Receptor
PDB id Resolution Class Description Source Keywords
2VUZ 1.7 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF CODAKINE IN COMPLEX WITH BIANTENNARY NONASACCHARIDE AT 1.7A RESOLUTION CODAKIA ORBICULARIS NONASACCHARIDE CODAKIA ORBICULARIS SUGAR-BINDING PROTEIN LECTIN CODAKINE BIANTENNARY INVERTEBRATE SUGAR BINDING
Ref.: HIGH AFFINITY INTERACTION BETWEEN A BIVALVE C-TYPE AND A BIANTENNARY COMPLEX-TYPE N-GLYCAN REVEALED BY CRYSTALLOGRAPHY AND MICROCALORIMETRY. J.BIOL.CHEM. V. 283 30112 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:201;
Part of Protein;
none;
submit data
40.078 Ca [Ca+2...
GOL A:211;
A:210;
A:209;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NAG NAG BMA MAN MAN NAG NAG B:1;
Valid;
none;
Kd = 0.432 uM
1301.21 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2VUZ 1.7 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF CODAKINE IN COMPLEX WITH BIANTENNARY NONASACCHARIDE AT 1.7A RESOLUTION CODAKIA ORBICULARIS NONASACCHARIDE CODAKIA ORBICULARIS SUGAR-BINDING PROTEIN LECTIN CODAKINE BIANTENNARY INVERTEBRATE SUGAR BINDING
Ref.: HIGH AFFINITY INTERACTION BETWEEN A BIVALVE C-TYPE AND A BIANTENNARY COMPLEX-TYPE N-GLYCAN REVEALED BY CRYSTALLOGRAPHY AND MICROCALORIMETRY. J.BIOL.CHEM. V. 283 30112 2008
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 2VUZ Kd = 0.432 uM NAG NAG BMA MAN MAN NAG NAG n/a n/a
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 2VUZ Kd = 0.432 uM NAG NAG BMA MAN MAN NAG NAG n/a n/a
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 2VUZ Kd = 0.432 uM NAG NAG BMA MAN MAN NAG NAG n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: NAG NAG BMA MAN MAN NAG NAG; Similar ligands found: 80
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG NAG BMA MAN MAN NAG NAG 1 1
2 NAG NAG BMA MAN MAN MAN MAN 0.792453 0.981132
3 NAG NAG BMA MAN MAN NAG GAL NAG 0.738318 0.924528
4 NDG BMA MAN MAN NAG GAL NAG 0.728972 0.924528
5 NAG NAG FUL BMA MAN MAN NAG GAL 0.719298 1
6 BMA MAN MAN NAG GAL NAG 0.688679 0.90566
7 NAG BMA MAN MAN NAG GAL NAG GAL 0.682243 0.924528
8 NAG NAG NAG 0.680851 1
9 NAG NAG NAG NAG 0.680851 1
10 NAG NAG NAG NAG NAG NAG NAG 0.680851 1
11 ALA ASN LYS NAG NAG BMA MAN MAN NAG NAG 0.661017 0.910714
12 NAG ASN NAG BMA MAN MAN NAG NAG 0.661017 0.894737
13 NAG NAG BMA MAN 0.656863 0.981132
14 C4W NAG FUC BMA MAN MAN NAG NAG 0.65 0.875
15 MAN MAN MAN NAG NAG 0.643564 0.90566
16 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.634783 0.90566
17 NAG NAG BMA MAN NAG 0.628571 0.924528
18 C4W NAG FUC BMA MAN MAN NAG GAL NAG 0.624 0.790323
19 NAG NAG BMA 0.616162 0.981132
20 NDG BMA MAN MAN NAG MAN MAN 0.603448 0.90566
21 NAG NAG BMA BMA 0.601942 0.981481
22 C4W NAG FUC BMA MAN MAN NAG 0.6 0.875
23 NAG BMA MAN MAN MAN MAN MAN MAN MAN MAN 0.561404 0.849057
24 YZ0 MAN MAN NAG MAN 0.544643 0.851852
25 MMA MAN NAG MAN NAG NAG 0.541284 0.907407
26 C4W NAG FUC BMA MAN NAG 0.540323 0.875
27 NAG NAG MAN MAN MAN 0.539823 0.90566
28 BGC GAL NAG NAG GAL GAL 0.539823 0.90566
29 MMA MAN NAG 0.514563 0.851852
30 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.512821 0.849057
31 MAN MAN NAG 0.504762 0.886792
32 C4W NAG FUC BMA MAN NAG GAL 0.503937 0.790323
33 BMA Z4Y NAG 0.5 0.833333
34 C4W NAG FUC BMA MAN MAN NAG GAL SIA NAG 0.5 0.809524
35 NAG GAL NAG 0.490566 0.90566
36 NAG BMA 0.484848 0.90566
37 YZ0 MAN Z4Y NAG MAN 0.484127 0.807018
38 NDG NAG NAG NAG NAG 0.480392 0.924528
39 NAG NAG NAG NAG NAG NAG 0.480392 0.924528
40 NAG NAG NAG NAG NAG NAG NAG NAG 0.480392 0.924528
41 NAG NAG NAG NAG NAG 0.480392 0.924528
42 GAL NAG GAL NAG GAL 0.477064 0.90566
43 BGC GAL NAG 0.476636 0.849057
44 NAG NOJ NAG 0.472727 0.894737
45 NAG NOJ NAG NAG 0.472727 0.912281
46 BGC GAL GLA NGA 0.468468 0.849057
47 NAG GAL NAG GAL NAG GAL 0.463636 0.924528
48 NAG GAL NAG GAL 0.463636 0.90566
49 Z4S NAG NAG 0.459459 0.859649
50 BMA MAN NAG 0.453704 0.849057
51 MAN NAG GAL 0.448598 0.849057
52 GAL NAG GAL 0.444444 0.849057
53 GDL NAG 0.441176 0.90566
54 C4W NAG FUC BMA MAN 0.440945 0.875
55 BGC GAL NGA 0.439252 0.849057
56 BGC FUC GAL NAG GAL 0.438017 0.867925
57 NAG BMA MAN MAN MAN MAN 0.436975 0.849057
58 NAG NGT NAG 0.434783 0.777778
59 BGC FUC GAL NAG 0.423729 0.867925
60 AMV NAG AMU NAG 0.423729 0.890909
61 MBG A2G 0.423077 0.851852
62 MAN NAG 0.421569 0.849057
63 GAL NGA 0.419048 0.867925
64 GLC GAL NAG GAL FUC A2G 0.418605 0.924528
65 BGC GAL NAG GAL FUC 0.418033 0.867925
66 Z3Q NGA 0.415929 0.777778
67 MAN BMA MAN MAN MAN MAN MAN 0.415254 0.62963
68 MBG NAG 0.413462 0.851852
69 6Y2 0.410256 0.720588
70 C4W NAG FUC BMA MAN NAG GAL SIA 0.408805 0.809524
71 MAN MAN MAN MAN MAN MAN MAN 0.408696 0.622642
72 GYP GZL NAG 0.408333 0.839286
73 BGC GAL NAG GAL FUC FUC 0.404762 0.886792
74 NDG GLA NAG GLC RAM 0.40458 0.924528
75 NDG NAG GLA NAG GLC RAM 0.40458 0.924528
76 C4W NAG FUC BMA 0.403226 0.875
77 1GN ACY GAL 1GN BGC ACY GAL BGC 0.401639 0.90566
78 NAA AMI NAA 0.401639 0.710145
79 AO3 0.401639 0.710145
80 UMG 0.4 0.816667
Similar Ligands (3D)
Ligand no: 1; Ligand: NAG NAG BMA MAN MAN NAG NAG; 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 : 2VUZ; Ligand: NAG NAG BMA MAN MAN NAG NAG; Similar sites found with APoc: 5
This union binding pocket(no: 1) in the query (biounit: 2vuz.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 1PWB GLC 36.4341
2 1PWB GLC 36.4341
3 5M62 BGC 37.9845
4 1RDL MMA 41.5929
5 1RDL MMA 41.5929
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