RICH SUGAR BINDING PROTEIN
Ref.: STRUCTURAL BASIS FOR SIALOGLYCAN BINDING BY THE STREPTOCOCCUS SANGUINIS SRPA ADHESIN. J.BIOL.CHEM. V. 291 7230 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:504;
A:503;
B:503;
A:505;
B:502;
B:501;
B:504;
 Part of Protein;
Part of Protein;
Invalid;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
none;
none;
none;
 submit data
40.078 Ca [Ca+2...
NA B:505;
 Invalid;
 none;
 submit data
22.99 Na [Na+]
ACT B:506;
A:506;
A:507;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
59.044 C2 H3 O2 CC(=O...
MBG NGC C:1;
 Valid;
 none;
 submit data
500.43 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5KIQ 1.64 Å NON-ENZYME: BINDING SRPA WITH SIALYL LEWISX STREPTOCOCCUS SANGUINIS (STRAIN SK36) ADHESIN CARBOHYDRATE BINDING IG FOLD SUGAR BINDING PROTEIN
Ref.: STRUCTURES OF THE STREPTOCOCCUS SANGUINIS SRPA BIND REGION WITH HUMAN SIALOGLYCANS SUGGEST FEATURES OF PHYSIOLOGICAL LIGAND. BIOCHEMISTRY 2016
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 552 families.
1 5IJ2 - NAG GAL SIA n/a n/a
2 5IJ3 - A2G GAL SIA n/a n/a
3 5IJ1 - BGC GAL SIA n/a n/a
4 5KIQ - NAG FUC GAL SIA n/a n/a
5 5EQ3 - MBG NGC n/a n/a
6 5IIY - GAL SIA n/a n/a
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 426 families.
1 5IJ2 - NAG GAL SIA n/a n/a
2 5IJ3 - A2G GAL SIA n/a n/a
3 5IJ1 - BGC GAL SIA n/a n/a
4 5KIQ - NAG FUC GAL SIA n/a n/a
5 5EQ3 - MBG NGC n/a n/a
6 5IIY - GAL SIA n/a n/a
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 322 families.
1 5IJ2 - NAG GAL SIA n/a n/a
2 5IJ3 - A2G GAL SIA n/a n/a
3 5IJ1 - BGC GAL SIA n/a n/a
4 5KIQ - NAG FUC GAL SIA n/a n/a
5 5EQ3 - MBG NGC n/a n/a
6 5IIY - GAL SIA n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: MBG NGC; Similar ligands found: 56
No: Ligand ECFP6 Tc MDL keys Tc
1 MBG NGC 1 1
2 GLC GAL NGC 0.71875 0.942308
3 NAG GAL NGC 0.7 0.943396
4 NGA POL GAL NGC AZI 0.630631 0.769231
5 A2G GAL SIA 0.62 0.907407
6 NAG GAL SIA 0.613861 0.907407
7 2FG SIA 0.612903 0.875
8 MAG FUC GAL SIA 0.590909 0.943396
9 NGA GAL SIA 0.584906 0.924528
10 GAL SIA NGA GAL SIA 0.568807 0.907407
11 GAL NGA GAL SIA 0.568807 0.907407
12 NDG GAL SIA SIA 0.563636 0.892857
13 NAG GAL SIA SIA 0.563636 0.890909
14 GAL SIA SIA 0.563107 0.890909
15 MN0 0.559524 0.903846
16 NGS GAL SIA 0.558559 0.720588
17 NAG 2FG SIA 0.551402 0.844828
18 NAG FUC GAL SIA 0.548673 0.907407
19 GAL SIA NGA 0.54717 0.907407
20 GAL 5N6 0.54 0.907407
21 BGC GAL SIA SIA 0.53913 0.890909
22 BGC GAL SIA NGA GAL SIA 0.525424 0.907407
23 BGC GAL GLA NGA GAL SIA 0.521008 0.907407
24 GAL NAG FUC GAL SIA 0.521008 0.907407
25 SIA GAL NGA GAL 0.513274 0.907407
26 GAL SIA NGA GAL 0.513274 0.890909
27 GAL SIA NGA GAL SIA SIA 0.508197 0.890909
28 BGC GAL SIA NAG 0.504274 0.907407
29 NGS FUC GLA SIA 0.504065 0.720588
30 GAL NGA GAL SIA SIA 0.504065 0.890909
31 SIA CMO 0.5 0.886792
32 NAG GAL PKM 0.495575 0.890909
33 BGC GAL SIA NGA GAL 0.483607 0.907407
34 Z3Q GAL 5N6 0.479339 0.793651
35 BGC 16C GAL SIA 0.470588 0.793651
36 BGC 18C GAL SIA 0.463768 0.793651
37 NGC 0.45977 0.862745
38 NGE 0.45977 0.862745
39 WIA SIA 0.456311 0.877193
40 GAL SIA 0.454545 0.90566
41 BGC GAL SIA NGA SIA 0.450382 0.890909
42 BGC GAL SIA NGA GAL FUC 0.443609 0.907407
43 BGC GAL SIA 0.438596 0.924528
44 MNA 0.438202 0.867925
45 GAL NAG GAL SIA 0.436975 0.890909
46 BGC CEQ GAL SLB NGA GAL SIA SIA 0.43662 0.793651
47 NAG GAL NAG GAL SIA 0.433071 0.890909
48 BGC GAL NAG GAL SIA 0.429688 0.890909
49 SIA SIA 0.417476 0.907407
50 SLB SIA SIA SIA SIA 0.413462 0.907407
51 SLB SIA SIA SIA 0.413462 0.907407
52 SLB SIA SIA 0.413462 0.907407
53 SIA SIA SIA SIA SIA SIA SIA 0.413462 0.907407
54 SIA SIA SIA 0.407407 0.907407
55 18D 0.402174 0.846154
56 NAG SIA 0.401869 0.859649
Similar Ligands (3D)
Ligand no: 1; Ligand: MBG NGC; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5KIQ; Ligand: NAG FUC GAL SIA; 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: 5kiq.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
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