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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(CC1...
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 1443 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 1205 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 1039 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: 178
No: Ligand ECFP6 Tc MDL keys Tc
1 BGC GLA 1 1
2 GAL GLC 1 1
3 GLA BGC 1 1
4 BGC GLC 1 1
5 GLA GLC 1 1
6 LAK 1 1
7 GAL GAL 1 1
8 GLC BGC 1 1
9 MLB 1 1
10 MAN BMA 1 1
11 MAN MAN 1 1
12 BMA GLA 1 1
13 BMA MAN 1 1
14 GLC GLC 1 1
15 GLA BMA 1 1
16 BMA MAN MAN 0.953488 1
17 GLC GLC GLC GLC GLC BGC 0.953488 1
18 MAN MAN MAN 0.953488 1
19 GLC GLC GLC 0.953488 1
20 GLC GLC GLC GLC BGC 0.953488 1
21 AHR AHR 0.75 0.857143
22 FUB AHR 0.75 0.857143
23 MAN MAN MAN MAN 0.732143 1
24 MAN MAN BMA MAN 0.732143 1
25 AHR AHR AHR AHR AHR AHR 0.702128 0.857143
26 FUB AHR AHR 0.702128 0.857143
27 MAN BMA MAN 0.672727 1
28 MAN MMA 0.66 0.942857
29 GLC GLC GLC BGC 0.633333 1
30 M5S 0.606557 1
31 MAN BMA MAN MAN MAN 0.606557 1
32 MAN MAN MAN BMA MAN 0.575758 1
33 BMA BMA GLA BMA BMA 0.546875 1
34 MAN MMA MAN 0.540984 0.942857
35 MAN MAN MAN MAN MAN MAN MAN 0.535211 1
36 RAF 0.515625 0.891892
37 GIV 0.511628 0.848485
38 GLA 0.511628 0.848485
39 WOO 0.511628 0.848485
40 MAN 0.511628 0.848485
41 GAL 0.511628 0.848485
42 GLC 0.511628 0.848485
43 BGC 0.511628 0.848485
44 GXL 0.511628 0.848485
45 BMA 0.511628 0.848485
46 ALL 0.511628 0.848485
47 STW 0.507692 0.891892
48 MAN MAN MAN BMA MAN MAN MAN 0.5 0.942857
49 BMA MAN MAN MAN MAN 0.485294 1
50 NGB 0.485294 0.622642
51 4CQ 0.483871 0.970588
52 WZ2 0.477612 0.868421
53 LBT 0.472727 1
54 N9S 0.472727 1
55 CBI 0.472727 1
56 MAB 0.472727 1
57 LAT 0.472727 1
58 CBK 0.472727 1
59 B2G 0.472727 1
60 BGC BMA 0.472727 1
61 GLC GAL 0.472727 1
62 GLA GLA 0.472727 1
63 BMA GAL 0.472727 1
64 GLA GAL 0.472727 1
65 MAL 0.472727 1
66 GAL BGC 0.472727 1
67 BGC GAL 0.472727 1
68 NAG MAN MAN 0.472222 0.733333
69 RGG 0.471698 0.882353
70 SUC GLA 0.471429 0.891892
71 DMJ MAN 0.466667 0.695652
72 NOJ BGC 0.466667 0.695652
73 WZ3 0.463768 0.916667
74 DEG 0.462963 0.769231
75 IFM MAN 0.459016 0.711111
76 EMZ 0.458333 0.783784
77 M6P 0.45098 0.674419
78 G6P 0.45098 0.674419
79 BG6 0.45098 0.674419
80 M6D 0.45098 0.674419
81 A6P 0.45098 0.674419
82 BGP 0.45098 0.674419
83 AHR AHR AHR 0.45 0.805556
84 EBG 0.446429 0.837838
85 M3M 0.446429 1
86 LB2 0.446429 1
87 NGR 0.446429 1
88 EBQ 0.446429 0.789474
89 MAN GLC 0.446429 1
90 MT7 0.440678 1
91 MAN BMA BMA BMA BMA BMA 0.440678 1
92 DXI 0.440678 1
93 GLC GAL GAL 0.440678 1
94 BGC BGC BGC BGC 0.440678 1
95 GLC BGC BGC BGC BGC BGC 0.440678 1
96 GLC BGC GLC 0.440678 1
97 CEX 0.440678 1
98 GLC BGC BGC BGC BGC 0.440678 1
99 BGC GLC GLC GLC GLC GLC GLC 0.440678 1
100 MLR 0.440678 1
101 BGC BGC BGC BGC BGC 0.440678 1
102 CE5 0.440678 1
103 MAN BMA BMA BMA BMA 0.440678 1
104 BMA BMA BMA BMA BMA 0.440678 1
105 MTT 0.440678 1
106 MAN MAN BMA BMA BMA BMA 0.440678 1
107 GLC GLC GLC GLC GLC 0.440678 1
108 BGC GLC GLC 0.440678 1
109 BMA MAN BMA 0.440678 1
110 BGC GLC GLC GLC 0.440678 1
111 GLA GAL GLC 0.440678 1
112 CT3 0.440678 1
113 BGC BGC BGC 0.440678 1
114 BGC BGC GLC 0.440678 1
115 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.440678 1
116 CTR 0.440678 1
117 CEY 0.440678 1
118 GLC BGC BGC 0.440678 1
119 GLA GAL BGC 0.440678 1
120 BMA BMA BMA BMA BMA BMA 0.440678 1
121 GLC GLC BGC 0.440678 1
122 CTT 0.440678 1
123 BGC BGC BGC BGC BGC BGC 0.440678 1
124 BGC BGC BGC GLC 0.440678 1
125 MAN BMA BMA 0.440678 1
126 B4G 0.440678 1
127 GAL GAL GAL 0.440678 1
128 BGC GLC GLC GLC GLC 0.440678 1
129 CE8 0.440678 1
130 BMA BMA BMA 0.440678 1
131 GLC BGC BGC BGC 0.440678 1
132 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.440678 1
133 CE6 0.440678 1
134 ACY 1GN GAL 1GN BGC ACY GAL BGC 0.439024 0.6875
135 1GN ACY GAL ACY 1GN BGC GAL BGC 0.439024 0.6875
136 JZR 0.438596 0.714286
137 BHG 0.438596 0.714286
138 GLC HEX 0.438596 0.714286
139 TRE 0.4375 1
140 BMA Z4Y NAG 0.435897 0.717391
141 B7G 0.431034 0.738095
142 KGM 0.431034 0.738095
143 2M4 0.428571 1
144 MBG 0.428571 0.857143
145 MMA 0.428571 0.857143
146 GYP 0.428571 0.857143
147 AMG 0.428571 0.857143
148 GAL GAL SO4 0.424242 0.66
149 BOG 0.423729 0.738095
150 BNG 0.423729 0.738095
151 HSJ 0.423729 0.738095
152 M1P 0.423077 0.697674
153 XGP 0.423077 0.697674
154 G1P 0.423077 0.697674
155 GL1 0.423077 0.697674
156 BGC BGC XYS BGC 0.418919 0.942857
157 GAL FUC 0.416667 0.941176
158 SER MAN 0.416667 0.72093
159 XYT 0.415385 0.767442
160 BQZ 0.415094 0.909091
161 6SA 0.414894 0.733333
162 GAL BGC NAG GAL 0.413333 0.733333
163 GAL BGC BGC XYS 0.410959 0.942857
164 BGC BGC BGC GLC BGC BGC 0.409836 1
165 GLC BGC BGC BGC BGC BGC BGC 0.409836 1
166 GLA EGA 0.409836 0.942857
167 DGD 0.409639 0.733333
168 BMA NAG MAN MAN MAN MAN MAN MAN MAN 0.409091 0.733333
169 NAG NAG BMA MAN MAN 0.406977 0.6875
170 T6P 0.40678 0.767442
171 GLA GAL GAL 0.40625 1
172 IAB 0.404494 0.733333
173 MAN MAN BMA 0.403226 1
174 BMA BMA MAN 0.403226 1
175 GLC BGC BGC XYS BGC XYS XYS 0.402597 0.942857
176 BGC BGC BGC XYS BGC XYS XYS 0.402597 0.942857
177 BGC BGC XYS BGC XYS BGC XYS 0.402597 0.942857
178 BMA MAN MAN MAN 0.4 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2DUR; Ligand: MAN MAN; Similar sites found with APoc: 222
This union binding pocket(no: 1) in the query (biounit: 2dur.bio2) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 2QCD U5P 1.18577
2 3BY8 MLT 1.40845
3 1RX0 FAD 1.58103
4 5DEY 59T 1.58103
5 2B1N LYS ALA SER VAL GLY 1.62602
6 2HF9 GSP 1.76991
7 4RLQ 3SK 1.97628
8 4I3V NAD 1.97628
9 1W8S FBP 1.97628
10 4FL3 ANP 1.97628
11 3CW9 01A 1.97628
12 3MI2 PFU 2.15054
13 6FK3 PPI 2.37154
14 1V8B NAD 2.37154
15 1WG8 SAM 2.37154
16 3ICT ADP 2.37154
17 4ZCC FAD 2.37154
18 4UP3 FAD 2.37154
19 3GE7 AFQ 2.37154
20 2AL2 PEP 2.37154
21 2AL2 2PG 2.37154
22 1VBO MAN MAN MAN 2.68456
23 1VBO MAN 2.68456
24 1TDF FAD 2.7668
25 5U3B 7TD 2.7668
26 1GUZ NAD 2.7668
27 1DQX BMP 2.7668
28 2IV2 2MD 2.7668
29 6CEP NAD 2.7668
30 4Z24 FAD 2.7668
31 5G4L NDP 2.7668
32 1FL2 FAD 2.7668
33 1X87 NAD 2.7668
34 4JBI NDP 2.7668
35 4ZLU 4PW 2.7668
36 2JL1 NAP 2.7668
37 4KCT PYR 2.7668
38 5TCI 79V 3.16206
39 5UR0 NAD 3.16206
40 4HKP TKW 3.16206
41 5KZD RCJ 3.16206
42 1HYH NAD 3.16206
43 1Q0H FOM 3.16206
44 1Q0H NDP 3.16206
45 1VL0 NAI 3.55731
46 5M67 NAD 3.55731
47 5M67 3D1 3.55731
48 5MLR GRQ 3.55731
49 5MLR NAP 3.55731
50 3NJ4 NAD 3.55731
51 1DIG NAP 3.55731
52 5Y9D FAD 3.55731
53 5G3U FDA 3.55731
54 5G3U ITW 3.55731
55 1GV0 NAD 3.55731
56 5ZBC FAD 3.55731
57 3JZ4 NAP 3.55731
58 3SLS ANP 3.55731
59 2O4C NAD 3.55731
60 1ZGS XMM 3.55731
61 2QZZ NAP 3.55731
62 2QZZ EMF 3.55731
63 5UFN SAH 3.78151
64 1LES GLC FRU 3.84615
65 5AYV KPL 3.95257
66 1DRV A3D 3.95257
67 4MIG G3F 3.95257
68 2UYT LRH 3.95257
69 2UYT ADP 3.95257
70 6EL3 NAP 3.95257
71 5EOW FAD 3.95257
72 1F74 NAY 3.95257
73 3WO0 ALA 3.95257
74 3WO0 ADP 3.95257
75 4IMG NGF 3.95257
76 2AZ5 307 4.05405
77 2HMT NAI 4.16667
78 3I6I NDP 4.34783
79 4EDK GTP 4.34783
80 4MOP 2H5 4.34783
81 4A0M NAD 4.34783
82 5KJK 6T1 4.34783
83 5KJK SAM 4.34783
84 2ZJ1 NAD 4.34783
85 2ZJ1 ARJ 4.34783
86 2P53 NNG 4.34783
87 1I8T FAD 4.34783
88 4KP7 1UQ 4.34783
89 3ABI NAD 4.34783
90 3WQQ IB3 4.34783
91 3WQQ NDP 4.34783
92 3KEE 30B 4.34783
93 4BX7 B4F 4.6875
94 3BXF 13P 4.74308
95 3B96 FAD 4.74308
96 5J60 FAD 4.74308
97 3ITJ FAD 4.74308
98 5GZ6 NDP 4.74308
99 5GZ6 7C3 4.74308
100 5ZZ6 NAD 4.80769
101 5ZZ6 ADP 4.80769
102 3PCJ INO 5.04202
103 5V6F MAN BMA MAN 5.07246
104 4F7E 0SH 5.10204
105 1YKJ FAD 5.13834
106 4CJX NAP 5.13834
107 3C1O NAP 5.13834
108 4ZGS NAD 5.13834
109 2PYW ADP 5.13834
110 1UGX GAL MGC 5.26316
111 2Y88 2ER 5.32787
112 5ML3 DL3 5.36913
113 2Q0L NAP 5.5336
114 1J49 NAD 5.5336
115 1SVM ATP 5.5336
116 4R4U COA 5.5336
117 3LAD FAD 5.92885
118 5L13 6ZE 5.92885
119 3GGO NAI 5.92885
120 1E1M NAP 5.92885
121 1E1M FAD 5.92885
122 2C7G FAD 5.92885
123 2C7G ODP 5.92885
124 2CVQ NDP 5.92885
125 2BOY BHO 5.92885
126 1N62 MCN 6.32411
127 3B20 NAD 6.32411
128 3B1J NAD 6.32411
129 2D2I NAP 6.32411
130 4M00 SUC 6.65434
131 4ZUL UN1 6.71937
132 3ORF NAD 6.77291
133 1MVQ MMA 6.77966
134 3V3L V3L 7.05882
135 3G08 FEE 7.07071
136 2AZC 3TL 7.07071
137 2BMZ XLM 7.0922
138 2ZSC BTN 7.0922
139 1T90 NAD 7.11462
140 5YS9 FAD 7.50988
141 1CX4 CMP 7.50988
142 1RM4 NDP 7.50988
143 5FBN 5WF 7.90514
144 4DPL NAP 7.90514
145 1ZK4 NAP 7.96813
146 1ZK4 AC0 7.96813
147 2YVJ NAI 8.25688
148 1LOF MAN BMA NAG NAG MAN NAG GAL GAL 8.28729
149 1LOB MMA 8.28729
150 1BUC FAD 8.3004
151 5DHU 5A8 8.3004
152 2XVF FAD 8.3004
153 2JE7 XMM 8.78661
154 2Q1W NAD 9.09091
155 3RUG DB6 9.31373
156 5YLT C7N 9.48617
157 5YLT SFG 9.48617
158 4L1F FAD 9.48617
159 4FG8 ATP 9.48617
160 5UIJ TYD 9.48617
161 2FMD MAN MAN 9.58333
162 5XFI NAG NAG BMA MAN MAN NAG GAL NAG 9.80392
163 2FCR FMN 9.82659
164 5JCA NDP 9.88142
165 4QYS PLP SEP 9.88142
166 5DF1 NAP 9.88142
167 5DF1 58X 9.88142
168 5K9B FMN 10.5556
169 5OCM NAP 10.6719
170 2V6G NAP 11.4625
171 1VHD NAP 11.4625
172 1P0Z FLC 12.2137
173 4K5S FAD 12.6482
174 1E6E FAD 13.2812
175 1KYQ NAD 13.4387
176 1C3M MAN MAN 13.6054
177 1XXR MAN 13.6646
178 5W10 CMP 14.359
179 5N5S NAP 15.0198
180 2BQP GLC 15.812
181 5HXI FAD 16.6008
182 5HXI 5HN 16.6008
183 6FLZ MMA 17.3611
184 1FWV SGA MAG FUC 17.9104
185 3ZYR NAG NAG BMA MAN MAN NAG NAG 19.3676
186 3ZYR ASN NAG NAG BMA MAN MAN NAG NAG 19.3676
187 1OFS SUC 19.7861
188 2PHT MAN MAN MAN BMA MAN 19.8413
189 2AUY NAG MAN MMA 19.8413
190 2PHU MAN MAN MAN BMA MAN 19.8413
191 2PHT MAN MAN MAN 19.8413
192 2GMM MAN MAN 19.8413
193 2GNM MAN 19.8413
194 2PHF MAN MAN BMA MAN 19.8413
195 2PHU MAN MAN 19.8413
196 2GNB MAN 19.8413
197 2PHF MAN MAN 19.8413
198 1Q8O MAN MMA 19.8413
199 2GN3 MMA 19.8413
200 2GN3 MAN 19.8413
201 2GND MAN 19.8413
202 1Q8V MAN MAN 19.8413
203 1Q8Q MAN MMA 19.8413
204 2GMP NAG MAN 19.8413
205 2PHW MAN MAN MAN BMA MAN MAN MAN 19.8413
206 1UKG MMA 19.8413
207 1Q8S MAN MMA 19.8413
208 1Q8V MAN MAN MAN 19.8413
209 1Q8P MAN MMA 19.8413
210 2PHR MAN MAN 19.8413
211 2GND MAN MMA 19.8413
212 2PHW MAN MAN 19.8413
213 2PHX MAN MAN MAN MAN 19.8413
214 2AR6 NAG MAN 19.8413
215 2PHR MAN MAN BMA MAN 19.8413
216 2PHX MAN MAN 19.8413
217 2AR6 NAG MAN MAN MAN NAG 19.8413
218 5EYY MDM 20
219 1AX2 NDG GAL 20.0837
220 2D3S TNR 28.9256
221 2PEL LAT 31.3559
222 2PEL LBT 31.3559
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