Receptor
PDB id Resolution Class Description Source Keywords
5M7I 2.1 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF GH125 1,6-ALPHA-MANNOSIDASE MUTANT FROM CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH 1,6-ALPHA-MANNOBIOS CLOSTRIDIUM PERFRINGENS (STRAIN 13 / TORGANISM_TAXID: 195102 MANNOSIDASE HYDROLASE CARBOHYDRATE CHEMISTRY
Ref.: COMPUTATIONAL DESIGN OF EXPERIMENT UNVEILS THE CONFORMATIONAL REACTION COORDINATE OF GH125 ALPHA-MANNOSIDASES. J. AM. CHEM. SOC. V. 139 1085 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BMA MAN B:1;
Valid;
none;
submit data
342.297 n/a O(C1O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6RQK 1.85 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF GH125 1,6-ALPHA-MANNOSIDASE FROM CLOSTR PERFRINGENS IN COMPLEX WITH MANNOIMIDAZOLE CLOSTRIDIUM PERFRINGENS STR. 13 CARBOHYDRATE INHIBITOR GLYCOSIDE HYDROLASE COMPLEX HYDRO
Ref.: DISTORTION OF MANNOIMIDAZOLE SUPPORTS A B2,5BOAT TR STATE FOR THE FAMILY GH125 ALPHA-1,6-MANNOSIDASE FR CLOSTRIDIUM PERFRINGENS. ORG.BIOMOL.CHEM. V. 17 7863 2019
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1579 families.
1 5M7Y - MAN MAN MAN n/a n/a
2 3QT9 - Z4Y MAN n/a n/a
3 5M7I - BMA MAN n/a n/a
4 6RQK Kd = 1.6 mM MVL C8 H12 N2 O4 c1cn2c(n1)....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1312 families.
1 5M7Y - MAN MAN MAN n/a n/a
2 3QT9 - Z4Y MAN n/a n/a
3 5M7I - BMA MAN n/a n/a
4 6RQK Kd = 1.6 mM MVL C8 H12 N2 O4 c1cn2c(n1)....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1130 families.
1 3QSP - BMA MAN n/a n/a
2 3QRY - DMJ C6 H13 N O4 C1[C@H]([C....
3 5M7Y - MAN MAN MAN n/a n/a
4 3QT9 - Z4Y MAN n/a n/a
5 5M7I - BMA MAN n/a n/a
6 6RQK Kd = 1.6 mM MVL C8 H12 N2 O4 c1cn2c(n1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: BMA MAN; Similar ligands found: 249
No: Ligand ECFP6 Tc MDL keys Tc
1 BGC GLC 1 1
2 2M4 1 1
3 BMA MAN 1 1
4 BMA BMA MAN 0.808511 1
5 MAN MAN BMA 0.808511 1
6 BGC BGC BGC BGC BGC BGC BGC 0.791667 1
7 BGC BGC BGC BGC BGC 0.791667 1
8 MAN MAN MAN GLC 0.690909 1
9 FUC GAL 0.66 0.941176
10 BQZ 0.622222 0.909091
11 GAL NAG MAN 0.612903 0.733333
12 LB2 0.612245 1
13 BMA BMA 0.612245 1
14 MAN GLC 0.612245 1
15 B2G 0.612245 1
16 BMA GAL 0.612245 1
17 GLA GAL 0.612245 1
18 BGC BMA 0.612245 1
19 MAL 0.612245 1
20 MAB 0.612245 1
21 GLC BGC 0.612245 1
22 GLC GLC 0.612245 1
23 GAL BGC 0.612245 1
24 M3M 0.612245 1
25 GLC GAL 0.612245 1
26 NGR 0.612245 1
27 LAT 0.612245 1
28 CBK 0.612245 1
29 GLA GLA 0.612245 1
30 LBT 0.612245 1
31 N9S 0.612245 1
32 BGC GAL 0.612245 1
33 CBI 0.612245 1
34 TRE 0.595238 1
35 GLA MBG 0.591837 0.942857
36 GLC GLC BGC 0.584906 1
37 GLC GLC GLC 0.584906 1
38 BGC BGC BGC GLC BGC BGC 0.584906 1
39 BGC BGC BGC BGC BGC BGC 0.584906 1
40 GLC GLC GLC GLC 0.584906 1
41 GLC BGC BGC BGC BGC BGC BGC 0.584906 1
42 BGC GLC GLC GLC GLC 0.566038 1
43 MAN BMA BMA BMA BMA 0.566038 1
44 BGC GLC GLC 0.566038 1
45 GLC GAL GAL 0.566038 1
46 CTT 0.566038 1
47 DXI 0.566038 1
48 BMA MAN BMA 0.566038 1
49 MT7 0.566038 1
50 BGC GLC GLC GLC GLC GLC GLC 0.566038 1
51 CT3 0.566038 1
52 BMA BMA BMA BMA BMA 0.566038 1
53 BGC BGC BGC BGC 0.566038 1
54 BMA BMA BMA BMA BMA BMA 0.566038 1
55 GLC BGC BGC BGC BGC BGC 0.566038 1
56 BGC BGC BGC 0.566038 1
57 CE6 0.566038 1
58 GLC BGC BGC BGC BGC 0.566038 1
59 GLA GAL BGC 0.566038 1
60 CE8 0.566038 1
61 BMA BMA BMA 0.566038 1
62 GLA GAL GLC 0.566038 1
63 CEX 0.566038 1
64 MLR 0.566038 1
65 CE5 0.566038 1
66 MAN MAN BMA BMA BMA BMA 0.566038 1
67 GAL GAL GAL 0.566038 1
68 B4G 0.566038 1
69 CTR 0.566038 1
70 MTT 0.566038 1
71 GLC GLC GLC GLC GLC 0.566038 1
72 CEY 0.566038 1
73 BGC BGC BGC GLC 0.566038 1
74 BGC BGC GLC 0.566038 1
75 GLC BGC BGC BGC 0.566038 1
76 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.566038 1
77 BGC GLC GLC GLC 0.566038 1
78 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.566038 1
79 MAN BMA BMA BMA BMA BMA 0.566038 1
80 MAN BMA BMA 0.566038 1
81 GLC BGC GLC 0.566038 1
82 GLC BGC BGC 0.566038 1
83 BMA MAN MAN MAN 0.561404 1
84 LAT GLA 0.56 1
85 GLA GAL GAL 0.54386 1
86 GLA GLA FUC 0.542373 0.970588
87 GLA GAL FUC 0.542373 0.970588
88 GAL GAL FUC 0.542373 0.970588
89 FUC GLA GLA 0.542373 0.970588
90 FUC GAL GLA 0.542373 0.970588
91 GAL FUC 0.537037 0.941176
92 U63 0.537037 0.891892
93 MAN MMA 0.528302 0.942857
94 MDM 0.528302 0.942857
95 MMA MAN 0.528302 0.942857
96 M13 0.528302 0.942857
97 DR5 0.528302 0.942857
98 RZM 0.528302 0.688889
99 GAL MBG 0.528302 0.942857
100 GLA EGA 0.527273 0.942857
101 DOM 0.518519 0.942857
102 BGC BGC 0.518519 0.914286
103 FMO 0.508772 0.868421
104 GAL A2G 0.508475 0.733333
105 NAG GAL 0.508475 0.733333
106 GAL NAG 0.508475 0.733333
107 GAL NGA 0.508475 0.733333
108 BGC BGC BGC BGC BGC BGC BGC BGC 0.508197 1
109 BMA BMA MAN GLA GLA 0.5 1
110 MAL EDO 0.491228 0.942857
111 GLA MAN ABE 0.484848 0.916667
112 GAL NDG 0.483333 0.733333
113 NLC 0.483333 0.733333
114 NOJ GLC 0.482759 0.695652
115 MMA 0.478261 0.857143
116 MBG 0.478261 0.857143
117 AMG 0.478261 0.857143
118 GYP 0.478261 0.857143
119 MAN MAN MAN 0.47541 1
120 MAN BMA MAN 0.47541 1
121 ABL 0.474576 0.702128
122 CGC 0.474576 0.941176
123 MVP 0.474576 0.733333
124 W9T 0.473684 0.842105
125 FRU GAL 0.473684 0.842105
126 BMA FRU 0.473684 0.842105
127 5QP 0.473684 0.885714
128 T6P 0.472727 0.767442
129 GDQ GLC 0.466667 0.666667
130 9MR 0.465517 0.744186
131 IFM BMA 0.465517 0.711111
132 BMA IFM 0.465517 0.711111
133 BGC OXZ 0.465517 0.666667
134 IFM BGC 0.465517 0.711111
135 FUC GLC BGC GAL 0.460317 0.970588
136 G2F BGC BGC BGC BGC BGC 0.460317 0.868421
137 A2G GAL 0.460317 0.653061
138 FUC BGC GAL 0.460317 0.970588
139 GAL GAL SO4 0.460317 0.66
140 GLA GAL BGC 5VQ 0.459016 0.891892
141 MAN MNM 0.457627 0.702128
142 GLC DMJ 0.457627 0.695652
143 NOY BGC 0.457627 0.702128
144 BMA MAN MAN MAN MAN 0.455882 1
145 XYT 0.451613 0.767442
146 MAN DGO 0.448276 0.914286
147 BMA BMA BMA GLA BMA 0.447761 1
148 BMA BMA GLA BMA BMA 0.447761 1
149 2GS 0.446809 0.857143
150 P3M 0.446154 0.767442
151 GLC GLC XYP 0.446154 1
152 GAL BGC BGC XYS 0.442857 0.942857
153 MAN G63 0.442623 0.653061
154 GLA GAL NAG 0.441176 0.733333
155 MAN BMA NAG 0.441176 0.733333
156 SOR GLC GLC 0.439394 0.970588
157 MAN MAN MAN MAN 0.439394 1
158 MAN MAN BMA MAN 0.439394 1
159 MAN 7D1 0.438596 0.888889
160 GLA GAL GLC NBU 0.4375 0.846154
161 NAG BMA 0.4375 0.653061
162 MAN MAN MAN BMA MAN 0.43662 1
163 GAL MGC 0.435484 0.702128
164 8VZ 0.435484 0.673469
165 GLC GLC GLC BGC 0.432836 1
166 M5S 0.432836 1
167 MAN BMA MAN MAN MAN 0.432836 1
168 GAL 0.431818 0.848485
169 GXL 0.431818 0.848485
170 GIV 0.431818 0.848485
171 BMA 0.431818 0.848485
172 WOO 0.431818 0.848485
173 MAN 0.431818 0.848485
174 ALL 0.431818 0.848485
175 GLC 0.431818 0.848485
176 BGC 0.431818 0.848485
177 GLA 0.431818 0.848485
178 BGC BGC BGC FRU 0.430769 0.868421
179 GLA BMA 0.428571 1
180 MLB 0.428571 1
181 BGC GLA 0.428571 1
182 GAL GLC 0.428571 1
183 MAN MAN 0.428571 1
184 GLA BGC 0.428571 1
185 LAK 0.428571 1
186 KHO 0.428571 0.888889
187 MAN BMA 0.428571 1
188 GAL GAL 0.428571 1
189 BMA GLA 0.428571 1
190 GLA GLC 0.428571 1
191 GLO GLC GLC GLC 0.426471 0.970588
192 LAG 0.426471 0.6
193 SOR GLC GLC GLC 0.426471 0.970588
194 GAL BGC NAG GAL 0.424658 0.733333
195 FUC GAL GLC BGC 0.424242 0.970588
196 G3I 0.424242 0.767442
197 UMQ 0.424242 0.785714
198 GLC GAL FUC 0.424242 0.970588
199 BGC GAL FUC 0.424242 0.970588
200 DMU 0.424242 0.785714
201 LMU 0.424242 0.785714
202 FUC GAL GLC 0.424242 0.970588
203 LAT FUC 0.424242 0.970588
204 LMT 0.424242 0.785714
205 G2I 0.424242 0.767442
206 OXZ BGC BGC 0.424242 0.6875
207 8B7 0.424242 0.970588
208 TUR 0.423729 0.842105
209 BTU 0.423729 0.842105
210 GLC FRU 0.423729 0.842105
211 GAL NAG GAL GLC 0.418919 0.733333
212 BGC GAL NAG GAL 0.418919 0.733333
213 BGC GLA GAL FUC 0.416667 0.970588
214 ISX 0.416667 0.761905
215 MAN MMA MAN 0.415385 0.942857
216 NPJ 0.414286 0.622642
217 BMA MAN MAN 0.413793 1
218 GLC GLC GLC GLC GLC BGC 0.413793 1
219 GLC GLC GLC GLC BGC 0.413793 1
220 NAG GAL GAL NAG GAL 0.413333 0.6875
221 G1P 0.411765 0.697674
222 GL1 0.411765 0.697674
223 XGP 0.411765 0.697674
224 ALX 0.411765 0.697674
225 M1P 0.411765 0.697674
226 BNX 0.411765 0.697674
227 GLC GLC XYS 0.411765 0.970588
228 56N 0.410714 0.833333
229 MAN IFM 0.409836 0.727273
230 GLC IFM 0.409836 0.727273
231 FUC NAG GAL 0.408451 0.717391
232 OPM MAN MAN 0.408451 0.804878
233 GAL NDG FUC 0.408451 0.717391
234 FUC NDG GAL 0.408451 0.717391
235 LAT NAG GAL 0.407895 0.733333
236 GLC GAL NAG GAL 0.407895 0.733333
237 MAN MAN MAN MAN MAN MAN MAN 0.407895 1
238 6UZ 0.405797 0.846154
239 LSE 0.405797 0.6875
240 GLC 7LQ 0.403226 0.885714
241 IDC 0.402985 0.6
242 MVL BMA 0.402985 0.6
243 GAL NGT 0.402985 0.66
244 NGT GAL 0.402985 0.66
245 BMA MVL 0.402985 0.6
246 GLO GLC GLC 0.402778 0.942857
247 RCB 0.402778 0.622642
248 GTM BGC BGC 0.4 0.868421
249 10M 0.4 0.733333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6RQK; Ligand: MVL; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 6rqk.bio2) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6RQK; Ligand: MVL; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 6rqk.bio2) has 10 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 6RQK; Ligand: MVL; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 6rqk.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 6RQK; Ligand: MVL; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 6rqk.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
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