Receptor
PDB id Resolution Class Description Source Keywords
3VYK 1.5 Å NON-ENZYME: BINDING CRYSTAL STRUCTURE OF C-TYPE LECTIN DOMAIN OF MURINE DENDRITI INHIBITORY RECEPTOR 2 IN COMPLEX WITH N-GLYCAN MUS MUSCULUS C-TYPE LECTIN FOLD CELL SURFACE CARBOHYDRATE BINDING PROTE
Ref.: RECOGNITION OF BISECTING N-ACETYLGLUCOSAMINE: STRUC BASIS FOR ASYMMETRIC INTERACTION WITH THE MOUSE LEC DENDRITIC CELL INHIBITORY RECEPTOR 2 J.BIOL.CHEM. V. 288 33598 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:1007;
 Part of Protein;
 none;
 submit data
40.078 Ca [Ca+2...
MMA MAN NAG MAN NAG NAG B:1;
 Valid;
 none;
 Kd = 0.000023 M
1128.05 n/a O=C(N...
SO4 A:1009;
A:1008;
 Invalid;
Invalid;
 none;
none;
 submit data
96.063 O4 S [O-]S...
EDO A:1010;
 Invalid;
 none;
 submit data
62.068 C2 H6 O2 C(CO)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3VYK 1.5 Å NON-ENZYME: BINDING CRYSTAL STRUCTURE OF C-TYPE LECTIN DOMAIN OF MURINE DENDRITI INHIBITORY RECEPTOR 2 IN COMPLEX WITH N-GLYCAN MUS MUSCULUS C-TYPE LECTIN FOLD CELL SURFACE CARBOHYDRATE BINDING PROTE
Ref.: RECOGNITION OF BISECTING N-ACETYLGLUCOSAMINE: STRUC BASIS FOR ASYMMETRIC INTERACTION WITH THE MOUSE LEC DENDRITIC CELL INHIBITORY RECEPTOR 2 J.BIOL.CHEM. V. 288 33598 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 552 families.
1 3VYK Kd = 0.000023 M MMA MAN NAG 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 426 families.
1 3VYK Kd = 0.000023 M MMA MAN NAG MAN NAG NAG n/a n/a
50% Homology Family (29)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 322 families.
1 4N33 - GAL NAG n/a n/a
2 3P5I - NAG G6S n/a n/a
3 3P5H - BGC BGC n/a n/a
4 4N37 - MMA C7 H14 O6 CO[C@@H]1[....
5 4N34 - 2F8 C9 H17 N O6 CC(=O)N[C@....
6 3P5E - MAN C6 H12 O6 C([C@@H]1[....
7 6PWR - MAN NAG n/a n/a
8 6PWS Ki = 1.6 mM MMA C7 H14 O6 CO[C@@H]1[....
9 5G6U ic50 = 0.22 uM SGN C6 H13 N O11 S2 C([C@@H]1[....
10 5VYB - BMA MAN MAN MAN MAN MAN MAN n/a n/a
11 1SL5 - GAL NAG FUC GAL n/a n/a
12 2IT5 - MAN MAN MAN n/a n/a
13 6LFJ Kd = 140 uM MAN IPD MAN n/a n/a
14 1K9J - MAN MAN MAN NAG NAG n/a n/a
15 1SL4 - MAN MAN MAN MAN n/a n/a
16 2IT6 - MAN MAN n/a n/a
17 1K9I - MAN MAN MAN NAG NAG n/a n/a
18 6GHV Kd = 52 uM EZ8 C35 H48 Cl N6 O10 c1cc(ccc1C....
19 3VYK Kd = 0.000023 M MMA MAN NAG MAN NAG NAG n/a n/a
20 4KZV - GLC GLC n/a n/a
21 4ZRV - GLC U8V n/a n/a
22 5KTH - GLC GLC 6X7 6X7 n/a n/a
23 5KTI - GLC GLC 6X6 n/a n/a
24 2OX9 - NAG FUC GAL n/a n/a
25 4ZES Ki = 9.4 mM MMA C7 H14 O6 CO[C@@H]1[....
26 3WH2 - FLC C6 H5 O7 C(C(=O)[O-....
27 5JPV - GLC GAL n/a n/a
28 5JQ1 - ZPF C9 H15 N O6 CC(=O)N[C@....
29 1SL6 - NDG FUC GAL n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: MMA MAN NAG MAN NAG NAG; Similar ligands found: 78
No: Ligand ECFP6 Tc MDL keys Tc
1 MMA MAN NAG MAN NAG NAG 1 1
2 MMA MAN NAG 0.658537 0.94
3 MAN MAN MAN NAG NAG 0.640449 0.96
4 YZ0 MAN MAN NAG MAN 0.610526 0.94
5 BMA Z4Y NAG 0.55914 0.882353
6 BMA MAN MAN NAG GAL NAG 0.558824 0.96
7 MBG NAG 0.548781 0.94
8 NDG BMA MAN MAN NAG GAL NAG 0.542056 0.98
9 NAG NAG BMA MAN MAN NAG NAG 0.541284 0.907407
10 NAG NAG BMA MAN MAN NAG GAL NAG 0.537037 0.98
11 MAN MAN NAG 0.533333 0.865385
12 YZ0 MAN Z4Y NAG MAN 0.53211 0.886792
13 MBG A2G 0.52381 0.94
14 GYP GZL NAG 0.520408 0.886792
15 C4W NAG FUC BMA MAN MAN NAG NAG 0.508475 0.924528
16 NAG ASN NAG BMA MAN MAN NAG NAG 0.504274 0.875
17 C4W NAG FUC BMA MAN NAG 0.5 0.924528
18 NAG BMA MAN MAN NAG GAL NAG GAL 0.495327 0.98
19 NAG NAG BMA MAN NAG 0.49505 0.98
20 ALA ASN LYS NAG NAG BMA MAN MAN NAG NAG 0.491525 0.890909
21 MAN NAG 0.488095 0.9
22 C4W NAG FUC BMA MAN MAN NAG GAL NAG 0.487805 0.830508
23 NM9 NAG 0.483871 0.980392
24 NDG BMA MAN MAN NAG MAN MAN 0.482143 0.96
25 AMV NAG AMU NAG 0.48 0.980392
26 GDL NAG 0.476744 0.96
27 C4W NAG FUC BMA MAN MAN NAG 0.47541 0.924528
28 NDG NAG 0.465909 0.98
29 MAG 0.461538 0.88
30 C4W NAG FUC BMA MAN NAG GAL 0.461538 0.830508
31 2F8 0.461538 0.88
32 NAG NAG NAG NAG NAG NAG 0.455556 0.98
33 NDG NAG NAG NAG NAG 0.455556 0.98
34 NAG NAG NAG NAG NAG NAG NAG NAG 0.455556 0.98
35 NAG NAG NAG NAG NAG 0.455556 0.98
36 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.448276 0.96
37 AMU NAG 0.443299 0.960784
38 Z3Q NGA 0.443299 0.786885
39 A2G NAG 0.443182 0.96
40 3QL 0.44086 0.888889
41 NAG NAG NAG 0.4375 0.907407
42 NAG GAL NAG 0.4375 0.96
43 NAG NAG NAG NAG 0.4375 0.907407
44 NAG NAG NAG NAG NAG NAG NAG 0.4375 0.907407
45 NAG BMA MAN MAN MAN MAN MAN MAN MAN MAN 0.436364 0.9
46 6Y2 0.435644 0.753846
47 GAL NGA 0.433333 0.846154
48 MAG GAL FUC FUC 0.43299 0.96
49 MAG FUC GAL FUC 0.43299 0.96
50 GAL FUC A2G 0.427083 0.92
51 BGC GAL NGA 0.425532 0.9
52 BGC GAL NAG 0.42268 0.9
53 GAL NAG 0.422222 0.9
54 NAG NGT NAG 0.421569 0.816667
55 Z4S NAG NAG 0.42 0.907407
56 BGC FUC GAL FUC A2G 0.419048 0.94
57 HSH A2G FUC 0.419048 0.810345
58 NGT NAG 0.418367 0.8
59 BGC GAL FUC A2G 0.415094 0.92
60 GAL NGA A2G 0.414894 0.96
61 NDG NAG GLA NAG GLC RAM 0.413793 0.98
62 NDG GLA NAG GLC RAM 0.413793 0.98
63 BMA MAN NAG 0.412371 0.9
64 NAG NGO 0.412371 0.839286
65 FHY 0.409524 0.943396
66 BGC FUC GAL NAG 0.409524 0.92
67 NAG NAG FUL BMA MAN MAN NAG GAL 0.408 0.907407
68 LEC NGA 0.407767 0.753846
69 NAG FUC GAL FUC A2G 0.407407 0.98
70 NAG GAL FUC FUC A2G 0.407407 0.98
71 NAG NOJ NAG 0.405941 0.842105
72 NAG NOJ NAG NAG 0.405941 0.859649
73 NAG NAG BMA MAN MAN MAN MAN 0.404959 0.888889
74 GUM 0.40367 0.859649
75 NDG GLA GLC NAG GLC RAM 0.403361 0.98
76 NAG GAL FUC A2G 0.402062 0.92
77 BGC GAL GLA NGA 0.401961 0.9
78 AH0 NAG 0.4 0.890909
Similar Ligands (3D)
Ligand no: 1; Ligand: MMA MAN NAG 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 : 3VYK; Ligand: MMA MAN NAG MAN NAG NAG; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 3vyk.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 6RYN GN1 32.8125
2 1PWB GLC GLC 37.9845
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