Receptor
PDB id Resolution Class Description Source Keywords
5KXC 1.8 Å NON-ENZYME: OTHER WISTERIA FLORIBUNDA LECTIN IN COMPLEX WITH GALNAC(BETA1-4)GL (LACDINAC) AT PH 8.5. 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
CA D:303;
A:304;
C:306;
B:303;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
6Y2 C:305;
B:302;
D:302;
A:303;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
545.494 C22 H31 N3 O13 CC(=O...
NAG B:301;
D:301;
Invalid;
Invalid;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
NAG FUC NAG BMA C:301;
Invalid;
none;
submit data n/a n/a n/a n/a
NAG FUC A:301;
Invalid;
none;
submit data
367.351 n/a O=C(N...
MN C:307;
A:305;
D:304;
B:304;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
54.938 Mn [Mn+2...
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 (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 5KXC - 6Y2 C22 H31 N3 O13 CC(=O)N[C@....
2 5KXD - 6Y2 C22 H31 N3 O13 CC(=O)N[C@....
3 4WV8 - LBT C12 H22 O11 C([C@@H]1[....
4 4U2A - A2G C8 H15 N O6 CC(=O)N[C@....
5 3WCS - MAN NAG GAL n/a n/a
6 3WOG - MAN NAG n/a n/a
7 1G9F - GAL NAG GAL NAG GAL n/a n/a
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: 6Y2; Similar ligands found: 108
No: Ligand ECFP6 Tc MDL keys Tc
1 6Y2 1 1
2 LEC 0.767123 0.953125
3 6ZC 0.767123 0.953125
4 LEC NGA 0.753086 1
5 NDG BDP BDP NPO NDG 0.677083 1
6 GAL A2G NPO 0.597701 0.984375
7 NPO A2G GAL 0.597701 0.984375
8 GUM 0.595745 0.73913
9 UMG 0.583333 0.73913
10 MBG A2G 0.5625 0.707692
11 A2G MBG 0.5625 0.707692
12 NAG NAG NAG 0.560976 0.765625
13 NAG NAG NAG NAG NDG 0.560976 0.765625
14 NAG NAG NDG 0.560976 0.765625
15 NAG NAG NAG NAG NAG 0.560976 0.765625
16 NAG NAG NAG NAG NDG NAG 0.560976 0.765625
17 NAG NAG NAG NAG NAG NAG NAG NAG 0.560976 0.765625
18 NDG NAG NAG NDG NAG 0.560976 0.765625
19 NDG NAG NAG NDG 0.560976 0.765625
20 NDG NAG NAG 0.560976 0.765625
21 CTO 0.560976 0.765625
22 NAG NAG NAG NAG NAG NAG 0.560976 0.765625
23 NAG NAG NAG NDG 0.560976 0.765625
24 NDG NAG NAG NAG 0.560976 0.765625
25 NAG NAG NAG NAG 0.560976 0.765625
26 CBS 0.55 0.75
27 CBS CBS 0.55 0.75
28 NAG NDG 0.55 0.75
29 NAG GDL 0.55 0.75
30 DLD 0.533333 0.768116
31 NPJ 0.523256 0.828125
32 RCB 0.511364 0.828125
33 NAG AMU NAG AMV 0.510417 0.769231
34 GNS BDP GNS BDP GNS BDP NPO 0.5 0.789474
35 NAG NAG NGT 0.494737 0.684932
36 NOJ NAG NAG NAG 0.494624 0.724638
37 NOJ NAG NAG 0.494624 0.710145
38 PNW 0.493671 0.796875
39 PNA 0.493671 0.796875
40 PNG 0.493671 0.796875
41 147 0.493671 0.796875
42 MBE 0.493671 0.796875
43 NBZ GLA 0.493671 0.796875
44 GLA NPO 0.493671 0.796875
45 GAL NPO 0.493671 0.796875
46 KHP 0.493506 0.742424
47 NGA GAL BGC 0.488636 0.703125
48 MAN NAG 0.487805 0.703125
49 NAG NGO 0.483146 0.705882
50 NAG MAN MMA 0.477778 0.707692
51 NAG MBG 0.47619 0.707692
52 NAG NAG NAG NAG NAG NAG NAG 0.474227 0.710145
53 NAG NAG 0.471264 0.691176
54 MAN MAN NAG 0.467391 0.681818
55 NAG GAL NAG 0.467391 0.75
56 NAA NAA AMI 0.466019 0.670886
57 AO3 0.465347 0.675325
58 NDG NAG 0.465116 0.765625
59 NGA GAL 0.464286 0.703125
60 GAL NAG 0.464286 0.703125
61 NAG GAL 0.464286 0.703125
62 NGT NAG 0.462366 0.671233
63 NAG NGA 0.458824 0.75
64 NAG A2G 0.458824 0.75
65 PNJ 0.457831 0.846154
66 NAG NM9 0.451613 0.742424
67 MAN NAG GAL 0.450549 0.703125
68 GAL NAG MAN 0.450549 0.703125
69 CTO TMX 0.446809 0.742857
70 GAL NAG GAL 0.446809 0.681818
71 TCG 0.446809 0.742857
72 NAG MUB 0.442105 0.78125
73 NAG AMU 0.442105 0.78125
74 GNS BDP GNS IDS GNS BDP NPO 0.441667 0.789474
75 2F8 0.441558 0.661538
76 MAG 0.441558 0.661538
77 3QL 0.43956 0.705882
78 NAG BMA NAG MAN MAN NAG NAG 0.436364 0.765625
79 NAG GAL BGC 0.43617 0.703125
80 MMA MAN NAG MAN NAG NAG 0.435644 0.753846
81 NAG MAN MAN 0.431579 0.703125
82 NAG MAN BMA 0.431579 0.703125
83 NAG MAN MAN MAN NAG 0.43 0.75
84 NGA GLA GAL BGC 0.428571 0.703125
85 NAG NDG BMA 0.427083 0.705882
86 NAG NAG BMA 0.427083 0.705882
87 AH0 NAG 0.427083 0.710145
88 NGB 0.423913 0.828125
89 NAG NAG BMA MAN NAG 0.423423 0.720588
90 SN5 SN5 0.420455 0.632353
91 NAG AH0 0.42 0.735294
92 GN1 0.419753 0.671429
93 NG1 0.419753 0.671429
94 A2G GAL NAG FUC 0.413462 0.765625
95 NGA GAL FUC 0.410526 0.71875
96 A2G GAL FUC 0.410526 0.71875
97 FUC GL0 A2G 0.410526 0.71875
98 FUC GAL A2G 0.410526 0.71875
99 A2G GLA FUC 0.410526 0.71875
100 FUC GLA A2G 0.410526 0.71875
101 NAG NAG BMA MAN MAN NAG NAG 0.410256 0.720588
102 NAG MAN BMA NDG MAN NAG GAL 0.408696 0.765625
103 NAG GAL GAL NAG GAL 0.408163 0.75
104 GAL NAG GAL NAG GAL NAG 0.408163 0.765625
105 NAG GAL GAL NAG 0.408163 0.75
106 GLC GAL NAG GAL 0.40404 0.703125
107 WZ5 0.401869 0.707692
108 NAG GDL PHJ 0.4 0.838235
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
Feedback