Receptor
PDB id Resolution Class Description Source Keywords
5U38 1.6 Å NON-ENZYME: BINDING CRYSTAL STRUCTURE OF NATIVE LECTIN FROM PLATYPODIUM ELEGANS (PELA) COMPLEXED WITH MAN1-3MAN-OME. PLATYPODIUM ELEGANS PLATYPODIUM ELEGANS LECTIN MAN1-3MAN-OME SUGAR BINDING PR
Ref.: STRUCTURAL STUDIES AND NOCICEPTIVE ACTIVITY OF A NA LECTIN FROM PLATYPODIUM ELEGANS SEEDS (NPELA). INT. J. BIOL. MACROMOL. V. 107 236 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAG A:301;
Invalid;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
CA A:303;
Part of Protein;
none;
submit data
40.078 Ca [Ca+2...
MN A:302;
Part of Protein;
none;
submit data
54.938 Mn [Mn+2...
MMA MAN B:1;
Valid;
none;
submit data
356.324 n/a O(CC1...
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: MMA MAN; Similar ligands found: 69
No: Ligand ECFP6 Tc MDL keys Tc
1 MMA MAN 1 1
2 BGC GLC GLC GLC GLC GLC 0.666667 0.942857
3 MMA MAN MAN 0.666667 1
4 BGC GLC GLC GLC GLC 0.666667 0.942857
5 AMG 0.651163 0.914286
6 GYP 0.651163 0.914286
7 MBG 0.651163 0.914286
8 MMA 0.651163 0.914286
9 BMA MAN MAN MAN 0.584615 0.972222
10 AHR AHR 0.56 0.810811
11 AHR AHR AHR AHR 0.557692 0.810811
12 AHR AHR AHR AHR AHR 0.557692 0.810811
13 AHR AHR AHR AHR AHR AHR 0.557692 0.810811
14 BGC GLC GLC 0.557377 0.942857
15 H1M MAN MAN 0.553846 0.921053
16 Z4R MAN MAN 0.542857 0.897436
17 Z9N GLC 0.534483 0.8
18 GLC GLC GLC 0.53125 0.891892
19 FRU GLC GLA 0.53125 0.846154
20 BMA MAN MAN 0.52459 0.942857
21 BGC GLC GLC GLC 0.523077 0.942857
22 GLC GLC GLC GLC GLC 0.523077 0.942857
23 GLC FRU GLA GLA GLA 0.523077 0.846154
24 GLC FRU GLA GLA 0.523077 0.846154
25 NGB 0.522388 0.6
26 BGC BGC BGC BGC 0.507463 0.942857
27 YZ0 MAN MAN NAG MAN 0.493827 0.744681
28 GLC FRU GLA 0.485714 0.846154
29 MAN MAN BMA 0.484375 0.891892
30 NOJ BGC 0.483333 0.666667
31 DEG 0.481481 0.775
32 IFM MAN 0.47541 0.680851
33 MGL GAL 0.473684 1
34 AXR BXY BXY BXX 0.472973 0.8
35 NAG BMA MAN MAN MAN MAN MAN 0.466667 0.921053
36 U1Y BGC 0.466667 0.921053
37 J5B 0.464286 0.794872
38 EBQ 0.464286 0.794872
39 RGG 0.462963 0.833333
40 BHG 0.45614 0.72093
41 HEX GLC 0.45614 0.72093
42 JZR 0.45614 0.72093
43 B7G 0.448276 0.744186
44 KGM 0.448276 0.744186
45 MBG GAL 0.448276 1
46 MBG GLA 0.446429 1
47 GYP GZL NAG 0.444444 0.7
48 BNG 0.440678 0.744186
49 HSJ 0.440678 0.744186
50 BOG 0.440678 0.744186
51 DGD 0.439024 0.73913
52 MAN MAN MAN MAN MAN MAN MAN 0.428571 0.942857
53 BMA BMA BMA BMA GLA 0.428571 0.942857
54 BMA MAN MAN MAN MAN 0.426667 0.891892
55 AXR BXY BXY BXY BXX BXX 0.425 0.8
56 HNV 0.41791 0.825
57 1GN ACY GAL 1GN BGC ACY GAL BGC 0.416667 0.693878
58 GL1 0.415094 0.666667
59 G1P 0.415094 0.666667
60 XGP 0.415094 0.666667
61 M1P 0.415094 0.666667
62 FK9 0.412698 0.704545
63 MAN MAN MAN 0.410959 0.916667
64 SER MAN 0.409836 0.688889
65 J7Z 0.406593 0.755556
66 GLC U8V 0.403226 0.918919
67 DR4 0.402985 0.785714
68 XNS 0.402985 0.785714
69 MAN BMA MAN MAN MAN MAN MAN 0.402439 1
Similar Ligands (3D)
Ligand no: 1; Ligand: MMA MAN; Similar ligands found: 39
No: Ligand Similarity coefficient
1 ZEL MAN 0.9952
2 MAN MAN 0.9802
3 MSX MAN 0.9611
4 DMJ MAN 0.9508
5 BMA MAN 0.9487
6 MAN GLC 0.9474
7 MMA LDY 0.9408
8 MAN MNM 0.9387
9 TW7 GLC 0.9341
10 MAN G63 0.9335
11 Z5L MAN 0.9318
12 GLC GLC 0.9313
13 MAN MVL 0.9185
14 7D1 MAN 0.9175
15 MAN IFM 0.9169
16 BDF GLC 0.9121
17 GLC DMJ 0.9115
18 RZM 0.9105
19 FRU GLC 0.9078
20 DGO MAN 0.9074
21 GLC FRU 0.9053
22 BMA GLA 0.9051
23 GLF B8D 0.9034
24 BGC GLC 0.8988
25 GMH GMH 0.8971
26 GLC BGC 0.8942
27 GLC GLA 0.8908
28 GPM GLC 0.8865
29 XMM 0.8864
30 MA1 GLC 0.8854
31 GLC IFM 0.8854
32 RR7 GLC 0.8831
33 DTK 0.8806
34 DGO Z61 0.8788
35 NOJ GLC 0.8731
36 BGC GLA 0.8698
37 GLA GLC 0.8654
38 GAL FUC 0.8593
39 FRU FRU 0.8590
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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