Receptor
PDB id Resolution Class Description Source Keywords
5KXB 2.33 Å NON-ENZYME: OTHER WISTERIA FLORIBUNDA LECTIN IN COMPLEX WITH GALNAC WISTERIA FLORIBUNDA CARBOHYDRATE-BINDING PROTEIN LECTIN SUGAR BINDING PROTEIN
Ref.: MOLECULAR BASIS FOR RECOGNITION OF THE CANCER GLYCOBIOMARKER, LACDINAC (GALNAC[ BETA 14]GLCNAC), WISTERIA FLORIBUNDA AGGLUTININ. J.BIOL.CHEM. V. 291 24085 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAG FUC NAG BMA XYP MAN A:301;
Invalid;
none;
submit data n/a n/a n/a n/a
CA B:306;
D:302;
A:308;
C:306;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
MN D:303;
B:307;
A:309;
C:307;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
54.938 Mn [Mn+2...
NAG FUC NAG BMA B:301;
C:301;
Invalid;
Invalid;
none;
none;
submit data n/a n/a n/a n/a
NGA A:307;
B:305;
D:301;
C:305;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5KXE 2.09 Å NON-ENZYME: OTHER WISTERIA FLORIBUNDA LECTIN IN COMPLEX WITH GALNAC(BETA1-4)GL (LACDINAC) AT PH 4.2 WISTERIA FLORIBUNDA CARBOHYDRATE-BINDING PROTEIN LECTIN SUGAR BINDING PROTEIN-COMPLEX
Ref.: MOLECULAR BASIS FOR RECOGNITION OF THE CANCER GLYCOBIOMARKER, LACDINAC (GALNAC[ BETA 14]GLCNAC), WISTERIA FLORIBUNDA AGGLUTININ. J.BIOL.CHEM. V. 291 24085 2016
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 5KXE Kd = 5.45 uM 6Y2 C22 H31 N3 O13 CC(=O)N[C@....
2 5KXB - NGA C8 H15 N O6 CC(=O)N[C@....
3 5KXC - 6Y2 C22 H31 N3 O13 CC(=O)N[C@....
4 5KXD - 6Y2 C22 H31 N3 O13 CC(=O)N[C@....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 1FNZ - A2G C8 H15 N O6 CC(=O)N[C@....
2 5KXE Kd = 5.45 uM 6Y2 C22 H31 N3 O13 CC(=O)N[C@....
3 5KXB - NGA C8 H15 N O6 CC(=O)N[C@....
4 4U36 - TNR C11 H20 N2 O8 CC(=O)N[C@....
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: NGA; Similar ligands found: 109
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG 1 1
2 HSQ 1 1
3 NGA 1 1
4 A2G 1 1
5 NDG 1 1
6 BM3 1 1
7 BGN 0.638298 0.888889
8 SIZ 0.630435 0.906977
9 YX1 0.625 0.65
10 GAL NGA A2G 0.614035 0.816327
11 STZ 0.612245 0.65
12 16G 0.591837 0.735849
13 BMX 0.591837 0.735849
14 4QY 0.591837 0.735849
15 SNG 0.5625 0.866667
16 NGS 0.54902 0.661017
17 NAG GDL 0.54386 0.833333
18 CBS 0.54386 0.833333
19 CBS CBS 0.54386 0.833333
20 NAG NDG 0.54386 0.833333
21 ASG 0.538462 0.661017
22 BG8 0.537037 0.906977
23 2F8 0.530612 0.909091
24 MAG 0.530612 0.909091
25 NLC 0.517857 0.888889
26 GAL NDG 0.517857 0.888889
27 NDG GAL 0.517857 0.888889
28 NAG A2G 0.517241 0.833333
29 4V5 0.517241 0.829787
30 NAG NGA 0.517241 0.833333
31 MAN NAG 0.508772 0.888889
32 4UZ 0.508475 0.808511
33 NDG NAG NAG 0.508197 0.816327
34 CTO 0.508197 0.816327
35 NAG NAG NDG 0.508197 0.816327
36 NAG NAG NAG NDG 0.508197 0.816327
37 NAG NAG NAG NAG NAG NAG NAG NAG 0.508197 0.816327
38 NDG NAG NAG NDG 0.508197 0.816327
39 NAG NAG NAG NAG 0.508197 0.816327
40 NAG NAG NAG 0.508197 0.816327
41 NAG NAG NAG NAG NDG NAG 0.508197 0.816327
42 NAG NAG NAG NAG NAG NAG 0.508197 0.816327
43 NDG NAG NAG NDG NAG 0.508197 0.816327
44 NDG NAG NAG NAG 0.508197 0.816327
45 NAG NAG NAG NAG NDG 0.508197 0.816327
46 NAG NAG NAG NAG NAG 0.508197 0.816327
47 NBG 0.5 0.951219
48 MQG 0.5 0.698113
49 A2G GAL 0.491228 0.888889
50 GAL A2G 0.491228 0.888889
51 GAL NGA 0.491228 0.888889
52 AMU 0.490909 0.930233
53 GN1 0.490566 0.754717
54 NG1 0.490566 0.754717
55 NDG NAG 0.47541 0.816327
56 NAG GAL 0.474576 0.888889
57 NGA GAL 0.474576 0.888889
58 NAG FUC 0.474576 0.866667
59 GAL NAG 0.474576 0.888889
60 NAG GAL NAG 0.455882 0.833333
61 FUC NAG 0.45 0.888889
62 3YW 0.448276 0.930233
63 GLA GAL NAG 0.446154 0.888889
64 MAN BMA NAG 0.446154 0.888889
65 NAG GAL GAL 0.446154 0.888889
66 FUL GAL NAG 0.426471 0.869565
67 G6S NAG 0.426471 0.677966
68 DR2 0.426471 0.869565
69 FUC GAL NDG 0.426471 0.869565
70 FUC GAL NAG 0.426471 0.869565
71 NDG GAL FUC 0.426471 0.869565
72 GYU 0.42623 0.740741
73 TNR 0.42623 0.833333
74 NAG BDP 0.421875 0.851064
75 NAG MBG 0.419355 0.851064
76 NGA GAL BGC 0.41791 0.888889
77 NAG NAG 0.415385 0.784314
78 AZC 0.415094 0.795918
79 SN5 SN5 0.412698 0.705882
80 MBG A2G 0.412698 0.851064
81 A2G MBG 0.412698 0.851064
82 HS2 0.411765 0.8125
83 5AX 0.411765 0.866667
84 6ZC 0.409091 0.655738
85 LEC 0.409091 0.655738
86 GAL BGC NAG GAL 0.408451 0.888889
87 TCG 0.408451 0.689655
88 CTO TMX 0.408451 0.689655
89 NAG NAG NAG NAG NAG NAG NAG 0.407895 0.740741
90 BMA 0.404762 0.7
91 WOO 0.404762 0.7
92 ALL 0.404762 0.7
93 GLA 0.404762 0.7
94 MAN 0.404762 0.7
95 GAL 0.404762 0.7
96 GLC 0.404762 0.7
97 GXL 0.404762 0.7
98 GIV 0.404762 0.7
99 BGC 0.404762 0.7
100 NAG AMU 0.402778 0.8
101 NAG MUB 0.402778 0.8
102 A2G GAL FUC 0.4 0.869565
103 DR3 0.4 0.869565
104 NAG GAL FUC 0.4 0.869565
105 FUC GL0 A2G 0.4 0.869565
106 A2G GLA FUC 0.4 0.869565
107 FUC GAL A2G 0.4 0.869565
108 NGA GAL FUC 0.4 0.869565
109 FUC GLA A2G 0.4 0.869565
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5KXE; Ligand: 6Y2; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5kxe.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5KXE; Ligand: 6Y2; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5kxe.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5KXE; Ligand: 6Y2; Similar sites found: 32
This union binding pocket(no: 3) in the query (biounit: 5kxe.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1KPG SAH 0.005335 0.44137 2.05761
2 5LOG SAH 0.02816 0.40034 3.00429
3 4PNE SAH 0.005109 0.44484 3.29218
4 2J5V PCA 0.002796 0.43576 3.29218
5 4BMX ADE 0.02144 0.40534 3.29218
6 1NBU PH2 0.01676 0.40261 3.36134
7 4IWN GEK 0.01626 0.41778 3.49345
8 4NEC SAH 0.01407 0.41026 3.78788
9 1KOJ PAN 0.009183 0.42624 4.11523
10 4KQR VPP 0.01147 0.42027 4.11523
11 5JGL SAM 0.01923 0.40515 4.11523
12 4WKB TDI 0.02738 0.40381 4.11523
13 2FK8 SAM 0.01011 0.42439 4.52675
14 1XSE NDP 0.04304 0.41328 4.52675
15 1IYK MIM 0.03286 0.40777 4.52675
16 4UP3 NDP 0.02532 0.40693 4.93827
17 3LCC SAH 0.02139 0.40346 5.10638
18 4M00 SUC 0.0006692 0.45497 6.17284
19 5DX0 SFG 0.02135 0.41523 6.17284
20 5DX1 SFG 0.03354 0.40287 6.17284
21 5DWQ SFG 0.03326 0.40011 6.17284
22 2GJP MAL 0.005141 0.41932 6.58436
23 3T7S SAM 0.02092 0.40486 6.58436
24 1NVU GTP 0.03052 0.40688 6.62651
25 1PJS NAD 0.01118 0.41918 8.64198
26 2C6Q NDP 0.0454 0.41434 9.46502
27 2C6Q IMP 0.02901 0.40692 9.46502
28 1OX5 1PR 0.01858 0.42112 11.1111
29 2CDU FAD 0.0391 0.41161 11.5226
30 4KXQ APR 0.03209 0.4025 11.5226
31 1ZC3 GNP 0.02842 0.40945 12.3894
32 4GKY MAN 0.0006924 0.4071 30.0412
Pocket No.: 4; Query (leader) PDB : 5KXE; Ligand: 6Y2; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5kxe.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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