Receptor
PDB id Resolution Class Description Source Keywords
3ZYR 1.65 Å NON-ENZYME: BINDING STRUCTURE OF THE LECTIN FROM PLATYPODIUM ELEGANS IN COMPLEX WITH 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
ASN NAG NAG BMA MAN MAN NAG NAG A:299;
Valid;
none;
Kd = 4.6 uM
1431.32 n/a O=C([...
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 B:300;
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)...
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 WITH 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 510 families.
1 3ZYR Kd = 4.6 uM ASN NAG NAG BMA MAN MAN NAG NAG n/a n/a
2 3ZVX - MAN MAN MAN n/a n/a
3 5U38 - MDM C13 H24 O11 CO[C@@H]1[....
70% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 391 families.
1 1S1A - MAN MMA n/a n/a
2 2ARB Ka = 26000 M^-1 NAG MAN n/a n/a
3 1N3Q - GLC BDF n/a n/a
4 2AR6 Ka = 63000 M^-1 NAG MAN MAN MAN 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 ASN NAG NAG BMA MAN MAN NAG NAG n/a n/a
10 3ZVX - MAN MAN MAN n/a n/a
11 5U38 - MDM C13 H24 O11 CO[C@@H]1[....
12 5EYX - MDM C13 H24 O11 CO[C@@H]1[....
13 5EYY - MDM C13 H24 O11 CO[C@@H]1[....
50% Homology Family (61)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 298 families.
1 5T55 Kd = 0.68 nM NGA GLA GAL BGC n/a n/a
2 5T54 Kd = 0.87 nM A2G GLA FUC 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 - MAN MMA n/a n/a
9 2ARB Ka = 26000 M^-1 NAG MAN n/a n/a
10 1N3Q - GLC BDF n/a n/a
11 2AR6 Ka = 63000 M^-1 NAG MAN MAN MAN 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 - FUC GAL MAG FUC n/a n/a
17 1GSL - FUC GAL MAG FUC n/a n/a
18 1V00 - LAT C12 H22 O11 C([C@@H]1[....
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 - GAL BGC 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 LAT C12 H22 O11 C([C@@H]1[....
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 FUC LAT n/a n/a
30 3ZYR Kd = 4.6 uM ASN NAG NAG BMA MAN MAN NAG NAG n/a n/a
31 3ZVX - MAN MAN MAN n/a n/a
32 5U38 - MDM C13 H24 O11 CO[C@@H]1[....
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 - LBT C12 H22 O11 C([C@@H]1[....
38 4U2A - A2G C8 H15 N O6 CC(=O)N[C@....
39 4U36 - TNR C11 H20 N2 O8 CC(=O)N[C@....
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 - MDM C13 H24 O11 CO[C@@H]1[....
44 5EYY - MDM C13 H24 O11 CO[C@@H]1[....
45 2BQP - GLC C6 H12 O6 C([C@@H]1[....
46 5T7P - XMM C14 H15 Br Cl N O6 c1cc(c(c2c....
47 2DVA - GAL MGC n/a n/a
48 2DV9 - GAL GAL n/a n/a
49 1V6K - GAL GLC n/a n/a
50 1V6L - GAL BGC n/a n/a
51 2DVD - GAL GAL n/a n/a
52 2TEP - GAL NGA n/a n/a
53 2DVB - GAL C6 H12 O6 C([C@@H]1[....
54 1V6I - GAL GLC n/a n/a
55 2PEL Ki = 1.37 mM LAT C12 H22 O11 C([C@@H]1[....
56 1G9F - GAL NAG GAL NAG GAL n/a n/a
57 2DTW - 2GS C7 H14 O6 CO[C@@H]1[....
58 1WBL - AMG C7 H14 O6 CO[C@@H]1[....
59 2ZMK - GLA EGA n/a n/a
60 2D3S - TNR C11 H20 N2 O8 CC(=O)N[C@....
61 2FMD - MAN MAN n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ASN NAG NAG BMA MAN MAN NAG NAG; Similar ligands found: 57
No: Ligand ECFP6 Tc MDL keys Tc
1 ASN NAG NAG BMA MAN MAN NAG NAG 1 1
2 NAG BMA NAG MAN MAN NAG NAG 0.702703 0.890909
3 NAG NAG BMA MAN MAN NAG GAL NAG 0.672414 0.890909
4 NAG MAN BMA NDG MAN NAG GAL 0.663793 0.890909
5 NAG NAG BMA MAN MAN NAG NAG 0.661017 0.894737
6 FUC C4W NAG BMA MAN MAN NAG NAG 0.622047 0.945455
7 MAN BMA NAG NAG MAN NAG GAL GAL 0.62069 0.890909
8 NAG MAN MAN MAN NAG GAL NAG GAL 0.62069 0.890909
9 NAG MAN BMA MAN NAG GAL 0.612069 0.872727
10 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.580645 0.872727
11 FUC C4W NAG BMA MAN MAN NAG 0.575758 0.945455
12 NAG MAN MAN MAN NAG 0.567568 0.872727
13 M5G 0.552 0.872727
14 NAG NAG BMA MAN NAG 0.536585 0.894737
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 FUC C4W NAG BMA MAN NAG 0.519084 0.945455
18 WZ5 0.508333 0.821429
19 NAG MAN MAN 0.504505 0.818182
20 NAG NAG BMA MAN MAN 0.491803 0.872727
21 MMA MAN NAG MAN NAG NAG 0.491525 0.875
22 NAG MAN MMA 0.477477 0.821429
23 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.472868 0.824561
24 BMA NAG MAN MAN MAN MAN MAN MAN MAN 0.468254 0.818182
25 BMA Z4Y NAG 0.466102 0.803571
26 NAG MAN BMA 0.455357 0.818182
27 WZ4 0.455224 0.779661
28 NAG AMU NAG AMV 0.454545 0.892857
29 NAG GAL NAG 0.443478 0.872727
30 NAG NAG NAG NAG NDG 0.432432 0.890909
31 NAG NAG NAG NDG 0.432432 0.890909
32 NAG NAG NAG NAG NAG NAG 0.432432 0.890909
33 NAG NAG NAG NAG NAG 0.432432 0.890909
34 NDG NAG NAG NAG 0.432432 0.890909
35 NAG NAG NAG NAG NAG NAG NAG NAG 0.432432 0.890909
36 NAG NAG NDG 0.432432 0.890909
37 NDG NAG NAG 0.432432 0.890909
38 NDG NAG NAG NDG 0.432432 0.890909
39 NAG NAG NDG NAG 0.432432 0.890909
40 CTO 0.432432 0.890909
41 MAN MAN NAG 0.431034 0.821429
42 NAG GAL BGC 0.431034 0.818182
43 LAT NAG GAL 0.428571 0.818182
44 GLC GAL NAG GAL 0.428571 0.818182
45 FUC C4W NAG BMA MAN 0.425373 0.945455
46 NGA GLA GAL BGC 0.425 0.818182
47 GAL NAG GAL NAG GAL NAG 0.420168 0.890909
48 NAG GAL GAL NAG GAL 0.420168 0.872727
49 NAG GAL GAL NAG 0.420168 0.872727
50 NAG NAG NAG NAG 0.40678 0.894737
51 NAG NAG NAG 0.40678 0.894737
52 GAL NAG GAL BGC 0.406504 0.821429
53 NAG NAG NGT 0.406504 0.753846
54 GAL NAG MAN 0.405172 0.818182
55 NOJ NAG NAG NAG 0.404959 0.913793
56 NOJ NAG NAG 0.404959 0.896552
57 NAG NAG BMA MAN 0.404762 0.877193
Ligand no: 2; Ligand: NAG NAG BMA MAN MAN NAG NAG; Similar ligands found: 101
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG NAG BMA MAN MAN NAG NAG 1 1
2 NAG NAG BMA MAN NAG 0.828283 1
3 NAG NAG BMA MAN MAN MAN MAN 0.792453 0.981132
4 NAG BMA NAG MAN MAN NAG NAG 0.77451 0.924528
5 NAG NAG BMA MAN MAN NAG GAL NAG 0.738318 0.924528
6 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.733333 0.924528
7 NAG MAN BMA NDG MAN NAG GAL 0.728972 0.924528
8 NAG NAG FUL BMA MAN MAN NAG GAL 0.719298 1
9 NAG MAN BMA MAN NAG GAL 0.688679 0.90566
10 MAN BMA NAG NAG MAN NAG GAL GAL 0.682243 0.924528
11 NAG MAN MAN MAN NAG GAL NAG GAL 0.682243 0.924528
12 NAG NAG NAG NAG 0.680851 1
13 NAG NAG NAG 0.680851 1
14 ASN NAG NAG BMA MAN MAN NAG NAG 0.661017 0.894737
15 NAG NAG BMA MAN 0.656863 0.981132
16 FUC C4W NAG BMA MAN MAN NAG NAG 0.65 0.875
17 NAG MAN MAN MAN NAG 0.643564 0.90566
18 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.634783 0.90566
19 NAG NAG BMA 0.616162 0.981132
20 NAG NDG BMA 0.616162 0.981132
21 NAG NAG 0.606383 0.962264
22 NAG NDG 0.606383 0.962264
23 M5G 0.603448 0.90566
24 NAG NAG BMA BMA 0.601942 0.981481
25 FUC C4W NAG BMA MAN MAN NAG 0.6 0.875
26 NAG MAN MAN 0.558824 0.849057
27 WZ5 0.544643 0.851852
28 MMA MAN NAG MAN NAG NAG 0.541284 0.907407
29 FUC C4W NAG BMA MAN NAG 0.540323 0.875
30 NAG NAG BMA MAN MAN 0.539823 0.90566
31 NAG MAN BMA 0.519608 0.849057
32 NAG MAN MMA 0.514563 0.851852
33 GAL NAG GAL BGC 0.513761 0.886792
34 BMA NAG MAN MAN MAN MAN MAN MAN MAN 0.512821 0.849057
35 MAN MAN NAG 0.504762 0.886792
36 BMA Z4Y NAG 0.5 0.833333
37 NAG GAL NAG 0.490566 0.90566
38 NAG BMA 0.484848 0.90566
39 WZ4 0.484127 0.807018
40 NDG NAG NAG NDG 0.480392 0.924528
41 NAG NAG NAG NAG NDG 0.480392 0.924528
42 NAG NAG NAG NAG NAG NAG 0.480392 0.924528
43 NAG NAG NAG NDG 0.480392 0.924528
44 NAG NAG NDG NAG 0.480392 0.924528
45 NDG NAG NAG NAG 0.480392 0.924528
46 NDG NAG NAG 0.480392 0.924528
47 NAG NAG NDG 0.480392 0.924528
48 NAG NAG NAG NAG NAG NAG NAG NAG 0.480392 0.924528
49 CTO 0.480392 0.924528
50 NAG NAG NAG NAG NAG 0.480392 0.924528
51 NAG GAL GAL NAG GAL 0.477064 0.90566
52 NAG GAL BGC 0.476636 0.849057
53 GLC GAL NAG GAL 0.472727 0.849057
54 NOJ NAG NAG NAG 0.472727 0.912281
55 NOJ NAG NAG 0.472727 0.894737
56 LAT NAG GAL 0.472727 0.849057
57 NGA GLA GAL BGC 0.468468 0.849057
58 GAL NAG GAL NAG GAL NAG 0.463636 0.924528
59 NAG GAL GAL NAG 0.463636 0.90566
60 Z4S NAG NAG 0.459459 0.859649
61 GAL NAG MAN 0.448598 0.849057
62 GAL NAG GAL 0.445455 0.886792
63 NDG NAG 0.441176 0.90566
64 CBS CBS 0.441176 0.90566
65 CBS 0.441176 0.90566
66 NAG GDL 0.441176 0.90566
67 FUC C4W NAG BMA MAN 0.440945 0.875
68 NGA GAL BGC 0.439252 0.849057
69 BMA MAN MAN MAN MAN 0.439252 0.622642
70 FUC BGC GAL NAG GAL 0.438017 0.867925
71 NAG BMA MAN MAN MAN MAN 0.436975 0.849057
72 NAG NAG NGT 0.434783 0.777778
73 NAG AMU NAG AMV 0.423729 0.890909
74 FUC BGC GAL NAG 0.423729 0.867925
75 MBG A2G 0.423077 0.851852
76 A2G MBG 0.423077 0.851852
77 NGA GAL 0.419048 0.867925
78 A2G GAL NAG FUC GAL GLC 0.418605 0.924528
79 GLC GAL NAG GAL FUC A2G 0.418605 0.924528
80 GAL GLC NAG GAL FUC 0.418033 0.867925
81 FUC GAL NAG GAL BGC 0.418033 0.867925
82 GLC NAG GAL GAL FUC 0.418033 0.867925
83 GAL NAG 0.417476 0.849057
84 NAG GAL 0.417476 0.849057
85 MAN MAN MAN BMA MAN MAN MAN 0.415254 0.62963
86 NAG MBG 0.413462 0.851852
87 DLD 0.412281 0.790323
88 6Y2 0.410256 0.720588
89 MAN MAN MAN MAN MAN MAN MAN 0.408696 0.622642
90 3PV 0.408333 0.839286
91 A2G GAL NAG FUC 0.404959 0.924528
92 FUC GAL NAG A2G 0.404959 0.924528
93 GLC GAL NAG GAL FUC FUC 0.404762 0.886792
94 BGC GAL NAG GAL FUC FUC 0.404762 0.886792
95 FUC C4W NAG BMA 0.403226 0.875
96 MAN MAN MAN BMA MAN 0.401786 0.622642
97 1GN ACY GAL ACY 1GN BGC GAL BGC 0.401639 0.90566
98 NAA NAA AMI 0.401639 0.710145
99 AO3 0.401639 0.710145
100 ACY 1GN GAL 1GN BGC ACY GAL BGC 0.401639 0.90566
101 UMG 0.4 0.816667
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: ASN 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: 2) in the query (biounit: 3zyr.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
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