Receptor
PDB id Resolution Class Description Source Keywords
6GVR 1.85 Å NON-ENZYME: BINDING TAILSPIKE PROTEIN MUTANT E372Q (DELTA N471/S472) OF E. COLI BACTERIOPHAGE HK620 IN COMPLEX WITH PENTASACCHARIDE SALMONELLA PHAGE HK620 BETA HELIX PROTEIN-CARBOHYDRATE COMPLEX PECTIN LYASE FOLDPROTEIN
Ref.: SOLVENT NETWORKS TUNE THERMODYNAMICS OF OLIGOSACCHA COMPLEX FORMATION IN AN EXTENDED PROTEIN BINDING SI J. AM. CHEM. SOC. V. 140 10447 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FMT A:1008;
A:1009;
A:1007;
A:1010;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
46.025 C H2 O2 C(=O)...
TRS A:1006;
 Invalid;
 none;
 submit data
122.143 C4 H12 N O3 C(C(C...
NA A:1012;
A:1011;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
22.99 Na [Na+]
NDG GLA NAG GLC RAM B:1;
 Valid;
 none;
 submit data
894.827 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: NDG GLA NAG GLC RAM; Similar ligands found: 95
No: Ligand ECFP6 Tc MDL keys Tc
1 NDG NAG GLA NAG GLC RAM 1 1
2 NDG GLA NAG GLC RAM 1 1
3 NDG GLA GLC NAG GLC RAM 0.90625 1
4 1GN ACY GAL 1GN BGC ACY GAL BGC 0.637255 0.979592
5 A2G NAG 0.588889 0.979592
6 NAG GAL FUC FUC A2G 0.570093 1
7 A2G GAL NAG 0.56 0.979592
8 NAG FUC GAL FUC A2G 0.555556 1
9 BGC FUC GAL NAG 0.54717 0.938776
10 C4W NAG FUC BMA MAN NAG 0.545455 0.942308
11 GAL FUC A2G 0.545455 0.938776
12 NAG FUC 0.543478 0.918367
13 C4W NAG FUC BMA MAN NAG GAL 0.532787 0.844828
14 C4W NAG FUC BMA MAN MAN NAG GAL NAG 0.530769 0.844828
15 A2G GAL 0.521739 0.918367
16 C4W NAG FUC BMA MAN MAN NAG 0.51938 0.942308
17 NAG GAL FUC 0.514852 0.938776
18 BGC FUC GAL FUC A2G 0.513761 0.959184
19 NAG BDP NAG BDP NAG BDP NAG 0.513761 0.98
20 NAG FUC GAL 0.51 0.938776
21 NDG BMA MAN MAN NAG MAN MAN 0.504132 0.979592
22 C4W NAG FUC BMA MAN MAN NAG NAG 0.503876 0.942308
23 NAG GAL GLC NAG GLC RAM 0.5 0.979592
24 BGC GAL FUC A2G 0.495495 0.938776
25 GLC GAL NAG GAL FUC A2G 0.491667 1
26 C4W NAG FUC BMA MAN 0.491667 0.942308
27 C4W NAG FUC BMA 0.491228 0.942308
28 YZ0 MAN MAN NAG MAN 0.482456 0.92
29 BGC FUC GAL NAG GAL 0.478261 0.938776
30 NAG NAG MAN MAN MAN 0.478261 0.979592
31 NAG NAG FUL BMA MAN MAN NAG GAL 0.476923 0.924528
32 NDG BMA MAN MAN NAG GAL NAG 0.471545 1
33 NAG NAG BMA MAN MAN NAG GAL NAG 0.467742 1
34 BMA Z4Y NAG 0.463636 0.9
35 NAG GAL FUC FUC 0.462264 0.959184
36 GAL NGA A2G 0.460784 0.979592
37 HSH A2G FUC 0.460177 0.824561
38 BMA MAN NAG 0.457143 0.918367
39 MAG SGA FUC 0.455357 0.723077
40 GAL NAG FUC GAL 0.454545 0.938776
41 GAL NAG 0.454545 0.918367
42 NDG FUC GAL FUC 0.448598 0.959184
43 BMA MAN MAN NAG GAL NAG 0.446281 0.979592
44 BGC GAL GLA NGA 0.445455 0.918367
45 BGC GAL NGA 0.442308 0.918367
46 BGC GAL NAG 0.439252 0.918367
47 NAG GAL NAG 0.439252 0.979592
48 GYP GZL NAG 0.434783 0.867925
49 MAN MAN MAN NAG NAG 0.433628 0.979592
50 AMU NAG 0.431193 0.98
51 NAG BMA MAN MAN NAG GAL NAG GAL 0.430894 1
52 GDL NAG 0.43 0.979592
53 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.429752 0.918367
54 C4W NAG FUC BMA MAN MAN NAG GAL SIA NAG 0.429448 0.803279
55 BGC GAL NAG NAG GAL GAL 0.428571 0.979592
56 NAG BMA MAN MAN MAN MAN 0.42735 0.918367
57 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.426357 0.979592
58 GLC GAL NAG GAL FUC GLA 0.42623 0.938776
59 EAG RAM RAM GLC RAM NAG RAM RAM GLC RAM 0.425 0.98
60 BGC GAL NAG GAL FUC 0.420168 0.938776
61 C4W NAG FUC BMA MAN NAG GAL SIA 0.419355 0.803279
62 BGC GAL NAG GAL 0.418182 0.918367
63 NAG BDP 0.417476 0.92
64 NGA THR GAL NAG 0.416667 0.960784
65 GLA NAG GAL FUC 0.415929 0.938776
66 BGC GAL GLA NGA GAL 0.415929 0.918367
67 GLC BGC FUC GAL 0.415842 0.693878
68 BGC FUC GAL 0.415842 0.693878
69 NAG BMA MAN MAN MAN MAN MAN MAN MAN MAN 0.414634 0.918367
70 GAL NAG GAL FUC FUC 0.413793 0.959184
71 MMA MAN NAG MAN NAG NAG 0.413793 0.98
72 NAG NAG NAG NAG NAG 0.413462 1
73 NDG NAG NAG NAG NAG 0.413462 1
74 NAG NAG NAG NAG NAG NAG NAG NAG 0.413462 1
75 NAG NAG NAG NAG NAG NAG 0.413462 1
76 BGC GAL NGA GAL 0.412844 0.918367
77 NAG GAL FUC GLA 0.412281 0.938776
78 BMA MAN MAN MAN 0.411215 0.7
79 MAN NAG 0.41 0.918367
80 NAG NAG BMA MAN MAN MAN MAN 0.409091 0.90566
81 NAG GAL BGC GAL 0.409091 0.918367
82 A2G THR GAL NAG 0.408333 0.960784
83 YZ0 MAN Z4Y NAG MAN 0.407692 0.867925
84 BGC GAL NAG GAL FUC FUC 0.406504 0.959184
85 BGC BGC BGC BGC 0.40566 0.673469
86 NAG NAG BMA MAN MAN NAG NAG 0.40458 0.924528
87 NAG NAG BMA MAN NAG 0.403361 1
88 MBG NAG 0.401961 0.92
89 3QL 0.401869 0.90566
90 NAG GAL NAG GAL NAG GAL 0.401786 1
91 NAG GAL NAG GAL 0.401786 0.979592
92 GAL NAG GAL NAG GAL 0.401786 0.979592
93 GLA NAG FUC GAL 0.401709 0.92
94 NM9 NAG 0.4 0.960784
95 NAG MEE FUC 0.4 0.867925
Similar Ligands (3D)
Ligand no: 1; Ligand: NDG GLA 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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