Receptor
PDB id Resolution Class Description Source Keywords
2VJJ 1.59 Å NON-ENZYME: BINDING TAILSPIKE PROTEIN OF E.COLI BACTERIOPHAGE HK620 IN COMPLEX W HEXASACCHARIDE SALMONELLA PHAGE HK620 VIRAL PROTEIN ENDO-N-ACETYLGLUCOSAMINIDASE VIRAL ADHESION RIGHT-HANDED PARALLEL BETA-HELIX HYDROLASE TAILSPIKE
Ref.: CRYSTAL STRUCTURE OF ESCHERICHIA COLI PHAGE HK620 T PODOVIRAL TAILSPIKE ENDOGLYCOSIDASE MODULES ARE EVOLUTIONARILY RELATED. MOL.MICROBIOL. V. 69 303 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:710;
 Part of Protein;
 none;
 submit data
40.078 Ca [Ca+2...
CL A:711;
 Invalid;
 none;
 submit data
35.453 Cl [Cl-]
GOL A:713;
A:714;
A:715;
A:716;
A:717;
A:718;
A:719;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
K A:712;
 Invalid;
 none;
 submit data
39.098 K [K+]
NAG GAL GLC NAG GLC RAM B:1;
 Valid;
 none;
 submit data
1061 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6G0X 1.41 Å NON-ENZYME: BINDING TAILSPIKE PROTEIN OF E. COLI BACTERIOPHAGE HK620 IN COMPLEX PENTASACCHARIDE SALMONELLA PHAGE HK620 BETA HELIX PROTEIN-CARBOHYDRATE COMPLEX PECTIN LYASE FOLDHYDROLASE
Ref.: SOLVENT NETWORKS TUNE THERMODYNAMICS OF OLIGOSACCHA COMPLEX FORMATION IN AN EXTENDED PROTEIN BINDING SI J. AM. CHEM. SOC. V. 140 10447 2018
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 552 families.
1 6G0X - NDG NAG GLA NAG GLC RAM n/a n/a
2 6GVR - NDG GLA NAG GLC RAM n/a n/a
3 6GVP - NDG GLA GLC NAG GLC RAM n/a n/a
4 2VJJ - NAG GAL GLC NAG GLC RAM n/a n/a
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 426 families.
1 6G0X - NDG NAG GLA NAG GLC RAM n/a n/a
2 6GVR - NDG GLA NAG GLC RAM n/a n/a
3 6GVP - NDG GLA GLC NAG GLC RAM n/a n/a
4 2VJJ - NAG GAL GLC NAG GLC RAM n/a n/a
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 322 families.
1 6G0X - NDG NAG GLA NAG GLC RAM n/a n/a
2 6GVR - NDG GLA NAG GLC RAM n/a n/a
3 6GVP - NDG GLA GLC NAG GLC RAM n/a n/a
4 2VJJ - NAG GAL GLC NAG GLC RAM n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: NAG GAL GLC NAG GLC RAM; Similar ligands found: 61
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG GAL GLC NAG GLC RAM 1 1
2 A2G NAG 0.689189 1
3 A2G GAL 0.584416 0.9375
4 NAG BDP NAG BDP NAG BDP NAG 0.580645 0.96
5 NAG GC4 0.534884 0.9
6 NAG FUC 0.530864 0.9375
7 GAL NGA A2G 0.523256 1
8 A2G GAL NAG 0.516484 1
9 NAG BDP 0.505882 0.9
10 NAG GAL FUC 0.5 0.958333
11 NDG GLA NAG GLC RAM 0.5 0.979592
12 NDG NAG GLA NAG GLC RAM 0.5 0.979592
13 GDL NAG 0.488095 1
14 BMA MAN NAG 0.483516 0.9375
15 GAL FUC A2G 0.483516 0.958333
16 MAN NAG 0.481928 0.9375
17 GAL NGA 0.476744 0.88
18 1GN ACY GAL 1GN BGC ACY GAL BGC 0.475248 1
19 AMU NAG 0.468085 0.96
20 NAG NAG NAG NAG NAG NAG NAG NAG 0.465909 0.979592
21 NDG NAG NAG NAG NAG 0.465909 0.979592
22 NAG NAG NAG NAG NAG NAG 0.465909 0.979592
23 NAG NAG NAG NAG NAG 0.465909 0.979592
24 NAG GAL NAG 0.462366 1
25 NDG NAG 0.45977 0.979592
26 NAG GAL FUC FUC A2G 0.456311 0.979592
27 NAG FUC GAL FUC A2G 0.456311 0.979592
28 MBG NAG 0.453488 0.938776
29 BGC GAL NGA 0.450549 0.9375
30 3QL 0.450549 0.923077
31 NDG GLA GLC NAG GLC RAM 0.447368 0.979592
32 BGC GAL NAG 0.446809 0.9375
33 NAG GAD 0.44086 0.865385
34 AH0 NAG 0.4375 0.888889
35 MBG A2G 0.431818 0.938776
36 MAN MAN NAG 0.431579 0.9
37 BGC FUC GAL NAG 0.431373 0.958333
38 BGC FUC GAL FUC A2G 0.427184 0.938776
39 BGC GAL GLA NGA 0.424242 0.9375
40 NAG BDP NAG BDP 0.422018 0.90566
41 2F8 0.417722 0.877551
42 MAG 0.417722 0.877551
43 NAG NAG NAG 0.416667 0.90566
44 NAG NAG NAG NAG 0.416667 0.90566
45 NAG NAG NAG NAG NAG NAG NAG 0.416667 0.90566
46 Z4S NAG NAG 0.414141 0.90566
47 MAN MAN MAN NAG NAG 0.411765 1
48 MMA MAN NAG 0.410526 0.938776
49 GAL NAG GAL 0.410526 0.9375
50 BGC GAL FUC A2G 0.409524 0.958333
51 NAG BDP NAG BDP NAG BDP 0.40708 0.923077
52 NAG NGO 0.40625 0.87037
53 GLA NAG GAL FUC 0.405941 0.958333
54 NAG NAG BMA MAN NAG 0.40566 0.979592
55 MGC GAL 0.402299 0.938776
56 BGC GAL NGA GAL 0.402062 0.9375
57 NM9 NAG 0.402062 0.941176
58 LEC NGA 0.401961 0.75
59 BMA Z4Y NAG 0.401961 0.918367
60 AMU 0.4 0.895833
61 NAG FUC GAL 0.4 0.958333
Similar Ligands (3D)
Ligand no: 1; Ligand: NAG GAL GLC NAG GLC RAM; 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 : 6G0X; Ligand: NDG NAG GLA NAG GLC RAM; 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: 6g0x.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
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