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Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PO4 A:309;
A:310;
C:306;
D:306;
B:312;
B:311;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
94.971 O4 P [O-]P...
6Y2 B:308;
C:303;
A:306;
D:303;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 5.45 uM
545.494 C22 H31 N3 O13 CC(=O...
CA D:305;
C:305;
A:308;
B:310;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
MN B:309;
C:304;
A:307;
D:304;
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 D:301;
C:301;
Invalid;
Invalid;
none;
none;
submit data
367.351 n/a O=C(N...
SO4 B:313;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
NAG FUC NAG BMA MAN A:301;
Invalid;
none;
submit data n/a n/a n/a n/a
NAG FUC NAG BMA XYP MAN MAN B:301;
Invalid;
none;
submit data n/a n/a n/a n/a
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 1443 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 (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 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 4WV8 - LBT C12 H22 O11 C([C@@H]1[....
5 4U2A - A2G C8 H15 N O6 CC(=O)N[C@....
6 4U36 - TNR C11 H20 N2 O8 CC(=O)N[C@....
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: 6Y2; Similar ligands found: 110
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 NPO A2G GAL 0.597701 0.984375
7 GAL A2G NPO 0.597701 0.984375
8 GUM 0.595745 0.73913
9 UMG 0.583333 0.73913
10 A2G MBG 0.5625 0.707692
11 MBG A2G 0.5625 0.707692
12 NAG NAG NAG NAG NDG 0.560976 0.765625
13 NAG NAG NAG NAG NAG NAG NAG NAG 0.560976 0.765625
14 CTO 0.560976 0.765625
15 NAG NAG NDG NAG 0.560976 0.765625
16 NDG NAG NAG NDG 0.560976 0.765625
17 NDG NAG NAG 0.560976 0.765625
18 NAG NAG NDG 0.560976 0.765625
19 NAG NAG NAG NAG NAG 0.560976 0.765625
20 NAG NAG NAG NAG NAG NAG 0.560976 0.765625
21 NDG NAG NAG NAG 0.560976 0.765625
22 NAG NAG NAG NDG 0.560976 0.765625
23 NAG GDL 0.55 0.75
24 NDG NAG 0.55 0.75
25 CBS 0.55 0.75
26 CBS CBS 0.55 0.75
27 DLD 0.533333 0.768116
28 NPJ 0.523256 0.828125
29 NAG NAG NAG NAG 0.516854 0.720588
30 NAG NAG NAG 0.516854 0.720588
31 RCB 0.511364 0.828125
32 NAG AMU NAG AMV 0.510417 0.769231
33 NAG NAG NGT 0.494737 0.684932
34 NOJ NAG NAG NAG 0.494624 0.714286
35 NOJ NAG NAG 0.494624 0.7
36 Z4S NAG NAG 0.494624 0.720588
37 GAL NPO 0.493671 0.796875
38 NBZ GLA 0.493671 0.796875
39 MBE 0.493671 0.796875
40 PNA 0.493671 0.796875
41 PNW 0.493671 0.796875
42 147 0.493671 0.796875
43 PNG 0.493671 0.796875
44 KHP 0.493506 0.742424
45 GNS BDP GNS BDP GNS BDP NPO 0.490741 0.769231
46 NGA GAL BGC 0.488636 0.703125
47 NGA GAL 0.482353 0.666667
48 NAG MAN MMA 0.477778 0.707692
49 NAG MBG 0.47619 0.707692
50 NAG NAG 0.471264 0.691176
51 NAG NDG 0.471264 0.691176
52 MAN MAN NAG 0.467391 0.681818
53 NAG GAL NAG 0.467391 0.75
54 NAG MAN BMA 0.466667 0.703125
55 AO3 0.465347 0.675325
56 NAA NAA AMI 0.465347 0.675325
57 GAL NAG 0.464286 0.703125
58 NAG GAL 0.464286 0.703125
59 NGT NAG 0.462366 0.671233
60 NAG A2G 0.458824 0.75
61 NAG NGA 0.458824 0.75
62 PNJ 0.457831 0.846154
63 NAG NM9 0.451613 0.742424
64 GAL NAG MAN 0.450549 0.703125
65 NAG MAN 0.448276 0.734375
66 TCG 0.446809 0.742857
67 GAL NAG GAL 0.446809 0.681818
68 NAG AMU 0.442105 0.78125
69 NAG MUB 0.442105 0.78125
70 MAG 0.441558 0.661538
71 2F8 0.441558 0.661538
72 3QL 0.43956 0.705882
73 NAG BMA NAG MAN MAN NAG NAG 0.436364 0.765625
74 NAG GAL BGC 0.43617 0.703125
75 MMA MAN NAG MAN NAG NAG 0.435644 0.753846
76 GNS BDP GNS IDS GNS BDP NPO 0.434426 0.769231
77 NAG MAN MAN 0.431579 0.703125
78 NAG MAN BMA MAN NAG GAL 0.431193 0.75
79 NAG MAN MAN MAN NAG 0.43 0.75
80 GAL NGA A2G 0.428571 0.75
81 NGA GLA GAL BGC 0.428571 0.703125
82 NAG NAG BMA 0.427083 0.705882
83 AH0 NAG 0.427083 0.710145
84 NAG NDG BMA 0.427083 0.705882
85 NGB 0.423913 0.828125
86 NAG NAG BMA MAN NAG 0.423423 0.720588
87 SN5 SN5 0.420455 0.632353
88 NAG AH0 0.42 0.735294
89 GN1 0.419753 0.671429
90 NG1 0.419753 0.671429
91 JXD 0.419643 0.65
92 NAG NAG BMA MAN MAN NAG GAL NAG 0.417391 0.765625
93 FUC GAL NAG A2G 0.413462 0.765625
94 A2G GAL NAG FUC 0.413462 0.765625
95 A2G GLA FUC 0.410526 0.71875
96 NGA GAL FUC 0.410526 0.71875
97 FUC GAL A2G 0.410526 0.71875
98 A2G GAL FUC 0.410526 0.71875
99 FUC GLA A2G 0.410526 0.71875
100 NAG NAG BMA MAN MAN NAG NAG 0.410256 0.720588
101 NAG MAN BMA NDG MAN NAG GAL 0.408696 0.765625
102 NAG GAL GAL NAG GAL 0.408163 0.75
103 GAL NAG GAL NAG GAL NAG 0.408163 0.765625
104 NAG GAL GAL NAG 0.408163 0.75
105 FHY 0.407767 0.720588
106 BMA Z4Y NAG 0.405941 0.692308
107 GLC GAL NAG GAL 0.40404 0.703125
108 LAT NAG GAL 0.40404 0.703125
109 WZ5 0.401869 0.707692
110 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 with APoc: 120
This union binding pocket(no: 1) in the query (biounit: 5kxe.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 1H74 ILE None
2 1H74 ADP None
3 2BES RES 1.16279
4 1WP4 NDP 1.23457
5 2ZA5 2FF 1.23457
6 6GAS FAD 1.64609
7 4QIJ 1HA 1.64609
8 2BLE 5GP 1.64609
9 5XDT GDP 1.64609
10 1UTJ ABN 1.65289
11 1GWN GTP 1.95122
12 1NW5 SAM 2.05761
13 6BQ6 TER 2.46914
14 4EHU ANP 2.46914
15 3H8V ATP 2.46914
16 3KLJ FAD 2.46914
17 3GUZ PAF 2.84091
18 2I7C AAT 2.88066
19 6F5W KG1 2.88066
20 2PT9 S4M 2.88066
21 2PT9 2MH 2.88066
22 5HXI 5HN 2.88066
23 5HXI FAD 2.88066
24 5T67 SAH 2.88066
25 12AS AMP 2.88066
26 3SBD GNP 3.20856
27 3CGD COA 3.29218
28 3CGD NAD 3.29218
29 3CGD FAD 3.29218
30 2J5V PCA 3.29218
31 4XQC 13D 3.29218
32 4BMX ADE 3.29218
33 2Q0L NAP 3.29218
34 5J60 FAD 3.29218
35 3GMB FAD 3.29218
36 4FFS BIG 3.34728
37 1ZOS MTM 3.47826
38 1BZL GCG 3.7037
39 1FL2 FAD 3.7037
40 2CXS F6P 3.7037
41 4YKG FAD 3.7037
42 5GT9 NAP 3.7037
43 4CQE CQE 3.7037
44 1IIM TTP 3.7037
45 1C3V NDP 3.7037
46 1VBO MAN 4.02685
47 1VBO MAN MAN MAN 4.02685
48 4KQR VPP 4.11523
49 5GWT SIN 4.11523
50 4WKB TDI 4.11523
51 1KOJ PAN 4.11523
52 3TLJ SAH 4.11523
53 5GM1 SAH 4.11523
54 5JGL SAM 4.11523
55 6AYR BIG 4.20168
56 3ZOK NAD 4.52675
57 1WYV PLP AOA 4.52675
58 3PT9 SAH 4.52675
59 1AL8 DHP 4.52675
60 1AL8 FMN 4.52675
61 1UAY ADN 4.54545
62 5FJN BE2 4.93827
63 5FJN FAD 4.93827
64 4UP3 NDP 4.93827
65 5GSN FAD 4.93827
66 3EYA FAD 4.93827
67 3FGC FMN 4.93827
68 1Q3Q ANP 4.93827
69 6FA4 GNP 5.20231
70 2WBP ZZU 5.34979
71 2WBP SIN 5.34979
72 1ON3 MCA 5.34979
73 2YAJ 4HP 5.76132
74 4K26 NDP 5.76132
75 4M00 SUC 6.17284
76 5VN0 FAD 6.17284
77 2DFV NAD 6.17284
78 3LL5 IPE 6.58436
79 3LL5 ADP 6.58436
80 2NP9 YE1 6.58436
81 6BVJ GNP 6.58683
82 2ZC0 PMP 6.99588
83 2VVL FAD 6.99588
84 1EP2 FMN 6.99588
85 6BVM GNP 7.18563
86 6D5H GNP 7.18563
87 6D59 GNP 7.18563
88 6BVL GNP 7.18563
89 6BVK GNP 7.18563
90 6D5M GNP 7.18563
91 6BVI GNP 7.18563
92 6D5G GNP 7.18563
93 1NVV GNP 7.22892
94 4AF0 IMP 7.40741
95 5C9P FUC 7.40741
96 4AUT FAD 7.81893
97 1KMQ GNP 8.15217
98 1GEX PLP HSA 8.23045
99 4WKC BIG 8.57143
100 1PJS NAD 8.64198
101 1IY8 NAD 8.64198
102 1CZA G6P 8.64198
103 5X40 ACP 9.0535
104 2C6Q IMP 9.46502
105 4UTG ANP 9.46502
106 2C6Q NDP 9.46502
107 4O1M NAD 9.87654
108 1S17 GNR 10
109 1S16 ANP 10.2881
110 1OX5 1PR 11.1111
111 2UYT ADP 11.5226
112 2UYT LRH 11.5226
113 1ZC3 GNP 12.3894
114 3NY4 SMX 16.4609
115 1CXZ GSP 17.4419
116 1QAW TRP 18.9189
117 4II2 ATP 21.4724
118 4GKY MAN 30.0412
119 2JE7 XMM 31.7992
120 1MVQ MMA 33.4746
Pocket No.: 2; Query (leader) PDB : 5KXE; Ligand: 6Y2; Similar sites found with APoc: 33
This union binding pocket(no: 2) in the query (biounit: 5kxe.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 3EWP APR 1.69492
2 3GFB NAD 2.05761
3 2X7J TPP 2.05761
4 3GD4 NAD 2.05761
5 1XL8 OCB 2.05761
6 1M7B GTP 2.17391
7 5F8F SFG 2.46914
8 5L95 AMP 2.46914
9 5T67 JHZ 2.88066
10 1KBJ FMN 2.88066
11 4XQC NAD 3.29218
12 4D04 NAP 3.7037
13 4D04 FAD 3.7037
14 3ABI NAD 3.7037
15 1L1E SAH 3.7037
16 5Z2M GTP 3.97727
17 3AB1 FAD 4.11523
18 2FK8 SAM 4.52675
19 4I9B 1KA 4.52675
20 3BL6 FMC 4.78261
21 2RDT 2RD 5.76132
22 4P53 NAI 5.76132
23 2GRU NAD 6.17284
24 4K81 GTP 6.43275
25 5MIT NAP 6.58436
26 5MIT FAD 6.58436
27 2VVM FAD 6.99588
28 3G5S FAD 7.40741
29 3ICR FAD 7.40741
30 3ICS FAD 7.40741
31 1LDN NAD 7.40741
32 1G8K MGD 9.02256
33 3DDC GNP 14.7239
Pocket No.: 3; Query (leader) PDB : 5KXE; Ligand: 6Y2; Similar sites found with APoc: 50
This union binding pocket(no: 3) in the query (biounit: 5kxe.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 1KPH SAH 2.05761
2 1KPG SAH 2.05761
3 3QF7 ANP 2.46914
4 5U3B 7TD 2.46914
5 5FWA J7C 2.88066
6 1KBI FMN 2.88066
7 1S7G NAD 2.88066
8 5LOG SAH 3.00429
9 1TPY SAH 3.29218
10 4PNE SAH 3.29218
11 1NBU PH2 3.36134
12 4IWN GEK 3.49345
13 4NEC SAH 3.78788
14 5GWT NAD 4.11523
15 1YC5 NCA 4.52675
16 1XSE NDP 4.52675
17 1IYK MIM 4.52675
18 5WP4 SAH 4.93827
19 1SZD APR 4.93827
20 3LCC SAH 5.10638
21 5TC4 NAD 5.76132
22 2RDT FMN 5.76132
23 4NBW NAD 5.76132
24 6ECT SAM 5.76132
25 4BMO FMN 5.88235
26 5DX8 SFG 6.17284
27 5DX1 SFG 6.17284
28 5DXA SFG 6.17284
29 5DX0 SFG 6.17284
30 5DWQ SFG 6.17284
31 4IS0 1R4 6.22407
32 2GJP MAL 6.58436
33 3T7S SAM 6.58436
34 6D55 GNP 7.18563
35 3AD8 NAD 7.40741
36 2YIC TPP 7.40741
37 1F2U ATP 7.43243
38 6C8R SAH 7.81893
39 4LZJ 22H 7.81893
40 3HDY FAD 8.23045
41 3HDY GDU 8.23045
42 5LU5 M7P 8.62944
43 5WP5 SAH 9.0535
44 1XHL NDP 9.0535
45 5ODQ 9SB 9.28571
46 5F52 ASP 9.87654
47 1XKQ NDP 11.1111
48 2CDU FAD 11.5226
49 4KXQ APR 11.5226
50 1GUA GNP 14.8148
Pocket No.: 4; Query (leader) PDB : 5KXE; Ligand: 6Y2; Similar sites found with APoc: 10
This union binding pocket(no: 4) in the query (biounit: 5kxe.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 3W8X FAD 2.05761
2 6F7L FAD 3.29218
3 2VK4 TPP 3.7037
4 6ER9 FAD 4.11523
5 1RQ5 CTT 4.11523
6 1O94 ADP 4.52675
7 3AXB FAD 6.99588
8 3AXB PRO 6.99588
9 6D56 GNP 7.18563
10 4Q9N NAI 10.2881
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