Receptor
PDB id Resolution Class Description Source Keywords
5VMG 2.45 Å NON-ENZYME: OTHER INFLUENZA HEMAGGLUTININ H1 MUTANT DH1E IN COMPLEX WITH 6'SLN INFLUENZA A VIRUS (A/NEW_YORK/1/18(H1NORGANISM_TAXID: 88775 INFLUENZA HEMAGGLUTININ RECEPTOR VIRAL PROTEIN
Ref.: DETERMINANT OF RECEPTOR-PREFERENCE SWITCH IN INFLUE HEMAGGLUTININ. VIROLOGY V. 513 98 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAG C:1001;
A:1004;
C:1002;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
NAG NAG BMA G:1;
Invalid;
none;
submit data
570.545 n/a O=C(N...
NAG NAG J:1;
Invalid;
none;
submit data
408.404 n/a O=C(N...
NAG GAL SIA K:1;
Valid;
none;
submit data
673.598 n/a O=C(N...
GAL SIA I:1;
H:1;
Valid;
Valid;
Atoms found LESS than expected: % Diff = 0.031;
Atoms found LESS than expected: % Diff = 0.031;
submit data
454.405 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5VMC 2.15 Å NON-ENZYME: OTHER INFLUENZA HEMAGGLUTININ H1 MUTANT DH1 IN COMPLEX WITH 6'SLN INFLUENZA A VIRUS (STRAIN A/BREVIG MISSION/1/1918 H1N1) INFLUENZA HEMAGGLUTININ RECEPTOR VIRAL PROTEIN
Ref.: DETERMINANT OF RECEPTOR-PREFERENCE SWITCH IN INFLUE HEMAGGLUTININ. VIROLOGY V. 513 98 2017
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 5VMF Kd = 0.305 uM NAG GAL SIA n/a n/a
2 5VMC - NAG GAL SIA n/a n/a
3 5VMG - NAG GAL SIA n/a n/a
70% Homology Family (30)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 44 families.
1 1RVZ - NAG GAL SIA n/a n/a
2 1RVX - NAG GAL SIA n/a n/a
3 1RV0 - NDG C8 H15 N O6 CC(=O)N[C@....
4 1RVT - BGC GAL NAG GAL SIA n/a n/a
5 4BH3 Kd = 12 mM NAG GAL SIA n/a n/a
6 4CQW - NAG GAL SIA n/a n/a
7 4BH0 Kd = 21 mM GAL SIA n/a n/a
8 3ZNL - NGS FUC GLA SIA n/a n/a
9 1JSO - SIA C11 H19 N O9 CC(=O)N[C@....
10 3ZP2 - GAL SIA n/a n/a
11 6VMZ - R3P C15 H20 Cl2 N2 O CC(C)N1CCC....
12 4CQY - NAG GAL SIA n/a n/a
13 4BGX Kd = 17 mM GAL SIA n/a n/a
14 4CQR - GAL SIA n/a n/a
15 4BH4 Kd = 32 mM NAG GAL SIA n/a n/a
16 1JSN - NAG GAL SIA n/a n/a
17 4CQX - NAG GAL SIA n/a n/a
18 4BH1 Kd = 1.1 mM NAG GAL SIA n/a n/a
19 6CFG - EZ7 C28 H27 N9 O3 CC(=O)Nc1c....
20 4KDO - SIA C11 H19 N O9 CC(=O)N[C@....
21 3ZNM - NAG FUC GLA SIA n/a n/a
22 4KDN - SIA C11 H19 N O9 CC(=O)N[C@....
23 4CQU - GAL SIA n/a n/a
24 5AJM - NAG GAL SIA n/a n/a
25 3UBQ - NAG GAL SIA n/a n/a
26 3UBE - SIA C11 H19 N O9 CC(=O)N[C@....
27 3UBJ - GAL SIA n/a n/a
28 5VMF Kd = 0.305 uM NAG GAL SIA n/a n/a
29 5VMC - NAG GAL SIA n/a n/a
30 5VMG - NAG GAL SIA n/a n/a
50% Homology Family (78)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 36 families.
1 1RVZ - NAG GAL SIA n/a n/a
2 1RVX - NAG GAL SIA n/a n/a
3 1RV0 - NDG C8 H15 N O6 CC(=O)N[C@....
4 1RVT - BGC GAL NAG GAL SIA n/a n/a
5 4BH3 Kd = 12 mM NAG GAL SIA n/a n/a
6 4CQW - NAG GAL SIA n/a n/a
7 4BH0 Kd = 21 mM GAL SIA n/a n/a
8 3ZNL - NGS FUC GLA SIA n/a n/a
9 1JSO - SIA C11 H19 N O9 CC(=O)N[C@....
10 3ZP2 - GAL SIA n/a n/a
11 6VMZ - R3P C15 H20 Cl2 N2 O CC(C)N1CCC....
12 4CQY - NAG GAL SIA n/a n/a
13 4BGX Kd = 17 mM GAL SIA n/a n/a
14 4CQR - GAL SIA n/a n/a
15 4BH4 Kd = 32 mM NAG GAL SIA n/a n/a
16 1JSN - NAG GAL SIA n/a n/a
17 4CQX - NAG GAL SIA n/a n/a
18 4BH1 Kd = 1.1 mM NAG GAL SIA n/a n/a
19 6CFG - EZ7 C28 H27 N9 O3 CC(=O)Nc1c....
20 4KDO - SIA C11 H19 N O9 CC(=O)N[C@....
21 3ZNM - NAG FUC GLA SIA n/a n/a
22 4KDN - SIA C11 H19 N O9 CC(=O)N[C@....
23 4CQU - GAL SIA n/a n/a
24 5AJM - NAG GAL SIA n/a n/a
25 6NSF - SIA C11 H19 N O9 CC(=O)N[C@....
26 6BKT - NAG GAL SIA n/a n/a
27 6AOS - NAG GAL SIA n/a n/a
28 6BKS - SIA C11 H19 N O9 CC(=O)N[C@....
29 6AOT - GAL SIA n/a n/a
30 6NSG - SIA C11 H19 N O9 CC(=O)N[C@....
31 6AOV - NAG GAL NAG GAL SIA n/a n/a
32 6BKR - NAG GAL SIA n/a n/a
33 3UBQ - NAG GAL SIA n/a n/a
34 3UBE - SIA C11 H19 N O9 CC(=O)N[C@....
35 3UBJ - GAL SIA n/a n/a
36 6TVB - NAG GAL SIA n/a n/a
37 6TXO - GAL SIA n/a n/a
38 4D00 - NAG GAL SIA n/a n/a
39 5TH1 - GAL SIA n/a n/a
40 6TVT - GAL SIA n/a n/a
41 6TVS - GAL SIA n/a n/a
42 4CYZ - NAG C8 H15 N O6 CC(=O)N[C@....
43 6TWI - NAG GAL SIA n/a n/a
44 6TVA - NAG GAL SIA n/a n/a
45 5TGU - NAG GAL SIA n/a n/a
46 4N62 - NGS GAL SIA n/a n/a
47 4BSH - GAL SIA n/a n/a
48 6IDB - NAG GAL SIA n/a n/a
49 4BSB - NAG GAL SIA n/a n/a
50 4LN8 - NAG SIA n/a n/a
51 4BSD - NAG GAL SIA n/a n/a
52 4LKK Kd = 0.33 uM GAL SIA n/a n/a
53 5T6S - 75U C22 H25 Br N2 O3 S CCOC(=O)c1....
54 1JSH - GAL SIA n/a n/a
55 1JSI - GLC GAL NAG GAL SIA n/a n/a
56 5XL7 - NAG GAL SIA n/a n/a
57 5XL6 - SIA C11 H19 N O9 CC(=O)N[C@....
58 5XLC - SIA C11 H19 N O9 CC(=O)N[C@....
59 5XL3 - SIA C11 H19 N O9 CC(=O)N[C@....
60 5XL4 - SIA C11 H19 N O9 CC(=O)N[C@....
61 5XLD - NAG GAL SIA n/a n/a
62 5VTY - GAL SIA n/a n/a
63 5VTR - SIA C11 H19 N O9 CC(=O)N[C@....
64 5VTV - GAL SIA n/a n/a
65 5VU4 - GAL SIA n/a n/a
66 4WE5 - NAG NAG BMA n/a n/a
67 6BKQ - NAG GAL SIA n/a n/a
68 5VTW - SIA C11 H19 N O9 CC(=O)N[C@....
69 3EYK - EYK C10 H14 O2 CC(C)(C)c1....
70 5VMF Kd = 0.305 uM NAG GAL SIA n/a n/a
71 5VMC - NAG GAL SIA n/a n/a
72 5VMG - NAG GAL SIA n/a n/a
73 4XKF - NAG GAL SIA n/a n/a
74 5BR6 - NAG GAL SIA n/a n/a
75 4XKG - SIA GAL n/a n/a
76 4XKE - NAG GAL SIA n/a n/a
77 5T0E - GAL SIA n/a n/a
78 5T0B - NAG GAL SIA n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: NAG GAL SIA; Similar ligands found: 74
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG GAL SIA 1 1
2 NAG GAL NGC 0.905263 0.962264
3 NGS GAL SIA 0.821782 0.787879
4 A2G GAL SIA 0.783505 1
5 NAG GAL PKM 0.782178 0.981132
6 GAL NGA GAL SIA 0.75 1
7 BGC GAL SIA SIA 0.724771 0.981132
8 NAG FUC GAL SIA 0.722222 1
9 NGA GAL SIA 0.721154 0.980769
10 GAL SIA NGA GAL SIA 0.716981 1
11 NAG GAL SIA SIA 0.71028 0.981132
12 GLC GAL NGC 0.708738 0.924528
13 BGC GAL SIA NGA GAL SIA 0.705357 1
14 BGC GAL GLA NGA GAL SIA 0.699115 1
15 NDG GAL SIA SIA 0.678899 0.945455
16 NAG GAL NAG GAL SIA 0.663793 0.981132
17 GAL NGA GAL SIA SIA 0.661017 0.981132
18 MAG FUC GAL SIA 0.660714 0.962264
19 GAL NAG FUC GAL SIA 0.655172 1
20 2FG SIA 0.642857 0.892857
21 BGC GAL SIA NGA GAL 0.641026 1
22 GAL SIA NGA GAL SIA SIA 0.638655 0.981132
23 NGS FUC GLA SIA 0.633333 0.787879
24 BGC GAL SIA NAG 0.626087 1
25 SIA GAL NGA GAL 0.625 1
26 NAG 2FG SIA 0.623853 0.928571
27 MBG NGC 0.613861 0.907407
28 NGA POL GAL NGC AZI 0.613445 0.784615
29 GAL SIA SIA 0.607477 0.981132
30 GAL SIA NGA 0.605505 1
31 NAG GAL 5N6 0.605263 0.962963
32 GAL 5N6 0.601942 0.962264
33 GAL SIA NGA GAL 0.596491 0.981132
34 BGC 16C GAL SIA 0.586466 0.83871
35 BGC GAL SIA NGA GAL FUC 0.585938 1
36 BGC GAL NAG GAL SIA 0.577236 0.981132
37 BGC GAL SIA 0.576577 0.943396
38 Z3Q GAL 5N6 0.570248 0.83871
39 BGC 18C GAL SIA 0.566176 0.83871
40 BGC GAL SIA NGA SIA 0.55814 0.981132
41 BGC CEQ GAL SLB NGA GAL SIA SIA 0.546763 0.83871
42 GAL NAG GAL SIA 0.516667 0.981132
43 SIA CMO 0.505376 0.87037
44 GAL SIA 0.490385 0.924528
45 NAG GAL GAL 0.489796 0.865385
46 CEQ BGC NGA GAL SIA SIA 0.486111 0.8
47 NAG GAL 0.473118 0.865385
48 NAG GAL NAG GAL NAG GAL 0.466667 0.942308
49 NAG GAL NAG GAL 0.466667 0.923077
50 NAG GAL NAG 0.466019 0.923077
51 BGC 18C GAL SIA NGA GAL 0.464968 0.83871
52 MNA 0.447917 0.851852
53 SIA SIA 0.440367 0.962264
54 NAG SIA 0.4375 0.910714
55 SLB SIA SIA SIA SIA 0.436364 0.962264
56 SLB SIA SIA 0.436364 0.962264
57 SLB SIA SIA SIA 0.436364 0.962264
58 SIA SIA SIA SIA SIA SIA SIA 0.436364 0.962264
59 SIA SIA SIA 0.429825 0.962264
60 NAG NAG BMA MAN NAG 0.426087 0.942308
61 NAG G6S 0.419048 0.727273
62 NAG GAL UNU 0.418182 0.90566
63 GDL NAG 0.414141 0.923077
64 WIA SIA 0.412281 0.894737
65 NDG NAG NAG NAG NAG 0.411765 0.942308
66 NAG NAG NAG NAG NAG NAG NAG NAG 0.411765 0.942308
67 NAG NAG NAG NAG NAG 0.411765 0.942308
68 NAG NAG NAG NAG NAG NAG 0.411765 0.942308
69 C4W NAG FUC BMA MAN NAG GAL SIA 0.409091 0.852459
70 NAG NAG 0.407767 0.942308
71 NAG NAG NAG TMX 0.407407 0.864407
72 NAG NAG MAN MAN MAN 0.403361 0.923077
73 C4W NAG FUC BMA MAN MAN NAG GAL SIA NAG 0.402439 0.852459
74 NAG BMA MAN MAN MAN MAN 0.401709 0.865385
Ligand no: 2; Ligand: GAL SIA; Similar ligands found: 60
No: Ligand ECFP6 Tc MDL keys Tc
1 GAL SIA 1 1
2 NAG SIA 0.710843 0.909091
3 SIA CMO 0.635135 0.867925
4 BGC GAL SIA 0.608247 0.980392
5 NDG GAL SIA SIA 0.592233 0.909091
6 GAL NAG GAL SIA 0.567308 0.943396
7 NAG GAL SIA SIA 0.561905 0.943396
8 MNA 0.558442 0.849057
9 2FG SIA 0.543478 0.890909
10 SIA SIA 0.516484 0.888889
11 NAG GAL NAG GAL SIA 0.513043 0.943396
12 SLB SIA SIA SIA 0.51087 0.888889
13 SLB SIA SIA SIA SIA 0.51087 0.888889
14 SLB SIA SIA 0.51087 0.888889
15 SIA SIA SIA SIA SIA SIA SIA 0.51087 0.888889
16 GAL SIA NGA GAL 0.509259 0.943396
17 BGC GAL NAG GAL SIA 0.508621 0.943396
18 NAG GAL 5N6 0.504587 0.925926
19 GAL SIA SIA 0.5 0.907407
20 A2G GAL SIA 0.495146 0.924528
21 NAG GAL SIA 0.490385 0.924528
22 GAL SIA NGA 0.485714 0.924528
23 SIA SIA SIA 0.484536 0.888889
24 GAL 5N6 0.474747 0.924528
25 NGS GAL SIA 0.473214 0.731343
26 SIA GAL NGA GAL 0.468468 0.924528
27 GAL NGA GAL SIA 0.468468 0.924528
28 GAL SIA NGA GAL SIA 0.468468 0.924528
29 NAG FUC GAL SIA 0.464912 0.924528
30 NAG 2FG SIA 0.462963 0.859649
31 SIA 0.4625 0.86
32 SLB 0.4625 0.86
33 MBG NGC 0.454545 0.90566
34 NGA GAL SIA 0.454545 0.90566
35 CNP 0.453488 0.796296
36 MAG FUC GAL SIA 0.452174 0.888889
37 NGS FUC GLA SIA 0.45082 0.731343
38 WIA SIA 0.44898 0.892857
39 MN0 0.447059 0.849057
40 NAG GAL NGC 0.446429 0.924528
41 GAL NAG FUC GAL SIA 0.441667 0.924528
42 BGC GAL SIA NAG 0.435897 0.924528
43 BGC GAL SIA NGA GAL SIA 0.433333 0.924528
44 BGC GAL SIA SIA 0.432203 0.907407
45 BGC GAL GLA NGA GAL SIA 0.429752 0.924528
46 BGC GAL SIA NGA GAL 0.429752 0.924528
47 SID 0.426966 0.781818
48 C5P SIA 0.425 0.662162
49 MUS 0.423077 0.793103
50 GAL SIA NGA GAL SIA SIA 0.419355 0.907407
51 NXD 0.417582 0.789474
52 GAL NGA GAL SIA SIA 0.416 0.907407
53 C4W NAG FUC BMA MAN NAG GAL SIA 0.414286 0.819672
54 423 0.407407 0.636364
55 6KL 0.406977 0.77193
56 GLY PRO ALA THR PRO ALA PRO A2G SIA 0.406897 0.724638
57 NGA POL GAL NGC AZI 0.406504 0.753846
58 GLC GAL NGC 0.401786 0.923077
59 PH5 0.4 0.888889
60 425 0.4 0.636364
Similar Ligands (3D)
Ligand no: 1; Ligand: NAG GAL SIA; Similar ligands found: 2
No: Ligand Similarity coefficient
1 GLC GAL SIA 0.9303
2 GAL BGC SIA 0.8989
Ligand no: 2; Ligand: GAL SIA; Similar ligands found: 1
No: Ligand Similarity coefficient
1 SIA GAL 0.9514
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5VMC; Ligand: NAG 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: 5vmc.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5VMC; Ligand: NAG 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: 2) in the query (biounit: 5vmc.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5VMC; Ligand: NAG 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: 3) in the query (biounit: 5vmc.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
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