Receptor
PDB id Resolution Class Description Source Keywords
2DUR 1.65 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF VIP36 EXOPLASMIC/LUMENAL DOMAIN, CA2+/M FORM CANIS LUPUS FAMILIARIS BETA SANDWICH CARBOHYDRATE BINDING PROTEIN CARGO RECEPTORTRANSPORT
Ref.: STRUCTURAL BASIS FOR RECOGNITION OF HIGH MANNOSE TY GLYCOPROTEINS BY MAMMALIAN TRANSPORT LECTIN VIP36 J.BIOL.CHEM. V. 282 28246 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:1;
B:2;
Part of Protein;
Part of Protein;
none;
none;
submit data
40.078 Ca [Ca+2...
CL A:10;
A:3;
A:5;
A:8;
A:9;
B:4;
B:6;
B:7;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
35.453 Cl [Cl-]
GOL A:11;
A:12;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
MAN MAN A:13;
B:15;
Valid;
Valid;
none;
none;
submit data
342.297 n/a O(C1O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2DUR 1.65 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF VIP36 EXOPLASMIC/LUMENAL DOMAIN, CA2+/M FORM CANIS LUPUS FAMILIARIS BETA SANDWICH CARBOHYDRATE BINDING PROTEIN CARGO RECEPTORTRANSPORT
Ref.: STRUCTURAL BASIS FOR RECOGNITION OF HIGH MANNOSE TY GLYCOPROTEINS BY MAMMALIAN TRANSPORT LECTIN VIP36 J.BIOL.CHEM. V. 282 28246 2007
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 2DUR - MAN MAN n/a n/a
2 2E6V - MAN C6 H12 O6 C([C@@H]1[....
3 2DUQ - MAN C6 H12 O6 C([C@@H]1[....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 2DUR - MAN MAN n/a n/a
2 2E6V - MAN C6 H12 O6 C([C@@H]1[....
3 2DUQ - MAN C6 H12 O6 C([C@@H]1[....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 2DUR - MAN MAN n/a n/a
2 2E6V - MAN C6 H12 O6 C([C@@H]1[....
3 2DUQ - MAN C6 H12 O6 C([C@@H]1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MAN MAN; Similar ligands found: 243
No: Ligand ECFP6 Tc MDL keys Tc
1 MAN MAN 1 1
2 BGC BGC 1 1
3 2M4 1 1
4 BMA BMA MAN 0.886364 0.970588
5 MAN MAN BMA 0.808511 1
6 MAN MAN MAN GLC 0.690909 1
7 FUC GAL 0.66 0.941176
8 GAL NAG MAN 0.612903 0.733333
9 MAN NAG GAL 0.612903 0.733333
10 BGC GLC 0.612245 1
11 GLC BGC 0.612245 1
12 B2G 0.612245 1
13 GLA GAL 0.612245 1
14 LAT 0.612245 1
15 GLC GAL 0.612245 1
16 CBK 0.612245 1
17 BGC GAL 0.612245 1
18 MAL MAL 0.612245 0.970588
19 GLA GLA 0.612245 1
20 GAL GLC 0.612245 1
21 BMA GAL 0.612245 1
22 MAB 0.612245 1
23 GAL BGC 0.612245 1
24 CBI 0.612245 1
25 BMA BMA 0.612245 1
26 BGC BMA 0.612245 1
27 LB2 0.612245 1
28 MAN GLC 0.612245 1
29 LBT 0.612245 1
30 N9S 0.612245 1
31 M3M 0.612245 1
32 MAL 0.612245 1
33 TRE 0.595238 1
34 GLA MBG 0.591837 0.942857
35 BGC BGC BGC ASO BGC BGC ASO 0.584906 1
36 GLC BGC BGC BGC BGC BGC BGC 0.584906 1
37 BGC BGC BGC 0.584906 1
38 BGC BGC BGC GLC BGC BGC 0.584906 1
39 BGC BGC BGC BGC BGC 0.584906 1
40 GLC BGC BGC BGC 0.584906 1
41 M6P MAN MAN 0.580645 0.785714
42 BMA MAN MAN 0.571429 1
43 GLA GAL GLC 0.566038 1
44 BGC GLC GLC GLC 0.566038 1
45 GAL GAL GAL 0.566038 1
46 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.566038 1
47 BGC BGC BGC BGC BGC BGC 0.566038 1
48 BMA MAN BMA 0.566038 1
49 GLC BGC BGC BGC BGC 0.566038 1
50 CE6 0.566038 1
51 BGC GLC GLC GLC GLC GLC GLC 0.566038 1
52 MTT 0.566038 1
53 GLC BGC BGC 0.566038 1
54 CEY 0.566038 1
55 MT7 0.566038 1
56 CE5 0.566038 1
57 BMA BMA BMA BMA BMA BMA 0.566038 1
58 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.566038 1
59 BGC BGC BGC GLC 0.566038 1
60 GLC GLC GLC GLC GLC GLC GLC GLC 0.566038 1
61 MLR 0.566038 1
62 BMA BMA BMA 0.566038 1
63 CEX 0.566038 1
64 BGC GLC GLC 0.566038 1
65 CTR 0.566038 1
66 BGC GLC GLC GLC GLC 0.566038 1
67 GLC BGC GLC 0.566038 1
68 CT3 0.566038 1
69 GLC GLC BGC GLC GLC GLC GLC 0.566038 1
70 MAN MAN BMA BMA BMA BMA 0.566038 1
71 CTT 0.566038 1
72 DXI 0.566038 1
73 MAN BMA BMA BMA BMA 0.566038 1
74 GLC GAL GAL 0.566038 1
75 BMA BMA BMA BMA BMA 0.566038 1
76 B4G 0.566038 1
77 MAN BMA BMA 0.566038 1
78 GLC BGC BGC BGC BGC BGC 0.566038 1
79 CE8 0.566038 1
80 GLC GLC GLC GLC GLC GLC GLC 0.566038 1
81 GLC GLC GLC GLC GLC 0.566038 1
82 GLC GLC BGC 0.566038 1
83 LAT GLA 0.56 1
84 MAN BMA BMA BMA BMA BMA 0.553571 0.970588
85 BMA BMA BMA BMA BMA BMA MAN 0.553571 0.970588
86 BGC BGC GLC 0.553571 1
87 MAN NAG 0.551724 0.733333
88 GLA GAL GAL 0.54386 1
89 GLA GAL BGC 0.54386 1
90 GAL GAL FUC 0.542373 0.970588
91 GLA GAL FUC 0.542373 0.970588
92 GLA GLA FUC 0.542373 0.970588
93 FUC GLA GLA 0.542373 0.970588
94 FUC GAL GLA 0.542373 0.970588
95 U63 0.537037 0.891892
96 GAL FUC 0.537037 0.941176
97 RZM 0.528302 0.688889
98 M13 0.528302 0.942857
99 MDM 0.528302 0.942857
100 GAL MBG 0.528302 0.942857
101 DR5 0.528302 0.942857
102 MMA MAN 0.528302 0.942857
103 GLA EGA 0.527273 0.942857
104 DOM 0.518519 0.942857
105 BMA MAN 0.518519 0.914286
106 FMO 0.508772 0.868421
107 A2G GAL 0.508475 0.733333
108 GAL A2G 0.508475 0.733333
109 GAL NGA 0.508475 0.733333
110 BGC BGC BGC BGC BGC BGC BGC BGC 0.508197 1
111 BGC BGC BGC BGC 0.508197 1
112 MAL EDO 0.491228 0.942857
113 GLA MAN ABE 0.484848 0.916667
114 NDG GAL 0.483333 0.733333
115 GAL NDG 0.483333 0.733333
116 NLC 0.483333 0.733333
117 NOJ GLC 0.482759 0.727273
118 AMG 0.478261 0.857143
119 MMA 0.478261 0.857143
120 GYP 0.478261 0.857143
121 MBG 0.478261 0.857143
122 GAL NGA A2G 0.476923 0.673469
123 ABL 0.474576 0.702128
124 MVP 0.474576 0.733333
125 CGC 0.474576 0.941176
126 5QP 0.473684 0.885714
127 FRU GAL 0.473684 0.842105
128 NOY BGC 0.473684 0.75
129 BMA FRU 0.473684 0.842105
130 T6P 0.472727 0.767442
131 GLC GLC GLC GLC GLC GLC 0.46875 1
132 GAL GAL SO4 0.467742 0.702128
133 BMA IFM 0.465517 0.744186
134 MAN MNM 0.465517 0.75
135 IFM BMA 0.465517 0.744186
136 9MR 0.465517 0.744186
137 BGC OXZ 0.465517 0.666667
138 IFM BGC 0.465517 0.744186
139 FUC BGC GAL 0.460317 0.970588
140 G2F BGC BGC BGC BGC BGC 0.460317 0.868421
141 GLA GAL BGC 5VQ 0.459016 0.891892
142 GLC DMJ 0.457627 0.727273
143 MAN DGO 0.448276 0.914286
144 BMA BMA GLA BMA BMA 0.447761 1
145 2GS 0.446809 0.857143
146 GLC GLC XYP 0.446154 1
147 P3M 0.446154 0.767442
148 GAL BGC BGC XYS 0.442857 0.942857
149 GLA GAL NAG 0.441176 0.733333
150 NAG GAL GAL 0.441176 0.733333
151 MAN BMA NAG 0.441176 0.733333
152 MAN MAN MAN MAN 0.439394 1
153 SOR GLC GLC 0.439394 0.970588
154 MAN MAN BMA MAN 0.439394 1
155 MAN 7D1 0.438596 0.888889
156 NAG BMA 0.4375 0.653061
157 GLC GLC GLC GLC 0.4375 1
158 GLA GAL GLC NBU 0.4375 0.846154
159 MAN MAN MAN BMA MAN 0.43662 1
160 8VZ 0.435484 0.673469
161 GAL MGC 0.435484 0.702128
162 GLC GLC GLC BGC 0.432836 1
163 MAN BMA MAN MAN MAN 0.432836 1
164 M5S 0.432836 1
165 MAN 0.431818 0.848485
166 GAL 0.431818 0.848485
167 BMA 0.431818 0.848485
168 ALL 0.431818 0.848485
169 WOO 0.431818 0.848485
170 GXL 0.431818 0.848485
171 GLC 0.431818 0.848485
172 GLA 0.431818 0.848485
173 BGC 0.431818 0.848485
174 GIV 0.431818 0.848485
175 BGC BGC G2F SHG 0.430556 0.846154
176 MLB 0.428571 1
177 BGC GLA 0.428571 1
178 KHO 0.428571 0.888889
179 GLA BGC 0.428571 1
180 MAN BMA 0.428571 1
181 GAL GAL 0.428571 1
182 LAK 0.428571 1
183 GLA GLC 0.428571 1
184 GLA BMA 0.428571 1
185 BMA GLA 0.428571 1
186 SOR GLC GLC GLC 0.426471 0.970588
187 LAG 0.426471 0.6
188 GAL BGC NAG GAL 0.424658 0.733333
189 OXZ BGC BGC 0.424242 0.6875
190 LAT FUC 0.424242 0.970588
191 BGC GAL FUC 0.424242 0.970588
192 FUC GAL GLC 0.424242 0.970588
193 UMQ 0.424242 0.785714
194 GLC GAL FUC 0.424242 0.970588
195 G3I 0.424242 0.767442
196 DMU 0.424242 0.785714
197 LMU 0.424242 0.785714
198 FUC LAT 0.424242 0.970588
199 LMT 0.424242 0.785714
200 G2I 0.424242 0.767442
201 BTU 0.423729 0.842105
202 TUR 0.423729 0.842105
203 LAT NAG GAL 0.418919 0.733333
204 BGC GAL NAG GAL 0.418919 0.733333
205 GAL NAG GAL BGC 0.418919 0.733333
206 BGC GLA GAL FUC 0.416667 0.970588
207 ISX 0.416667 0.761905
208 MAN MMA MAN 0.415385 0.942857
209 NPJ 0.414286 0.622642
210 GLC GLC GLC 0.413793 1
211 MAN MAN MAN 0.413793 1
212 GLC GLC GLC GLC GLC BGC 0.413793 1
213 GLC GLC GLC GLC BGC 0.413793 1
214 NAG GAL GAL NAG GAL 0.413333 0.6875
215 GLC GLC XYS 0.411765 0.970588
216 G1P 0.411765 0.697674
217 ALX 0.411765 0.697674
218 GL1 0.411765 0.697674
219 BNX 0.411765 0.697674
220 M1P 0.411765 0.697674
221 XGP 0.411765 0.697674
222 56N 0.410714 0.833333
223 MAN IFM 0.409836 0.761905
224 GLC IFM 0.409836 0.761905
225 FUC NDG GAL 0.408451 0.717391
226 OPM MAN MAN 0.408451 0.804878
227 GAL NDG FUC 0.408451 0.717391
228 FUC NAG GAL 0.408451 0.717391
229 GAL NAG FUC 0.408451 0.717391
230 GLC GAL NAG GAL 0.407895 0.733333
231 LSE 0.405797 0.6875
232 6UZ 0.405797 0.846154
233 GLC 7LQ 0.403226 0.885714
234 GAL NGT 0.402985 0.66
235 BMA MVL 0.402985 0.6
236 MVL BMA 0.402985 0.6
237 IDC 0.402985 0.6
238 NGT GAL 0.402985 0.66
239 RCB 0.402778 0.622642
240 GLO GLC GLC 0.402778 0.942857
241 GTM BGC BGC 0.4 0.868421
242 GLC GLC BGC XYS BGC XYS 0.4 0.942857
243 10M 0.4 0.733333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2DUR; Ligand: MAN MAN; Similar sites found: 87
This union binding pocket(no: 1) in the query (biounit: 2dur.bio2) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3BY8 MLT 0.003389 0.41051 1.40845
2 1W8S FBP 0.0111 0.41179 1.97628
3 4FL3 ANP 0.01793 0.41147 1.97628
4 3MI2 PFU 0.04042 0.40705 2.15054
5 1V8B NAD 0.02548 0.42549 2.37154
6 1WG8 SAM 0.01461 0.41615 2.37154
7 1VBO MAN MAN MAN 0.005908 0.40493 2.68456
8 1VBO MAN 0.007053 0.40176 2.68456
9 4JBI NDP 0.01641 0.41218 2.7668
10 4J36 FAD 0.01186 0.4331 2.89157
11 4HKP TKW 0.01403 0.40837 3.16206
12 1VL0 NAI 0.004054 0.44876 3.55731
13 5M67 3D1 0.02895 0.4223 3.55731
14 5G3U FDA 0.03798 0.41755 3.55731
15 3SLS ANP 0.02204 0.41146 3.55731
16 2O4C NAD 0.03083 0.41014 3.55731
17 2QZZ NAP 0.0331 0.40053 3.55731
18 2QZZ EMF 0.03428 0.40053 3.55731
19 1LES GLC FRU 0.0000003836 0.63517 3.84615
20 5AYV KPL 0.008594 0.451 3.95257
21 4MIG G3F 0.04279 0.42258 3.95257
22 5EOW FAD 0.03137 0.41362 3.95257
23 3I6I NDP 0.008952 0.44801 4.34783
24 4KP7 1UQ 0.02721 0.40748 4.34783
25 2P53 NNG 0.01718 0.40435 4.34783
26 3KEE 30B 0.02639 0.40261 4.34783
27 3ABI NAD 0.04079 0.40068 4.34783
28 3BXF 13P 0.0105 0.42551 4.74308
29 5J60 FAD 0.02771 0.4231 4.74308
30 3ITJ FAD 0.04081 0.42247 4.74308
31 4F7E 0SH 0.02962 0.41286 5.10204
32 3C1O NAP 0.02064 0.4091 5.13834
33 2PYW ADP 0.01659 0.40317 5.13834
34 5ML3 DL3 0.03398 0.4107 5.36913
35 3KC1 2T6 0.01328 0.41978 5.92885
36 1E1M NAP 0.04387 0.41501 5.92885
37 1E1M FAD 0.04387 0.41501 5.92885
38 1N62 MCN 0.02243 0.41412 6.32411
39 4M00 SUC 0.000007865 0.55458 6.65434
40 3V3L V3L 0.02129 0.40567 7.05882
41 3G08 FEE 0.02887 0.43041 7.07071
42 5FBN 5WF 0.01179 0.44752 7.90514
43 1LOB MMA 0.0000002134 0.52282 8.28729
44 1LOF MAN BMA NAG NAG MAN NAG GAL GAL 0.00001966 0.43352 8.28729
45 5DHU 5A8 0.03876 0.41998 8.3004
46 4FG8 ATP 0.01365 0.41397 9.48617
47 5JCA NDP 0.04093 0.42259 9.88142
48 5AV7 MMA MAN NAG MAN NAG NAG 0.003512 0.456 9.93377
49 1E6E FAD 0.02292 0.41908 13.2812
50 1XXR MAN 0.0002578 0.47611 13.6646
51 5W10 CMP 0.01045 0.42291 14.359
52 2BQP GLC 0.00000007716 0.67007 15.812
53 3ZYR NAG NAG BMA MAN MAN NAG NAG 0.00000106 0.4075 19.3676
54 3ZYR ASN NAG NAG BMA MAN MAN NAG NAG 0.00000129 0.40612 19.3676
55 1OFS SUC 0.0000001357 0.59203 19.7861
56 1Q8O MAN MMA 0.0000003388 0.65228 19.8413
57 2AR6 NAG MAN 0.0000008081 0.65144 19.8413
58 2AR6 NAG MAN MAN MAN NAG 0.000001248 0.6498 19.8413
59 2GMM MAN MAN 0.0000002028 0.61612 19.8413
60 1Q8V MAN MAN MAN 0.00001265 0.57515 19.8413
61 2PHF MAN MAN BMA MAN 0.00001517 0.57468 19.8413
62 2GNB MAN 0.000006763 0.57177 19.8413
63 2PHR MAN MAN 0.00001594 0.5682 19.8413
64 2PHR MAN MAN BMA MAN 0.00001874 0.56781 19.8413
65 2PHF MAN MAN 0.0000164 0.56737 19.8413
66 1Q8V MAN MAN 0.00001396 0.56194 19.8413
67 2PHT MAN MAN MAN 0.0000003854 0.55166 19.8413
68 2GNM MAN 0.000005554 0.55041 19.8413
69 2PHU MAN MAN 0.000009505 0.51611 19.8413
70 2GND MAN 0.00001053 0.51349 19.8413
71 2GN3 MMA 0.00007676 0.49785 19.8413
72 2PHT MAN MAN MAN BMA MAN 0.0000004908 0.4931 19.8413
73 2GN3 MAN 0.0000893 0.49268 19.8413
74 2PHW MAN MAN MAN BMA MAN MAN MAN 0.0000005707 0.4913 19.8413
75 2PHU MAN MAN MAN BMA MAN 0.0000006345 0.48997 19.8413
76 2AUY NAG MAN MMA 0.000000685 0.47494 19.8413
77 1Q8P MAN MMA 0.00001301 0.47491 19.8413
78 2GMP NAG MAN 0.0005707 0.4747 19.8413
79 2GND MAN MMA 0.00001629 0.47138 19.8413
80 2PHW MAN MAN 0.00001642 0.47126 19.8413
81 2PHX MAN MAN MAN MAN 0.00001687 0.47086 19.8413
82 1UKG MMA 0.0003167 0.46618 19.8413
83 1Q8Q MAN MMA 0.0002644 0.45434 19.8413
84 1Q8S MAN MMA 0.0004265 0.44452 19.8413
85 2PHX MAN MAN 0.0004653 0.4431 19.8413
86 2D3S TNR 0.01386 0.40119 28.9256
87 2PEL LAT 0.007182 0.41412 31.3559
Feedback