Receptor
PDB id Resolution Class Description Source Keywords
1DL2 1.54 Å EC: 3.2.1.113 CRYSTAL STRUCTURE OF CLASS I ALPHA-1,2-MANNOSIDASE FROM SACC CEREVISIAE AT 1.54 ANGSTROM RESOLUTION SACCHAROMYCES CEREVISIAE ALPHA-ALPHA HELIX BARREL HYDROLASE
Ref.: CRYSTAL STRUCTURE OF A CLASS I ALPHA1,2-MANNOSIDASE IN N-GLYCAN PROCESSING AND ENDOPLASMIC RETICULUM QU CONTROL. EMBO J. V. 19 581 2000
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:901;
Part of Protein;
none;
submit data
40.078 Ca [Ca+2...
GOL A:900;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NDG NAG NDG BMA MAN MAN MAN MAN A:601;
Valid;
none;
submit data n/a n/a n/a n/a
NAG A:700;
Valid;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
NAG NAG BMA A:800;
Valid;
none;
submit data
570.545 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1DL2 1.54 Å EC: 3.2.1.113 CRYSTAL STRUCTURE OF CLASS I ALPHA-1,2-MANNOSIDASE FROM SACC CEREVISIAE AT 1.54 ANGSTROM RESOLUTION SACCHAROMYCES CEREVISIAE ALPHA-ALPHA HELIX BARREL HYDROLASE
Ref.: CRYSTAL STRUCTURE OF A CLASS I ALPHA1,2-MANNOSIDASE IN N-GLYCAN PROCESSING AND ENDOPLASMIC RETICULUM QU CONTROL. EMBO J. V. 19 581 2000
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1DL2 - NDG NAG NDG BMA MAN MAN MAN MAN n/a n/a
2 1G6I - DMJ C6 H13 N O4 C1[C@H]([C....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1DL2 - NDG NAG NDG BMA MAN MAN MAN MAN n/a n/a
2 1G6I - DMJ C6 H13 N O4 C1[C@H]([C....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5KKB - BMA NAG MAN MAN MAN MAN MAN MAN MAN n/a n/a
2 2RI9 Ki = 0.6 mM MMA LDY n/a n/a
3 5KIJ - NAG BMA MAN MAN MAN MAN MAN MAN MAN n/a n/a
4 1FO2 ic50 = 20 uM DMJ C6 H13 N O4 C1[C@H]([C....
5 1FO3 ic50 = 0.2 uM KIF C8 H12 N2 O6 C([C@@H]1[....
6 5KK7 - SMD C13 H24 O10 S CO[C@@H]1[....
7 1DL2 - NDG NAG NDG BMA MAN MAN MAN MAN n/a n/a
8 1G6I - DMJ C6 H13 N O4 C1[C@H]([C....
9 1X9D Kd = 110 uM SMD C13 H24 O10 S CO[C@@H]1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NDG NAG NDG BMA MAN MAN MAN MAN; Similar ligands found: 0
No: Ligand ECFP6 Tc MDL keys Tc
Ligand no: 2; Ligand: NAG; Similar ligands found: 109
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG 1 1
2 HSQ 1 1
3 NGA 1 1
4 A2G 1 1
5 NDG 1 1
6 BM3 1 1
7 BGN 0.638298 0.888889
8 SIZ 0.630435 0.906977
9 YX1 0.625 0.65
10 GAL NGA A2G 0.614035 0.816327
11 STZ 0.612245 0.65
12 16G 0.591837 0.735849
13 BMX 0.591837 0.735849
14 4QY 0.591837 0.735849
15 SNG 0.5625 0.866667
16 NGS 0.54902 0.661017
17 NAG GDL 0.54386 0.833333
18 CBS 0.54386 0.833333
19 CBS CBS 0.54386 0.833333
20 NAG NDG 0.54386 0.833333
21 ASG 0.538462 0.661017
22 BG8 0.537037 0.906977
23 2F8 0.530612 0.909091
24 MAG 0.530612 0.909091
25 NLC 0.517857 0.888889
26 GAL NDG 0.517857 0.888889
27 NDG GAL 0.517857 0.888889
28 NAG A2G 0.517241 0.833333
29 4V5 0.517241 0.829787
30 NAG NGA 0.517241 0.833333
31 MAN NAG 0.508772 0.888889
32 4UZ 0.508475 0.808511
33 NDG NAG NAG 0.508197 0.816327
34 CTO 0.508197 0.816327
35 NAG NAG NDG 0.508197 0.816327
36 NAG NAG NAG NDG 0.508197 0.816327
37 NAG NAG NAG NAG NAG NAG NAG NAG 0.508197 0.816327
38 NDG NAG NAG NDG 0.508197 0.816327
39 NAG NAG NAG NAG 0.508197 0.816327
40 NAG NAG NAG 0.508197 0.816327
41 NAG NAG NAG NAG NDG NAG 0.508197 0.816327
42 NAG NAG NAG NAG NAG NAG 0.508197 0.816327
43 NDG NAG NAG NDG NAG 0.508197 0.816327
44 NDG NAG NAG NAG 0.508197 0.816327
45 NAG NAG NAG NAG NDG 0.508197 0.816327
46 NAG NAG NAG NAG NAG 0.508197 0.816327
47 NBG 0.5 0.951219
48 MQG 0.5 0.698113
49 A2G GAL 0.491228 0.888889
50 GAL A2G 0.491228 0.888889
51 GAL NGA 0.491228 0.888889
52 AMU 0.490909 0.930233
53 GN1 0.490566 0.754717
54 NG1 0.490566 0.754717
55 NDG NAG 0.47541 0.816327
56 NAG GAL 0.474576 0.888889
57 NGA GAL 0.474576 0.888889
58 NAG FUC 0.474576 0.866667
59 GAL NAG 0.474576 0.888889
60 NAG GAL NAG 0.455882 0.833333
61 FUC NAG 0.45 0.888889
62 3YW 0.448276 0.930233
63 GLA GAL NAG 0.446154 0.888889
64 MAN BMA NAG 0.446154 0.888889
65 NAG GAL GAL 0.446154 0.888889
66 FUL GAL NAG 0.426471 0.869565
67 G6S NAG 0.426471 0.677966
68 DR2 0.426471 0.869565
69 FUC GAL NDG 0.426471 0.869565
70 FUC GAL NAG 0.426471 0.869565
71 NDG GAL FUC 0.426471 0.869565
72 GYU 0.42623 0.740741
73 TNR 0.42623 0.833333
74 NAG BDP 0.421875 0.851064
75 NAG MBG 0.419355 0.851064
76 NGA GAL BGC 0.41791 0.888889
77 NAG NAG 0.415385 0.784314
78 AZC 0.415094 0.795918
79 SN5 SN5 0.412698 0.705882
80 MBG A2G 0.412698 0.851064
81 A2G MBG 0.412698 0.851064
82 HS2 0.411765 0.8125
83 5AX 0.411765 0.866667
84 6ZC 0.409091 0.655738
85 LEC 0.409091 0.655738
86 GAL BGC NAG GAL 0.408451 0.888889
87 TCG 0.408451 0.689655
88 CTO TMX 0.408451 0.689655
89 NAG NAG NAG NAG NAG NAG NAG 0.407895 0.740741
90 BMA 0.404762 0.7
91 WOO 0.404762 0.7
92 ALL 0.404762 0.7
93 GLA 0.404762 0.7
94 MAN 0.404762 0.7
95 GAL 0.404762 0.7
96 GLC 0.404762 0.7
97 GXL 0.404762 0.7
98 GIV 0.404762 0.7
99 BGC 0.404762 0.7
100 NAG AMU 0.402778 0.8
101 NAG MUB 0.402778 0.8
102 A2G GAL FUC 0.4 0.869565
103 DR3 0.4 0.869565
104 NAG GAL FUC 0.4 0.869565
105 FUC GL0 A2G 0.4 0.869565
106 A2G GLA FUC 0.4 0.869565
107 FUC GAL A2G 0.4 0.869565
108 NGA GAL FUC 0.4 0.869565
109 FUC GLA A2G 0.4 0.869565
Ligand no: 3; Ligand: NAG NAG BMA; Similar ligands found: 199
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG NDG BMA 1 1
2 NAG NAG BMA 1 1
3 NAG NAG BMA MAN 0.88 1
4 NAG BMA 0.80303 0.923077
5 NAG NAG BMA BMA 0.779221 0.962963
6 NAG NAG NAG NAG NAG NAG NAG 0.746835 0.962963
7 NAG NAG 0.732394 0.980769
8 NAG NAG BMA MAN NAG 0.719101 0.981132
9 NAG NAG BMA MAN MAN MAN MAN 0.6875 1
10 GAL NAG GAL 0.679487 0.903846
11 MAN NAG GAL 0.649351 0.865385
12 GAL NAG MAN 0.649351 0.865385
13 NAG GAL GAL NAG GAL 0.621951 0.923077
14 NAG NAG BMA MAN MAN NAG NAG 0.616162 0.981132
15 NAG GAL GAL NAG 0.60241 0.923077
16 GAL NAG GAL NAG GAL NAG 0.60241 0.90566
17 GLC GAL NAG GAL 0.595238 0.865385
18 NDG GAL 0.567568 0.865385
19 GAL NDG 0.567568 0.865385
20 NLC 0.567568 0.865385
21 NAG NAG NAG NAG NDG 0.556962 0.90566
22 NAG NAG NAG NAG NAG NAG NAG NAG 0.556962 0.90566
23 NAG NAG NAG 0.556962 0.90566
24 NDG NAG NAG NAG 0.556962 0.90566
25 NDG NAG NAG NDG 0.556962 0.90566
26 NAG NAG NAG NAG 0.556962 0.90566
27 CTO 0.556962 0.90566
28 NAG NAG NAG NAG NAG 0.556962 0.90566
29 NAG NAG NAG NAG NAG NAG 0.556962 0.90566
30 NAG NAG NAG NAG NDG NAG 0.556962 0.90566
31 NAG NAG NAG NDG 0.556962 0.90566
32 NDG NAG NAG 0.556962 0.90566
33 NAG NAG NDG 0.556962 0.90566
34 NDG NAG NAG NDG NAG 0.556962 0.90566
35 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.555556 0.942308
36 8VZ 0.546667 0.90566
37 NAG NAG BMA MAN MAN 0.536842 0.923077
38 NAG MAN GAL MAN MAN NAG GAL 0.536842 0.923077
39 FUC BGC GAL NAG GAL 0.536842 0.884615
40 MAN MAN NAG MAN NAG 0.536842 0.923077
41 NGA GAL BGC 0.518072 0.865385
42 NAG GDL 0.506329 0.923077
43 CBS 0.506329 0.923077
44 NAG NDG 0.506329 0.923077
45 CBS CBS 0.506329 0.923077
46 GLA GAL NAG 0.506024 0.865385
47 NAG GAL GAL 0.506024 0.865385
48 MAN BMA NAG 0.506024 0.865385
49 TCG 0.505747 0.774194
50 CTO TMX 0.505747 0.774194
51 NAG MAN GAL BMA NDG MAN NAG GAL 0.490196 0.90566
52 MAN BMA NAG NAG MAN NAG GAL GAL 0.490196 0.90566
53 NAG MAN GAL BMA NAG MAN NAG GAL 0.490196 0.90566
54 NAG MAN MAN MAN NAG GAL NAG GAL 0.490196 0.90566
55 NOJ NAG NAG 0.488889 0.927273
56 NOJ NAG NAG NAG 0.488889 0.910714
57 A2G MBG 0.481481 0.867925
58 MBG A2G 0.481481 0.867925
59 NAG GAL NAG 0.477273 0.923077
60 GAL NOK 0.47561 0.875
61 NOK GAL 0.47561 0.875
62 FUC GAL NAG A2G 0.474227 0.962963
63 BMA MAN 0.472973 0.653846
64 GAL BGC NAG GAL 0.47191 0.865385
65 G2F BGC BGC BGC BGC BGC 0.469136 0.607143
66 GAL NGA 0.468354 0.865385
67 A2G GAL 0.468354 0.865385
68 GAL A2G 0.468354 0.865385
69 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.46789 0.923077
70 NGA GLA GAL BGC 0.467391 0.865385
71 NAG MAN BMA NDG MAN NAG GAL 0.46729 0.90566
72 NAG GAL BGC 0.460674 0.865385
73 NAG NAG NGT 0.457447 0.761905
74 LAT NAG GAL 0.450549 0.865385
75 BGC GAL NAG GAL 0.450549 0.865385
76 GAL NAG GAL BGC 0.450549 0.865385
77 GAL MGC 0.45 0.867925
78 GAL NGA GLA BGC GAL 0.446809 0.865385
79 DLD 0.445652 0.803279
80 FUC NAG GLA GAL 0.443299 0.903846
81 NAG AMU NAG AMV 0.443299 0.872727
82 GAL NAG 0.439024 0.865385
83 NAG GAL 0.439024 0.865385
84 NGA GAL 0.439024 0.865385
85 G6S NAG 0.438202 0.681818
86 3QL 0.431818 0.857143
87 GLA NAG GAL FUC 0.431579 0.884615
88 GAL NAG GAL FUC 0.431579 0.884615
89 5AX 0.430556 0.846154
90 GAL NGA A2G 0.430233 0.90566
91 AO3 0.43 0.695652
92 NAG BMA NAG MAN MAN NAG NAG 0.429907 0.90566
93 NAG BMA MAN MAN MAN MAN 0.428571 0.865385
94 MAN MAN NAG 0.428571 0.903846
95 6Y2 0.427083 0.705882
96 FUC NDG GAL 0.426966 0.884615
97 GAL NAG FUC 0.426966 0.884615
98 FUC NAG GAL 0.426966 0.884615
99 GAL NDG FUC 0.426966 0.884615
100 MAN NAG 0.426829 0.865385
101 GAL GC2 0.423913 0.742424
102 GLC GLC XYP 0.423529 0.634615
103 NAG FUC 0.421687 0.846154
104 MMA MAN 0.421053 0.641509
105 DR5 0.421053 0.641509
106 LAT GLA 0.418919 0.634615
107 NAA NAA AMI 0.417476 0.666667
108 NAG NGA 0.416667 0.923077
109 NAG A2G 0.416667 0.923077
110 UMG 0.413462 0.8
111 LAT 0.413333 0.634615
112 BGC GAL 0.413333 0.634615
113 BGC BMA 0.413333 0.634615
114 BGC GLC 0.413333 0.634615
115 GLA GLA 0.413333 0.634615
116 CBI 0.413333 0.634615
117 N9S 0.413333 0.634615
118 GLA GAL 0.413333 0.634615
119 GLC BGC 0.413333 0.634615
120 MAL 0.413333 0.634615
121 GLC GAL 0.413333 0.634615
122 LBT 0.413333 0.634615
123 GAL BGC 0.413333 0.634615
124 CBK 0.413333 0.634615
125 BMA BMA 0.413333 0.634615
126 GAL GLC 0.413333 0.634615
127 BMA GAL 0.413333 0.634615
128 MAL MAL 0.413333 0.622642
129 MAB 0.413333 0.634615
130 B2G 0.413333 0.634615
131 MAG FUC GAL 0.411111 0.851852
132 NAG NGO 0.411111 0.824561
133 M5G 0.410714 0.923077
134 MAN MAN BMA BMA BMA BMA 0.410256 0.634615
135 BGC GLC GLC GLC GLC 0.410256 0.634615
136 BGC GLC GLC 0.410256 0.634615
137 GLC BGC BGC BGC BGC BGC 0.410256 0.634615
138 GLC GLC GLC GLC GLC 0.410256 0.634615
139 GLC GAL GAL 0.410256 0.634615
140 BMA BMA BMA 0.410256 0.634615
141 DXI 0.410256 0.634615
142 MAN BMA BMA BMA BMA 0.410256 0.634615
143 CTR 0.410256 0.634615
144 MLR 0.410256 0.634615
145 CTT 0.410256 0.634615
146 GLC GLC GLC GLC GLC GLC GLC 0.410256 0.634615
147 CE6 0.410256 0.634615
148 GAL NAG SIA GAL 0.410256 0.909091
149 GLA GAL GLC 0.410256 0.634615
150 CE5 0.410256 0.634615
151 BGC BGC BGC GLC 0.410256 0.634615
152 CE8 0.410256 0.634615
153 BGC GLC GLC GLC 0.410256 0.634615
154 GLC BGC GLC 0.410256 0.634615
155 CT3 0.410256 0.634615
156 GLC GLC BGC GLC GLC GLC GLC 0.410256 0.634615
157 SIA GAL NAG GAL 0.410256 0.909091
158 GLC GLC BGC 0.410256 0.634615
159 BMA BMA BMA BMA BMA 0.410256 0.634615
160 CEX 0.410256 0.634615
161 B4G 0.410256 0.634615
162 BGC BGC BGC BGC BGC BGC 0.410256 0.634615
163 MAN BMA BMA 0.410256 0.634615
164 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.410256 0.634615
165 BMA BMA BMA BMA BMA BMA 0.410256 0.634615
166 GLC BGC BGC BGC BGC 0.410256 0.634615
167 MTT 0.410256 0.634615
168 BMA MAN BMA 0.410256 0.634615
169 MT7 0.410256 0.634615
170 BGC GLC GLC GLC GLC GLC GLC 0.410256 0.634615
171 GLC GLC GLC GLC GLC GLC GLC GLC 0.410256 0.634615
172 CEY 0.410256 0.634615
173 GLC BGC BGC 0.410256 0.634615
174 GAL GAL GAL 0.410256 0.634615
175 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.410256 0.634615
176 NAG GCU NAG GCD 0.409091 0.859649
177 BGC BGC GLC 0.407407 0.634615
178 NDG NAG 0.406977 0.90566
179 NDG GAL FUC 0.406593 0.884615
180 FUC GAL NAG 0.406593 0.884615
181 FUC GAL NDG 0.406593 0.884615
182 DR2 0.406593 0.884615
183 FUL GAL NAG 0.406593 0.884615
184 8VW 0.405941 0.842105
185 A2G GAL NAG FUC 0.405941 0.90566
186 NDG BDP BDP NPO NDG 0.405405 0.705882
187 GLA EGA 0.405063 0.641509
188 AH0 NAG 0.404255 0.827586
189 GAL LOG 0.402299 0.741935
190 LOG GAL 0.402299 0.741935
191 NGA GAL FUC 0.402174 0.884615
192 FUC GLA A2G 0.402174 0.884615
193 A2G GLA FUC 0.402174 0.884615
194 A2G GAL FUC 0.402174 0.884615
195 FUC GAL A2G 0.402174 0.884615
196 FUC GL0 A2G 0.402174 0.884615
197 NA1 NAA AMI 0.401869 0.685714
198 FUC BGC GAL NAG 0.4 0.884615
199 NAG MBG 0.4 0.867925
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1DL2; Ligand: NAG NAG BMA; Similar sites found: 29
This union binding pocket(no: 1) in the query (biounit: 1dl2.bio1) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2AMV BIN 0.02554 0.40723 1.95695
2 3HDY GDU 0.04621 0.41976 2.01511
3 3HDY FDA 0.04532 0.41976 2.01511
4 3E7O 35F 0.03966 0.40944 2.22222
5 1SW0 PGA 0.003423 0.40706 2.41935
6 2Q46 NAP 0.02618 0.40216 2.7668
7 1HG4 LPP 0.003315 0.43278 2.86738
8 3BLI ACO 0.0228 0.40631 2.96736
9 1KOR ANP 0.04026 0.42724 3.5
10 1KOR ARG 0.03968 0.42724 3.5
11 1KOR SIN 0.03968 0.42724 3.5
12 3P7I P7I 0.0123 0.40333 4.04984
13 1ZVX FIN 0.01616 0.43339 4.29448
14 2EVL GAL SPH EIC 0.03357 0.40409 4.30622
15 1LCP PLU 0.0451 0.41241 4.33884
16 1VB3 KPA 0.01326 0.40038 4.89237
17 4M0R 644 0.04473 0.41533 5.01319
18 3KPB SAM 0.008731 0.40866 5.7377
19 2R0N FAD 0.04012 0.40605 6.09137
20 4B7P 9UN 0.01538 0.41874 6.52174
21 4WZV E40 0.01379 0.40745 6.875
22 4EKQ NPO 0.002867 0.40351 6.95187
23 2BTM PGA 0.001303 0.44696 7.14286
24 2VZZ SCA 0.0227 0.40275 7.33945
25 5CSD ACD 0.01135 0.42767 7.54717
26 3KXC PLM 0.01104 0.40133 8.76289
27 1PZ4 PLM 0.00329 0.43332 11.2069
28 1QDS PGA 0.001535 0.43796 17.1315
29 4ELG 52J 0.02652 0.40458 21.0843
Pocket No.: 2; Query (leader) PDB : 1DL2; Ligand: NAG; Similar sites found: 4
This union binding pocket(no: 2) in the query (biounit: 1dl2.bio1) has 5 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2E22 MAN 0.000766 0.52676 2.15264
2 4NG2 OHN 0.003824 0.41159 3.80435
3 3RDE OYP 0.005349 0.40384 4.30528
4 1XKD ICT 0.009443 0.42621 4.82759
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