Receptor
PDB id Resolution Class Description Source Keywords
2VUZ 1.7 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF CODAKINE IN COMPLEX WITH BIANTENNARY NONASACCHARIDE AT 1.7A RESOLUTION CODAKIA ORBICULARIS NONASACCHARIDE CODAKIA ORBICULARIS SUGAR-BINDING PROTEIN LECTIN CODAKINE BIANTENNARY INVERTEBRATE SUGAR BINDING
Ref.: HIGH AFFINITY INTERACTION BETWEEN A BIVALVE C-TYPE AND A BIANTENNARY COMPLEX-TYPE N-GLYCAN REVEALED BY CRYSTALLOGRAPHY AND MICROCALORIMETRY. J.BIOL.CHEM. V. 283 30112 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:1130;
Part of Protein;
none;
submit data
40.078 Ca [Ca+2...
GOL A:1136;
A:1137;
A:1138;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NAG BMA NAG MAN MAN NAG NAG A:1139;
Valid;
none;
Kd = 0.432 uM
1317.21 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2VUZ 1.7 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF CODAKINE IN COMPLEX WITH BIANTENNARY NONASACCHARIDE AT 1.7A RESOLUTION CODAKIA ORBICULARIS NONASACCHARIDE CODAKIA ORBICULARIS SUGAR-BINDING PROTEIN LECTIN CODAKINE BIANTENNARY INVERTEBRATE SUGAR BINDING
Ref.: HIGH AFFINITY INTERACTION BETWEEN A BIVALVE C-TYPE AND A BIANTENNARY COMPLEX-TYPE N-GLYCAN REVEALED BY CRYSTALLOGRAPHY AND MICROCALORIMETRY. J.BIOL.CHEM. V. 283 30112 2008
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 2VUZ Kd = 0.432 uM NAG BMA NAG MAN MAN NAG NAG n/a n/a
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 2VUZ Kd = 0.432 uM NAG BMA NAG MAN MAN NAG NAG n/a n/a
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 2VUZ Kd = 0.432 uM NAG BMA NAG MAN MAN NAG NAG n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NAG BMA NAG MAN MAN NAG NAG; Similar ligands found: 150
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG BMA NAG MAN MAN NAG NAG 1 1
2 NAG MAN BMA NDG MAN NAG GAL 0.934783 1
3 MAN BMA NAG NAG MAN NAG GAL GAL 0.880435 1
4 NAG MAN GAL BMA NAG MAN NAG GAL 0.880435 1
5 NAG MAN MAN MAN NAG GAL NAG GAL 0.880435 1
6 NAG MAN GAL BMA NDG MAN NAG GAL 0.880435 1
7 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.81 0.979592
8 NAG NAG BMA MAN MAN NAG NAG 0.77451 0.924528
9 M5G 0.772277 0.979592
10 NAG NAG BMA MAN MAN 0.704082 0.979592
11 MAN MAN NAG MAN NAG 0.704082 0.979592
12 ASN NAG NAG BMA MAN MAN NAG NAG 0.696429 0.907407
13 NAG MAN MAN MAN NAG 0.691489 0.979592
14 NAG MAN GAL MAN MAN NAG GAL 0.686869 0.979592
15 BMA NAG MAN MAN MAN MAN MAN MAN MAN 0.666667 0.918367
16 NAG GAL NAG 0.659341 0.979592
17 NAG NAG NAG NAG NAG NAG NAG NAG 0.655172 1
18 NDG NAG NAG NDG NAG 0.655172 1
19 NAG NAG NAG NDG 0.655172 1
20 NAG NAG NAG 0.655172 1
21 NAG NAG NDG 0.655172 1
22 NAG NAG NAG NAG 0.655172 1
23 CTO 0.655172 1
24 NDG NAG NAG NDG 0.655172 1
25 NAG NAG NAG NAG NAG NAG 0.655172 1
26 NAG NAG NAG NAG NDG 0.655172 1
27 NAG NAG NAG NAG NDG NAG 0.655172 1
28 NDG NAG NAG 0.655172 1
29 NAG NAG NAG NAG NAG 0.655172 1
30 NDG NAG NAG NAG 0.655172 1
31 NAG NAG BMA MAN NAG 0.626168 0.924528
32 GAL NAG GAL NAG GAL NAG 0.621053 1
33 NAG GAL GAL NAG 0.621053 0.979592
34 NAG MAN BMA 0.617021 0.918367
35 NAG MAN MAN 0.617021 0.918367
36 NAG GDL 0.609195 0.979592
37 CBS 0.609195 0.979592
38 CBS CBS 0.609195 0.979592
39 NAG NDG 0.609195 0.979592
40 NAG NAG BMA MAN MAN MAN MAN 0.605263 0.90566
41 NAG BMA MAN MAN MAN MAN 0.594059 0.918367
42 WZ5 0.580952 0.92
43 MMA MAN NAG MAN NAG NAG 0.563107 0.98
44 NAG NAG NAG NAG NAG NAG NAG 0.558824 0.907407
45 NAG MAN MMA 0.552083 0.92
46 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.548673 0.849057
47 NAG GAL BGC 0.540816 0.918367
48 A2G GAL NAG FUC 0.537736 1
49 MAN BMA NAG 0.536842 0.918367
50 NAG GAL GAL 0.536842 0.918367
51 GLA GAL NAG 0.536842 0.918367
52 CTO TMX 0.535354 0.844828
53 TCG 0.535354 0.844828
54 GLC GAL NAG GAL 0.534653 0.918367
55 NGA GLA GAL BGC 0.529412 0.918367
56 FUL GAL NAG 0.520408 0.938776
57 DR2 0.520408 0.938776
58 NDG GAL FUC 0.520408 0.938776
59 FUC GAL NAG 0.520408 0.938776
60 FUC GAL NDG 0.520408 0.938776
61 WZ4 0.512605 0.867925
62 NAG GAL GAL NAG GAL 0.509804 0.979592
63 NGA GAL BGC 0.5 0.918367
64 MAN MAN NAG 0.49505 0.882353
65 GAL NAG MAN 0.494949 0.918367
66 MAN NAG GAL 0.494949 0.918367
67 NDG GAL 0.48913 0.918367
68 NLC 0.48913 0.918367
69 GAL NDG 0.48913 0.918367
70 GAL BGC NAG GAL 0.475728 0.918367
71 NAG NAG BMA MAN 0.472727 0.90566
72 FUC GAL NAG GAL BGC 0.469027 0.938776
73 SN5 SN5 0.46875 0.811321
74 MAN NAG 0.468085 0.918367
75 GLC GAL NAG GAL FUC A2G 0.466667 1
76 A2G GAL NAG FUC GAL GLC 0.466667 1
77 FUC BGC GAL NAG GAL 0.464912 0.938776
78 NDG NAG 0.463918 1
79 NAG NAG NGT 0.462963 0.830508
80 G6S NAG 0.460784 0.714286
81 MAN MAN MAN BMA MAN MAN MAN 0.454545 0.68
82 MBG A2G 0.453608 0.92
83 A2G MBG 0.453608 0.92
84 GLC GAL NAG GAL FUC FUC 0.452991 0.959184
85 BGC GAL NAG GAL FUC FUC 0.452991 0.959184
86 ACY 1GN GAL 1GN BGC ACY GAL BGC 0.451327 0.979592
87 1GN ACY GAL ACY 1GN BGC GAL BGC 0.451327 0.979592
88 FUC GAL NAG A2G 0.451327 0.907407
89 FUC BGC GAL NAG 0.45045 0.938776
90 NAG AMU NAG AMV 0.45045 0.960784
91 NOJ NAG NAG 0.448598 0.872727
92 NOJ NAG NAG NAG 0.448598 0.890909
93 NGA GAL 0.447917 0.918367
94 NAG FUC 0.447917 0.897959
95 GAL NAG 0.447917 0.918367
96 NAG GAL 0.447917 0.918367
97 NAG MBG 0.443299 0.92
98 NAG NGA 0.443299 0.979592
99 NAG A2G 0.443299 0.979592
100 A2G GAL BGC FUC 0.442478 0.938776
101 MAN MAN MAN BMA MAN 0.442308 0.673469
102 DLD 0.439252 0.813559
103 NAG NGO 0.436893 0.87037
104 6Y2 0.436364 0.765625
105 GAL NAG GAL 0.433962 0.882353
106 3PV 0.433628 0.867925
107 LAT NAG GAL 0.429907 0.918367
108 NAG NAG BMA 0.429907 0.90566
109 NAG MUB 0.429907 0.98
110 BGC GAL NAG GAL 0.429907 0.918367
111 GAL NAG GAL BGC 0.429907 0.918367
112 NAG AMU 0.429907 0.98
113 NAG NDG BMA 0.429907 0.90566
114 GAL NGA GLA BGC GAL 0.427273 0.918367
115 AO3 0.426087 0.753846
116 AML MAN MAN MAN MAN MAN MAN MAN MAN 0.426087 0.618182
117 UMG 0.423729 0.875
118 NAG NAG BMA BMA 0.423423 0.907407
119 NAG GAL FUC FUC A2G 0.422414 1
120 FUC GAL NAG A2G FUC 0.422414 1
121 NAG GCU NAG GCD 0.419355 0.907407
122 NDG BDP BDP NPO NDG 0.416 0.765625
123 NAA NAA AMI 0.415254 0.720588
124 NGA GAL FUC 0.415094 0.938776
125 A2G GAL FUC 0.415094 0.938776
126 A2G GLA FUC 0.415094 0.938776
127 FUC GL0 A2G 0.415094 0.938776
128 FUC GAL A2G 0.415094 0.938776
129 FUC GLA A2G 0.415094 0.938776
130 NAG NAG 0.411765 0.886792
131 BGC FUC GAL FUC A2G 0.408696 0.959184
132 GLC FUC GAL FUC A2G 0.408696 0.959184
133 BCW 0.407407 0.959184
134 FUC GAL NDG FUC 0.407407 0.959184
135 BDZ 0.407407 0.959184
136 FUC GAL NAG FUC 0.407407 0.959184
137 GAL NDG FUC FUC 0.407407 0.959184
138 FUC NDG GAL FUC 0.407407 0.959184
139 NGT NAG 0.407407 0.813559
140 FUC NAG GAL FUC 0.407407 0.959184
141 GAL NAG FUC FUC 0.407407 0.959184
142 GUM 0.40678 0.875
143 SIA GAL NAG GAL GLC 0.405797 0.924528
144 SIA GAL NAG GAL BGC 0.405797 0.924528
145 BGC GAL NAG SIA GAL 0.405797 0.924528
146 UNU GAL NAG 0.405405 0.96
147 NAG GAL FUC 0.401869 0.938776
148 DR3 0.401869 0.938776
149 GLA GAL NAG FUC GAL GLC 0.401639 0.938776
150 FUC GAL NAG GAL FUC 0.4 0.959184
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2VUZ; Ligand: NAG BMA NAG MAN MAN NAG NAG; Similar sites found: 65
This union binding pocket(no: 1) in the query (biounit: 2vuz.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2BW7 APC 0.04539 0.41989 None
2 2BW7 ECS 0.0417 0.41989 None
3 1TKE SER 0.01951 0.40755 None
4 4LTN FMN 0.02313 0.40588 None
5 4LTN NAI 0.02657 0.40588 None
6 1I9G SAM 0.02858 0.40058 1.55039
7 2GZM DGL 0.01355 0.40288 2.32558
8 3UTU 1TS 0.04559 0.40664 3.10078
9 2JFN GLU 0.01611 0.40171 3.10078
10 5K9B FMN 0.005686 0.4361 3.87597
11 2Z48 A2G 0.002672 0.43199 3.87597
12 3UR0 SVR 0.03995 0.41886 3.87597
13 5JWC FAD 0.03255 0.41592 3.87597
14 1EWY FAD 0.02024 0.41494 3.87597
15 2Z49 AMG 0.0003323 0.40551 3.87597
16 4O4K 2PK 0.0298 0.40229 3.87597
17 1NP7 FAD 0.04687 0.40056 3.87597
18 1USF FMN 0.01258 0.43033 4.65116
19 1USF NAP 0.01499 0.42937 4.65116
20 1KRH FAD 0.00891 0.4263 4.65116
21 4XTX 590 0.02144 0.41652 4.65116
22 1F20 FAD 0.01886 0.40942 4.65116
23 1ZC9 PMP 0.01915 0.40736 4.65116
24 1WY7 SAH 0.03202 0.40074 4.65116
25 1FC4 AKB PLP 0.0274 0.40049 4.65116
26 4JYD SAH 0.0356 0.40647 5.42636
27 2Q3O FMN 0.03564 0.40269 5.42636
28 2CET PGI 0.03596 0.40066 5.42636
29 4O8O AHR 0.01092 0.41559 6.20155
30 3B2Q ATP 0.03248 0.40164 6.20155
31 4KOT CE3 0.01146 0.44092 7.75194
32 5GXU FMN 0.00962 0.4243 7.75194
33 2G7C GLA GAL NAG 0.005696 0.42173 7.75194
34 1H4H XYP XYS XYP 0.01744 0.40817 7.75194
35 2JFQ DGL 0.01628 0.40149 9.30233
36 1NLU IVA PHI TYB 0.01476 0.40515 10.8527
37 4KQR VPP 0.02461 0.40156 10.8527
38 1RC0 KT5 0.02139 0.41966 11.6279
39 2DWU DGL 0.01394 0.40233 12.4031
40 4KIB SAH 0.02021 0.4054 13.1783
41 3CEV ARG 0.04393 0.40144 13.1783
42 5AX9 4KT 0.02127 0.4042 14.7287
43 2VVT I24 0.04376 0.40163 14.7287
44 4C2V YJA 0.02121 0.41764 15.9091
45 5D63 FUC GAL GLA 0.02263 0.41855 18.6047
46 1G1T SIA GAL MAG FUC 0.001292 0.43765 25.5814
47 1TLG GAL 0.000004204 0.58741 28
48 1PWB GLC GLC 0.000000001334 0.53522 36.4341
49 1PWB GLC 0.00000000242 0.52799 36.4341
50 4KZV TRE 0.000001275 0.52964 39.5349
51 3WH2 FLC 0.00008872 0.45683 39.5349
52 3P7G MAN 0.0000003541 0.65444 40.3101
53 1RDL MMA 0.000000002736 0.60257 41.5929
54 4WQQ MAN 0.0000005026 0.54708 41.8605
55 1BCJ NGA 0.00002109 0.5453 41.8605
56 5JQ1 ZPF 0.000007937 0.53953 41.8605
57 4ZES MMA 0.000000006442 0.51722 42.6357
58 2OX9 GAL NAG FUC 0.0000001618 0.67072 43.4109
59 3VYK MMA MAN NAG MAN NAG NAG 0.00000345 0.58128 43.4109
60 1JZN BGC GAL 0.00000002279 0.53638 43.4109
61 3ALT MLB 0.000527 0.45705 44.186
62 1K9J NAG MAN MAN MAN NAG 0.00001045 0.56798 44.9612
63 1SL4 MAN MAN MAN MAN 0.00000121 0.62229 45.7364
64 2MSB NAG BMA MAN MAN MAN MAN MAN 0.0000001951 0.65982 46.087
65 1SL6 GAL NDG FUC 0.0000002471 0.55909 48.8372
Feedback