Receptor
PDB id Resolution Class Description Source Keywords
3ZYR 1.65 Å NON-ENZYME: BINDING STRUCTURE OF THE LECTIN FROM PLATYPODIUM ELEGANS IN COMPLEX HEPTASACCHARIDE PLATYPODIUM ELEGANS SUGAR BINDING PROTEIN N-GLYCAN PLANT LECTIN
Ref.: A LECTIN FROM PLATYPODIUM ELEGANS WITH UNUSUAL SPEC AND AFFINITY FOR ASYMMETRIC COMPLEX N-GLYCANS. J.BIOL.CHEM. V. 287 26352 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:401;
B:401;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
40.078 Ca [Ca+2...
GOL A:402;
A:405;
A:406;
B:403;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
MN A:400;
B:400;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
54.938 Mn [Mn+2...
NAG NAG BMA MAN MAN NAG NAG D:1;
 Valid;
 none;
 submit data
1301.21 n/a O=C(N...
URE A:403;
B:404;
 Invalid;
Invalid;
 none;
none;
 submit data
60.055 C H4 N2 O C(=O)...
NAG ASN NAG BMA MAN MAN NAG NAG C:1;
 Valid;
 none;
 Kd = 4.6 uM
1430.31 n/a O=C([...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3ZYR 1.65 Å NON-ENZYME: BINDING STRUCTURE OF THE LECTIN FROM PLATYPODIUM ELEGANS IN COMPLEX HEPTASACCHARIDE PLATYPODIUM ELEGANS SUGAR BINDING PROTEIN N-GLYCAN PLANT LECTIN
Ref.: A LECTIN FROM PLATYPODIUM ELEGANS WITH UNUSUAL SPEC AND AFFINITY FOR ASYMMETRIC COMPLEX N-GLYCANS. J.BIOL.CHEM. V. 287 26352 2012
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 552 families.
1 3ZYR Kd = 4.6 uM NAG ASN NAG BMA MAN MAN NAG NAG n/a n/a
2 3ZVX - MAN MAN MAN n/a n/a
3 5U38 - MMA MAN n/a n/a
70% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 426 families.
1 1S1A - MMA MAN n/a n/a
2 2ARB Ka = 26000 M^-1 MAN NAG n/a n/a
3 1N3Q - FRU GLC n/a n/a
4 2AR6 Ka = 63000 M^-1 MAN MAN MAN NAG NAG n/a n/a
5 1N3O - GYP C7 H14 O6 CO[C@@H]1[....
6 1N3P - GLC FRU n/a n/a
7 2ARX - MAN MAN n/a n/a
8 2ARE Ka = 1900 M^-1 MAN C6 H12 O6 C([C@@H]1[....
9 3ZYR Kd = 4.6 uM NAG ASN NAG BMA MAN MAN NAG NAG n/a n/a
10 3ZVX - MAN MAN MAN n/a n/a
11 5U38 - MMA MAN n/a n/a
12 5EYX - MMA MAN n/a n/a
13 5EYY - MMA MAN n/a n/a
50% Homology Family (67)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 322 families.
1 5T55 Kd = 0.68 nM BGC GAL GLA NGA n/a n/a
2 5T54 Kd = 0.87 nM GLA FUC A2G n/a n/a
3 5T5J Kd = 0.73 nM ACA SER SER VAL GLY A2G n/a n/a
4 5T52 Kd = 0.54 nM NGA C8 H15 N O6 CC(=O)N[C@....
5 5T5L Kd = 0.73 nM ACE SER SER VAL GLY A2G n/a n/a
6 5T5P Kd = 0.71 nM ACE SER THR VAL GLY A2G n/a n/a
7 1FNZ - A2G C8 H15 N O6 CC(=O)N[C@....
8 1S1A - MMA MAN n/a n/a
9 2ARB Ka = 26000 M^-1 MAN NAG n/a n/a
10 1N3Q - FRU GLC n/a n/a
11 2AR6 Ka = 63000 M^-1 MAN MAN MAN NAG NAG n/a n/a
12 1N3O - GYP C7 H14 O6 CO[C@@H]1[....
13 1N3P - GLC FRU n/a n/a
14 2ARX - MAN MAN n/a n/a
15 2ARE Ka = 1900 M^-1 MAN C6 H12 O6 C([C@@H]1[....
16 1LED - MAG GAL FUC FUC n/a n/a
17 1GSL - MAG FUC GAL FUC n/a n/a
18 1V00 - BGC GAL n/a n/a
19 3N3H - CIT C6 H8 O7 C(C(=O)O)C....
20 3N36 - GLA C6 H12 O6 C([C@@H]1[....
21 1AX0 Ka = 1340 M^-1 A2G C8 H15 N O6 CC(=O)N[C@....
22 1UZY - BGC GAL n/a n/a
23 1LTE - BGC GAL n/a n/a
24 1AX1 Ka = 1940 M^-1 BGC GAL n/a n/a
25 1AX2 Ka = 9730 M^-1 NDG GAL n/a n/a
26 1GZC Kd = 0.32 mM BGC GAL n/a n/a
27 3N35 - A2G C8 H15 N O6 CC(=O)N[C@....
28 1AXZ Ka = 1570 M^-1 GAL C6 H12 O6 C([C@@H]1[....
29 1GZ9 Kd = 0.31 mM BGC GAL FUC n/a n/a
30 3ZYR Kd = 4.6 uM NAG ASN NAG BMA MAN MAN NAG NAG n/a n/a
31 3ZVX - MAN MAN MAN n/a n/a
32 5U38 - MMA MAN n/a n/a
33 5KXE Kd = 5.45 uM 6Y2 C22 H31 N3 O13 CC(=O)N[C@....
34 5KXB - NGA C8 H15 N O6 CC(=O)N[C@....
35 5KXC - 6Y2 C22 H31 N3 O13 CC(=O)N[C@....
36 5KXD - 6Y2 C22 H31 N3 O13 CC(=O)N[C@....
37 4WV8 - GLC GAL n/a n/a
38 4U2A - A2G C8 H15 N O6 CC(=O)N[C@....
39 4U36 - SER A2G n/a n/a
40 1JXN - MFU C7 H14 O5 C[C@H]1[C@....
41 3WCS - MAN NAG GAL n/a n/a
42 3WOG - MAN NAG n/a n/a
43 5EYX - MMA MAN n/a n/a
44 5EYY - MMA MAN n/a n/a
45 2BQP - GLC C6 H12 O6 C([C@@H]1[....
46 5T7P - XMM C14 H15 Br Cl N O6 c1cc(c(c2c....
47 2DVA - MGC GAL n/a n/a
48 6VC4 Kd = 360 uM QWG C22 H37 N3 O14 S2 CO[C@@H]1[....
49 6VGF Kd = 180 uM WA3 C42 H68 N6 O27 S4 c1c(nnn1C[....
50 2DV9 - GAL GAL n/a n/a
51 1V6K - GLC GAL n/a n/a
52 1V6L - BGC GAL n/a n/a
53 2DVD - GAL GAL n/a n/a
54 6VC3 Kd = 482 uM QWJ C15 H24 O9 S2 C#CCSC[C@@....
55 2TEP - NGA GAL n/a n/a
56 6V95 Kd = 495 uM QSG C32 H48 N10 O20 c1c(nnn1[C....
57 6VAV Kd = 690 uM QTY C32 H48 N10 O16 c1c(nnn1[C....
58 2DVB - GAL C6 H12 O6 C([C@@H]1[....
59 1V6I - GLC GAL n/a n/a
60 6VAW Kd = 1563 uM S3W C20 H33 N5 O12 CO[C@@H]1[....
61 2PEL Ki = 1.37 mM BGC GAL n/a n/a
62 1G9F - GAL NAG GAL NAG GAL n/a n/a
63 2DTW - 2GS C7 H14 O6 CO[C@@H]1[....
64 1WBL - AMG C7 H14 O6 CO[C@@H]1[....
65 2ZMK - EGA GLA n/a n/a
66 2D3S - SER A2G n/a n/a
67 2FMD - MAN MAN 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
Ligand no: 2; Ligand: NAG ASN NAG BMA MAN MAN NAG NAG; Similar ligands found: 52
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG ASN NAG BMA MAN MAN NAG NAG 1 1
2 ALA ASN LYS NAG NAG BMA MAN MAN NAG NAG 0.837838 0.981818
3 NAG NAG BMA MAN MAN NAG GAL NAG 0.672414 0.890909
4 NDG BMA MAN MAN NAG GAL NAG 0.663793 0.890909
5 NAG NAG BMA MAN MAN NAG NAG 0.661017 0.894737
6 C4W NAG FUC BMA MAN MAN NAG NAG 0.622047 0.945455
7 NAG BMA MAN MAN NAG GAL NAG GAL 0.62069 0.890909
8 BMA MAN MAN NAG GAL NAG 0.612069 0.872727
9 C4W NAG FUC BMA MAN MAN NAG GAL NAG 0.598485 0.852459
10 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.580645 0.872727
11 C4W NAG FUC BMA MAN MAN NAG 0.575758 0.945455
12 NAG NAG BMA MAN NAG 0.570175 0.890909
13 MAN MAN MAN NAG NAG 0.567568 0.872727
14 NDG BMA MAN MAN NAG MAN MAN 0.552 0.872727
15 NAG NAG BMA MAN MAN MAN MAN 0.523077 0.877193
16 NAG NAG FUL BMA MAN MAN NAG GAL 0.522388 0.894737
17 C4W NAG FUC BMA MAN NAG 0.519084 0.945455
18 C4W NAG FUC BMA MAN MAN NAG GAL SIA NAG 0.512346 0.84127
19 NAG BMA MAN MAN MAN MAN MAN MAN MAN MAN 0.512195 0.818182
20 YZ0 MAN MAN NAG MAN 0.508333 0.821429
21 MMA MAN NAG MAN NAG NAG 0.504274 0.875
22 NAG NAG MAN MAN MAN 0.491803 0.872727
23 BGC GAL NAG NAG GAL GAL 0.491803 0.872727
24 C4W NAG FUC BMA MAN NAG GAL 0.485075 0.852459
25 MMA MAN NAG 0.477477 0.821429
26 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.468254 0.818182
27 BMA Z4Y NAG 0.466102 0.803571
28 NAG ASN FUC 0.457627 0.981818
29 YZ0 MAN Z4Y NAG MAN 0.455224 0.779661
30 AMV NAG AMU NAG 0.454545 0.892857
31 NAG GAL NAG 0.443478 0.872727
32 NAG NAG NAG NAG NAG NAG 0.432432 0.890909
33 NDG NAG NAG NAG NAG 0.432432 0.890909
34 NAG NAG NAG NAG NAG 0.432432 0.890909
35 NAG NAG NAG NAG NAG NAG NAG NAG 0.432432 0.890909
36 BGC GAL NAG 0.431034 0.818182
37 C4W NAG FUC BMA MAN 0.425373 0.945455
38 BGC GAL GLA NGA 0.425 0.818182
39 C4W NAG FUC BMA MAN NAG GAL SIA 0.423313 0.84127
40 NAG GAL NAG GAL NAG GAL 0.420168 0.890909
41 GAL NAG GAL NAG GAL 0.420168 0.872727
42 NAG GAL NAG GAL 0.420168 0.872727
43 MAN MAN NAG 0.418803 0.821429
44 NAG NAG NAG 0.40678 0.894737
45 NAG NAG NAG NAG 0.40678 0.894737
46 NAG NAG NAG NAG NAG NAG NAG 0.40678 0.894737
47 NAG NGT NAG 0.406504 0.753846
48 MAN NAG GAL 0.405172 0.818182
49 NAG NOJ NAG 0.404959 0.896552
50 NAG NOJ NAG NAG 0.404959 0.913793
51 NAG NAG BMA MAN 0.404762 0.877193
52 Z3Q NGA 0.4 0.78125
Similar Ligands (3D)
Ligand no: 1; Ligand: NAG NAG BMA MAN MAN NAG NAG; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; Ligand: NAG ASN 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 : 3ZYR; Ligand: NAG NAG BMA MAN MAN NAG NAG; 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: 3zyr.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3ZYR; Ligand: NAG ASN NAG BMA MAN MAN NAG NAG; 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: 3zyr.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
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