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 (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 473 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
70% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 355 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 5EYX - MDM C13 H24 O11 CO[C@@H]1[....
12 5EYY - MDM C13 H24 O11 CO[C@@H]1[....
50% Homology Family (59)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 272 families.
1 5T54 Kd = 0.87 nM A2G GLA FUC n/a n/a
2 5T5J Kd = 0.73 nM ACA SER SER VAL GLY A2G n/a n/a
3 5T52 Kd = 0.54 nM NGA C8 H15 N O6 CC(=O)N[C@....
4 5T5L Kd = 0.73 nM ACE SER SER VAL GLY A2G n/a n/a
5 5T5P Kd = 0.71 nM ACE SER THR VAL GLY A2G n/a n/a
6 1FNZ - A2G C8 H15 N O6 CC(=O)N[C@....
7 1S1A - MAN MMA n/a n/a
8 2ARB Ka = 26000 M^-1 NAG MAN n/a n/a
9 1N3Q - GLC BDF n/a n/a
10 2AR6 Ka = 63000 M^-1 NAG MAN MAN MAN NAG n/a n/a
11 1N3O - GYP C7 H14 O6 CO[C@@H]1[....
12 1N3P - GLC FRU n/a n/a
13 2ARX - MAN MAN n/a n/a
14 2ARE Ka = 1900 M^-1 MAN C6 H12 O6 C([C@@H]1[....
15 1LED - FUC GAL MAG FUC n/a n/a
16 1GSL - FUC GAL MAG FUC n/a n/a
17 1V00 - LAT C12 H22 O11 C([C@@H]1[....
18 3N3H - CIT C6 H8 O7 C(C(=O)O)C....
19 3N36 - GLA C6 H12 O6 C([C@@H]1[....
20 1AX0 Ka = 1340 M^-1 A2G C8 H15 N O6 CC(=O)N[C@....
21 1UZY - GAL BGC n/a n/a
22 1LTE - BGC GAL n/a n/a
23 1AX1 Ka = 1940 M^-1 BGC GAL n/a n/a
24 1AX2 Ka = 9730 M^-1 NDG GAL n/a n/a
25 1GZC Kd = 0.32 mM LAT C12 H22 O11 C([C@@H]1[....
26 3N35 - A2G C8 H15 N O6 CC(=O)N[C@....
27 1AXZ Ka = 1570 M^-1 GAL C6 H12 O6 C([C@@H]1[....
28 1GZ9 Kd = 0.31 mM FUC LAT n/a n/a
29 3ZYR Kd = 4.6 uM ASN NAG NAG BMA MAN MAN NAG NAG n/a n/a
30 3ZVX - MAN MAN MAN n/a n/a
31 5KXE Kd = 5.45 uM 6Y2 C22 H31 N3 O13 CC(=O)N[C@....
32 5KXB - NGA C8 H15 N O6 CC(=O)N[C@....
33 5KXC - 6Y2 C22 H31 N3 O13 CC(=O)N[C@....
34 5KXD - 6Y2 C22 H31 N3 O13 CC(=O)N[C@....
35 4WV8 - LBT C12 H22 O11 C([C@@H]1[....
36 4U2A - A2G C8 H15 N O6 CC(=O)N[C@....
37 4U36 - TNR C11 H20 N2 O8 CC(=O)N[C@....
38 1JXN - MFU C7 H14 O5 C[C@H]1[C@....
39 3WCS - MAN NAG GAL n/a n/a
40 3WOG - MAN NAG n/a n/a
41 5EYX - MDM C13 H24 O11 CO[C@@H]1[....
42 5EYY - MDM C13 H24 O11 CO[C@@H]1[....
43 2BQP - GLC C6 H12 O6 C([C@@H]1[....
44 5T7P - XMM C14 H15 Br Cl N O6 c1cc(c(c2c....
45 2DVA - GAL MGC n/a n/a
46 2DV9 - GAL GAL n/a n/a
47 1V6K - GAL GLC n/a n/a
48 1V6L - GAL BGC n/a n/a
49 2DVD - GAL GAL n/a n/a
50 2TEP - GAL NGA n/a n/a
51 2DVB - GAL C6 H12 O6 C([C@@H]1[....
52 1V6I - GAL GLC n/a n/a
53 2PEL Ki = 1.37 mM LAT C12 H22 O11 C([C@@H]1[....
54 1G9F - GAL NAG GAL NAG GAL n/a n/a
55 2DTW - 2GS C7 H14 O6 CO[C@@H]1[....
56 1WBL - AMG C7 H14 O6 CO[C@@H]1[....
57 2ZMK - GLA EGA n/a n/a
58 2D3S - TNR C11 H20 N2 O8 CC(=O)N[C@....
59 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: 52
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 0.696429 0.907407
3 NAG MAN BMA NDG MAN NAG GAL 0.65812 0.907407
4 NAG NAG BMA MAN MAN NAG NAG 0.655462 0.910714
5 NAG MAN GAL BMA NAG MAN NAG GAL 0.615385 0.907407
6 NAG MAN MAN MAN NAG GAL NAG GAL 0.615385 0.907407
7 MAN BMA NAG NAG MAN NAG GAL GAL 0.615385 0.907407
8 NAG MAN GAL BMA NDG MAN NAG GAL 0.615385 0.907407
9 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.576 0.888889
10 NAG MAN GAL MAN MAN NAG GAL 0.564103 0.888889
11 NAG MAN MAN MAN NAG 0.5625 0.888889
12 M5G 0.547619 0.888889
13 NAG NAG BMA MAN NAG 0.532258 0.910714
14 NAG NAG BMA MAN MAN MAN MAN 0.519084 0.892857
15 WZ5 0.504132 0.836364
16 NAG MAN MAN 0.5 0.833333
17 NAG MAN BMA 0.5 0.833333
18 MAN MAN NAG MAN NAG 0.487805 0.888889
19 NAG NAG BMA MAN MAN 0.487805 0.888889
20 MMA MAN NAG MAN NAG NAG 0.487395 0.890909
21 NAG MAN MMA 0.473214 0.836364
22 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.469231 0.839286
23 BMA NAG MAN MAN MAN MAN MAN MAN MAN 0.464567 0.833333
24 WZ4 0.462687 0.793103
25 NAG AMU NAG AMV 0.45082 0.909091
26 NAG GAL NAG 0.439655 0.888889
27 NAG NAG NAG NAG NAG NAG NAG NAG 0.428571 0.907407
28 NAG NAG NAG NDG 0.428571 0.907407
29 NDG NAG NAG NDG 0.428571 0.907407
30 NAG NAG NAG NAG 0.428571 0.907407
31 NDG NAG NAG 0.428571 0.907407
32 CTO 0.428571 0.907407
33 NAG NAG NDG 0.428571 0.907407
34 NAG NAG NAG 0.428571 0.907407
35 NAG NAG NAG NAG NDG 0.428571 0.907407
36 NAG NAG NAG NAG NAG 0.428571 0.907407
37 NDG NAG NAG NDG NAG 0.428571 0.907407
38 NAG NAG NAG NAG NAG NAG 0.428571 0.907407
39 NDG NAG NAG NAG 0.428571 0.907407
40 NAG NAG NAG NAG NDG NAG 0.428571 0.907407
41 NAG GAL BGC 0.42735 0.833333
42 GLC GAL NAG GAL 0.425 0.833333
43 NGA GLA GAL BGC 0.421488 0.833333
44 NAG GAL GAL NAG GAL 0.416667 0.888889
45 NAG GAL GAL NAG 0.416667 0.888889
46 GAL NAG GAL NAG GAL NAG 0.416667 0.907407
47 MAN MAN NAG 0.415254 0.836364
48 NAG BMA MAN MAN MAN MAN 0.404762 0.833333
49 NAG NAG NGT 0.403226 0.765625
50 GAL NAG MAN 0.401709 0.833333
51 MAN NAG GAL 0.401709 0.833333
52 NAG NAG BMA MAN 0.401575 0.892857
Ligand no: 2; Ligand: NAG NAG BMA MAN MAN NAG NAG; Similar ligands found: 91
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 BMA MAN MAN MAN MAN MAN MAN MAN 0.733333 0.924528
6 NAG MAN BMA NDG MAN NAG GAL 0.728972 0.924528
7 MAN BMA NAG NAG MAN NAG GAL GAL 0.682243 0.924528
8 NAG MAN GAL BMA NDG MAN NAG GAL 0.682243 0.924528
9 NAG MAN GAL BMA NAG MAN NAG GAL 0.682243 0.924528
10 NAG MAN MAN MAN NAG GAL NAG GAL 0.682243 0.924528
11 NAG NAG BMA MAN 0.656863 0.981132
12 ASN NAG NAG BMA MAN MAN NAG NAG 0.655462 0.910714
13 NAG MAN MAN MAN NAG 0.643564 0.90566
14 NAG MAN GAL MAN MAN NAG GAL 0.641509 0.90566
15 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.634783 0.90566
16 NAG NAG NAG NAG NAG NAG NAG 0.627451 0.981481
17 NAG NDG BMA 0.616162 0.981132
18 NAG NAG BMA 0.616162 0.981132
19 NAG NAG 0.606383 0.962264
20 M5G 0.603448 0.90566
21 NAG NAG BMA BMA 0.601942 0.981481
22 NAG MAN BMA 0.558824 0.849057
23 NAG MAN MAN 0.558824 0.849057
24 WZ5 0.544643 0.851852
25 MMA MAN NAG MAN NAG NAG 0.541284 0.907407
26 NAG NAG BMA MAN MAN 0.539823 0.90566
27 MAN MAN NAG MAN NAG 0.539823 0.90566
28 NAG MAN MMA 0.514563 0.851852
29 BMA NAG MAN MAN MAN MAN MAN MAN MAN 0.512821 0.849057
30 MAN MAN NAG 0.504762 0.886792
31 NAG GAL NAG 0.490566 0.90566
32 NAG BMA 0.484848 0.90566
33 WZ4 0.484127 0.807018
34 NAG NAG NDG 0.480392 0.924528
35 NAG NAG NAG NDG 0.480392 0.924528
36 NAG NAG NAG NAG NAG NAG 0.480392 0.924528
37 NDG NAG NAG NAG 0.480392 0.924528
38 NAG NAG NAG NAG NAG NAG NAG NAG 0.480392 0.924528
39 NAG NAG NAG NAG 0.480392 0.924528
40 NDG NAG NAG NDG NAG 0.480392 0.924528
41 NAG NAG NAG NAG NAG 0.480392 0.924528
42 NAG NAG NAG NAG NDG NAG 0.480392 0.924528
43 NDG NAG NAG 0.480392 0.924528
44 CTO 0.480392 0.924528
45 NDG NAG NAG NDG 0.480392 0.924528
46 NAG NAG NAG 0.480392 0.924528
47 NAG NAG NAG NAG NDG 0.480392 0.924528
48 NAG GAL GAL NAG GAL 0.477064 0.90566
49 NAG GAL BGC 0.476636 0.849057
50 GLC GAL NAG GAL 0.472727 0.849057
51 NGA GLA GAL BGC 0.468468 0.849057
52 NAG GAL GAL NAG 0.463636 0.90566
53 GAL NAG GAL NAG GAL NAG 0.463636 0.924528
54 MAN NAG GAL 0.448598 0.849057
55 GAL NAG MAN 0.448598 0.849057
56 NAG BMA MAN MAN MAN MAN 0.448276 0.849057
57 GAL NAG GAL 0.445455 0.886792
58 CBS 0.441176 0.90566
59 NAG GDL 0.441176 0.90566
60 CBS CBS 0.441176 0.90566
61 NAG NDG 0.441176 0.90566
62 NGA GAL BGC 0.439252 0.849057
63 FUC BGC GAL NAG GAL 0.438017 0.867925
64 FUC GAL NAG A2G 0.436975 0.981481
65 NAG NAG NGT 0.434783 0.777778
66 NOJ NAG NAG NAG 0.433628 0.928571
67 NOJ NAG NAG 0.433628 0.910714
68 NAG AMU NAG AMV 0.423729 0.890909
69 FUC BGC GAL NAG 0.423729 0.867925
70 A2G MBG 0.423077 0.851852
71 MBG A2G 0.423077 0.851852
72 MAN NAG 0.421569 0.849057
73 A2G GAL NAG FUC GAL GLC 0.418605 0.924528
74 GLC GAL NAG GAL FUC A2G 0.418605 0.924528
75 FUC GAL NAG GAL BGC 0.418033 0.867925
76 NAG GAL 0.417476 0.849057
77 NGA GAL 0.417476 0.849057
78 GAL NAG 0.417476 0.849057
79 MAN MAN MAN BMA MAN MAN MAN 0.415254 0.62963
80 NAG MBG 0.413462 0.851852
81 DLD 0.412281 0.790323
82 6Y2 0.410256 0.720588
83 3PV 0.408333 0.839286
84 A2G GAL NAG FUC 0.404959 0.924528
85 GLC GAL NAG GAL FUC FUC 0.404762 0.886792
86 BGC GAL NAG GAL FUC FUC 0.404762 0.886792
87 MAN MAN MAN BMA MAN 0.401786 0.622642
88 ACY 1GN GAL 1GN BGC ACY GAL BGC 0.401639 0.90566
89 AO3 0.401639 0.710145
90 1GN ACY GAL ACY 1GN BGC GAL BGC 0.401639 0.90566
91 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: 34
This union binding pocket(no: 1) in the query (biounit: 3zyr.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3VY6 BGC BGC 0.000005001 0.55656 1.41844
2 4MO2 FDA 0.007187 0.41699 1.53257
3 1PS9 FAD 0.01944 0.40137 1.53257
4 1BZL FAD 0.0149 0.43488 2.29885
5 3I7S PYR 0.005632 0.41934 2.29885
6 1GPM CIT 0.02178 0.40661 2.29885
7 5VE5 GSH 0.0344 0.4024 2.29885
8 3QV9 QV7 0.03103 0.40045 2.29885
9 4N2Z CTR 0.01453 0.41534 3.06513
10 3BP1 GUN 0.0176 0.41396 3.06513
11 4H4D 10E 0.01203 0.4075 3.06513
12 4ZNO SUC 0.00004571 0.53283 3.44828
13 3LAD FAD 0.005738 0.42638 3.83142
14 5TE1 7A2 0.008677 0.42289 3.83142
15 5TQZ GLC 0.000004184 0.41696 4
16 1YRO UDP 0.02448 0.40218 4.87805
17 2WPF WPF 0.01893 0.43054 5.74713
18 2WPF FAD 0.01932 0.42883 5.74713
19 4REP FAD 0.01086 0.41097 6.13027
20 3R51 MMA 0.002359 0.45248 6.25
21 3F8D FAD 0.01728 0.42192 6.51341
22 4RPL FAD 0.01855 0.41696 6.51341
23 2GUC MAN 0.0000004498 0.65263 6.55738
24 2GUD MAN 0.0000005799 0.64426 6.55738
25 2NU5 NAG 0.0000006568 0.62612 6.55738
26 2HYR BGC GLC 0.0000006617 0.62566 6.55738
27 2NUO BGC 0.000003691 0.56273 6.55738
28 2GUE NAG 0.00002526 0.4507 6.55738
29 4AKB GAL 0.008569 0.43623 6.76692
30 3LLZ GAL NGA 0.007687 0.42561 7.5188
31 4XFR CIT 0.01135 0.42594 9.1954
32 4RDN 6MD 0.01926 0.40977 14.3713
33 5ITZ GTP 0.009254 0.40005 17.3228
34 2DUR MAN MAN 0.00000106 0.4075 19.3676
Pocket No.: 2; Query (leader) PDB : 3ZYR; Ligand: ASN NAG NAG BMA MAN MAN NAG NAG; Similar sites found: 45
This union binding pocket(no: 2) in the query (biounit: 3zyr.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3VY6 BGC BGC 0.000006685 0.55023 1.41844
2 4MO2 FDA 0.007949 0.41504 1.53257
3 1PS9 FAD 0.02006 0.40075 1.53257
4 2CUN 3PG 0.0041 0.44063 2.29885
5 1BZL FAD 0.01442 0.43559 2.29885
6 5VE5 GSH 0.03328 0.4033 2.29885
7 4N2Z CTR 0.01539 0.41378 3.06513
8 3BP1 GUN 0.01785 0.41339 3.06513
9 1TDF NAP 0.02633 0.41307 3.06513
10 1TDF FAD 0.01695 0.40834 3.06513
11 4H4D 10E 0.01375 0.40473 3.06513
12 4JWK CTN 0.01633 0.41413 3.10881
13 4ZNO SUC 0.00005539 0.52618 3.44828
14 1MO9 FAD 0.01157 0.43414 3.83142
15 1MO9 KPC 0.01229 0.43337 3.83142
16 3LAD FAD 0.005693 0.42654 3.83142
17 5TE1 7A2 0.008873 0.42241 3.83142
18 2DVZ GLU 0.01794 0.403 3.83142
19 2V2G BEZ 0.02959 0.40171 3.86266
20 5TQZ GLC 0.000004759 0.41636 4
21 1YRO UDP 0.01672 0.40947 4.87805
22 2WPF WPF 0.02003 0.42805 5.74713
23 2WPF FAD 0.01963 0.42805 5.74713
24 2A9G ARG 0.0126 0.41476 5.74713
25 1TUU ADP 0.01511 0.41522 6.13027
26 4REP FAD 0.01686 0.40234 6.13027
27 3R51 MMA 0.003004 0.44596 6.25
28 4RPL 3UC 0.03681 0.40436 6.51341
29 2GUC MAN 0.000000523 0.63124 6.55738
30 2HYR BGC GLC 0.0000007056 0.62286 6.55738
31 2GUD MAN 0.0000006728 0.62236 6.55738
32 2NU5 NAG 0.0000007874 0.61821 6.55738
33 2NUO BGC 0.000005694 0.55479 6.55738
34 2GUE NAG 0.00004434 0.43303 6.55738
35 4AKB GAL 0.009199 0.4343 6.76692
36 1U1J MET 0.005881 0.42395 6.89655
37 3LLZ GAL NGA 0.009851 0.41283 7.5188
38 4XFR CIT 0.01029 0.42828 9.1954
39 2X2T GAL NGA 0.01862 0.40985 9.80392
40 1KC7 PPR 0.02871 0.40062 12.2605
41 4RDN 6MD 0.0181 0.41116 14.3713
42 1FEC FAD 0.01241 0.41459 15.3257
43 5ITZ GTP 0.008098 0.40254 17.3228
44 2DUR MAN MAN 0.00000129 0.40612 19.3676
45 2F5Z FAD 0.01392 0.40976 25
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