Receptor
PDB id Resolution Class Description Source Keywords
3GD9 1.8 Å EC: 3.2.1.39 CRYSTAL STRUCTURE OF LAMINARIPENTAOSE-PRODUCING BETA-1,3- GLUCANASE IN COMPLEX WITH LAMINARITETRAOSE STREPTOMYCES MATENSIS GLYCOSIDE HYDROLASES LAMINARIPENTAOSE-PRODUCING BETA-1 3- GLUCNASE (LPHASE) MULTI-WAVELENGTH ANOMALOUS DISPERSION (MAD)
Ref.: STRUCTURE, MECHANISTIC ACTION, AND ESSENTIAL RESIDUES OF A GH-64 ENZYME, LAMINARIPENTAOSE-PRODUCING BETA-1,3-GLUCANASE. J.BIOL.CHEM. V. 284 26708 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GLC BGC BGC BGC A:1;
Valid;
none;
submit data
666.579 n/a O(C1O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3GD9 1.8 Å EC: 3.2.1.39 CRYSTAL STRUCTURE OF LAMINARIPENTAOSE-PRODUCING BETA-1,3- GLUCANASE IN COMPLEX WITH LAMINARITETRAOSE STREPTOMYCES MATENSIS GLYCOSIDE HYDROLASES LAMINARIPENTAOSE-PRODUCING BETA-1 3- GLUCNASE (LPHASE) MULTI-WAVELENGTH ANOMALOUS DISPERSION (MAD)
Ref.: STRUCTURE, MECHANISTIC ACTION, AND ESSENTIAL RESIDUES OF A GH-64 ENZYME, LAMINARIPENTAOSE-PRODUCING BETA-1,3-GLUCANASE. J.BIOL.CHEM. V. 284 26708 2009
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3GD9 - GLC BGC BGC BGC 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 5 families.
1 3GD9 - GLC BGC BGC BGC 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 3 families.
1 3GD9 - GLC BGC BGC BGC n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GLC BGC BGC BGC; Similar ligands found: 229
No: Ligand ECFP6 Tc MDL keys Tc
1 BGC BGC BGC 1 1
2 GLC BGC BGC BGC 1 1
3 GLC BGC BGC BGC BGC BGC BGC 1 1
4 BGC BGC BGC BGC BGC 1 1
5 BGC BGC BGC ASO BGC BGC ASO 1 1
6 BGC BGC BGC GLC BGC BGC 1 1
7 MAN GLC 0.888889 1
8 M3M 0.888889 1
9 LB2 0.888889 1
10 BGC BGC GLC 0.754717 1
11 P3M 0.754386 0.767442
12 BMA MAN MAN 0.709091 1
13 GLA GAL GAL 0.709091 1
14 GLA GAL BGC 0.709091 1
15 BGC BGC BGC BGC 0.689655 1
16 BGC BGC BGC BGC BGC BGC BGC BGC 0.689655 1
17 NAG GAL GAL NAG GAL 0.647059 0.6875
18 M13 0.641509 0.942857
19 MDM 0.641509 0.942857
20 GAL MBG 0.641509 0.942857
21 MAN MAN MAN GLC 0.622951 1
22 MAN BMA MAN MAN MAN 0.619048 1
23 M5S 0.619048 1
24 GAL GAL SO4 0.616667 0.702128
25 BMA BMA MAN 0.589286 0.970588
26 2M4 0.584906 1
27 BGC BGC 0.584906 1
28 MAN MAN 0.584906 1
29 GLC GLC GLC GLC 0.580645 1
30 CGC 0.576271 0.941176
31 MAN BMA NAG 0.575758 0.733333
32 GLA GAL NAG 0.575758 0.733333
33 NAG GAL GAL 0.575758 0.733333
34 GAL GLC 0.545455 1
35 BGC GAL 0.545455 1
36 GLA GLA 0.545455 1
37 BMA GAL 0.545455 1
38 GAL BGC 0.545455 1
39 CBK 0.545455 1
40 CBI 0.545455 1
41 BGC BMA 0.545455 1
42 MAB 0.545455 1
43 GLA GAL 0.545455 1
44 BMA BMA 0.545455 1
45 GLC GAL 0.545455 1
46 LBT 0.545455 1
47 LAT 0.545455 1
48 BGC GLC 0.545455 1
49 GLC BGC 0.545455 1
50 MAL 0.545455 1
51 N9S 0.545455 1
52 B2G 0.545455 1
53 MAL MAL 0.545455 0.970588
54 MAN BMA BMA BMA BMA 0.534483 1
55 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.534483 1
56 GAL GAL GAL 0.534483 1
57 GLC GAL GAL 0.534483 1
58 GLC GLC BGC 0.534483 1
59 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.534483 1
60 GLC GLC GLC GLC GLC 0.534483 1
61 GLA GAL GLC 0.534483 1
62 BMA BMA BMA 0.534483 1
63 BGC BGC BGC BGC BGC BGC 0.534483 1
64 CE6 0.534483 1
65 GLC BGC BGC BGC BGC 0.534483 1
66 MLR 0.534483 1
67 BMA MAN BMA 0.534483 1
68 GLC GLC GLC GLC GLC GLC GLC 0.534483 1
69 CEY 0.534483 1
70 GLC BGC BGC 0.534483 1
71 GLC GLC GLC GLC GLC GLC GLC GLC 0.534483 1
72 BGC GLC GLC 0.534483 1
73 B4G 0.534483 1
74 MT7 0.534483 1
75 MAN MAN BMA BMA BMA BMA 0.534483 1
76 BMA BMA BMA BMA BMA 0.534483 1
77 CEX 0.534483 1
78 BMA BMA BMA BMA BMA BMA 0.534483 1
79 BGC GLC GLC GLC GLC GLC GLC 0.534483 1
80 BGC GLC GLC GLC GLC 0.534483 1
81 MTT 0.534483 1
82 CE5 0.534483 1
83 CT3 0.534483 1
84 CE8 0.534483 1
85 CTR 0.534483 1
86 CTT 0.534483 1
87 BGC GLC GLC GLC 0.534483 1
88 DXI 0.534483 1
89 GLC BGC GLC 0.534483 1
90 MAN BMA BMA 0.534483 1
91 GLC GLC BGC GLC GLC GLC GLC 0.534483 1
92 GLC BGC BGC BGC BGC BGC 0.534483 1
93 BGC BGC BGC GLC 0.534483 1
94 MAN MAN MAN MAN 0.530303 1
95 MAN MAN BMA MAN 0.530303 1
96 MAN BMA BMA BMA BMA BMA 0.52459 0.970588
97 BMA BMA BMA BMA BMA BMA MAN 0.52459 0.970588
98 TRE 0.520833 1
99 GAL NAG GAL BGC 0.520548 0.733333
100 LAT NAG GAL 0.520548 0.733333
101 BGC GAL NAG GAL 0.520548 0.733333
102 BMA MAN 0.517241 0.914286
103 NAG GAL 0.515625 0.733333
104 NGA GAL 0.515625 0.733333
105 GAL NAG 0.515625 0.733333
106 GLA NAG GAL FUC 0.513158 0.717391
107 GAL NAG GAL FUC 0.513158 0.717391
108 GAL NGA GLA BGC GAL 0.513158 0.733333
109 GAL FUC 0.508475 0.941176
110 GLC GAL NAG GAL 0.506667 0.733333
111 NOY BGC 0.5 0.75
112 LAT GLA 0.5 1
113 GAL AAL GAL AAL GAL AAL 0.493333 0.891892
114 AAL GAL AAL GAL 0.493333 0.891892
115 NAG GAL GAL NAG 0.493333 0.6875
116 GAL NAG GAL NAG GAL NAG 0.493333 0.673469
117 AAL GAL AAL GLA 0.493333 0.891892
118 MAN MAN BMA 0.491803 1
119 MAN MMA MAN 0.484848 0.942857
120 FUC BGC GAL 0.484848 0.970588
121 GAL A2G 0.484375 0.733333
122 A2G GAL 0.484375 0.733333
123 GAL NGA 0.484375 0.733333
124 U63 0.483333 0.891892
125 NGA GLA GAL BGC 0.480519 0.733333
126 MAN MAN MAN BMA MAN 0.479452 1
127 GLA EGA 0.47541 0.942857
128 DR5 0.474576 0.942857
129 MMA MAN 0.474576 0.942857
130 GLA MBG 0.473684 0.942857
131 NAG GAL BGC 0.472973 0.733333
132 FUC BGC GAL NAG GAL 0.470588 0.717391
133 GLA GLA FUC 0.469697 0.970588
134 GAL GAL FUC 0.469697 0.970588
135 GLA GAL FUC 0.469697 0.970588
136 FUC GAL GLA 0.469697 0.970588
137 FUC GLA GLA 0.469697 0.970588
138 47N 0.46875 0.891892
139 AAL GAL 0.46875 0.891892
140 DOM 0.466667 0.942857
141 NAG NAG BMA MAN 0.463415 0.634615
142 NOJ GLC 0.460317 0.727273
143 GLC DMJ 0.460317 0.727273
144 GLA MAN RAM TYV GLA MAN RAM TYV 0.454545 0.868421
145 GLA MAN RAM ABE GLA MAN RAM ABE 0.454545 0.868421
146 MAN MAN MAN MAN MAN MAN MAN MAN 0.452381 0.846154
147 OPM MAN MAN 0.452055 0.804878
148 5QP 0.451613 0.885714
149 FUC BGC GAL NAG 0.451219 0.717391
150 T6P 0.45 0.767442
151 RZM 0.45 0.688889
152 GLC GLC GLC GLC GLC GLC 0.449275 1
153 IFM BGC 0.444444 0.744186
154 IFM BMA 0.444444 0.744186
155 MAN MNM 0.444444 0.75
156 BMA IFM 0.444444 0.744186
157 9MR 0.444444 0.744186
158 GLA MAN ABE 0.444444 0.916667
159 MAL EDO 0.444444 0.942857
160 BGC OXZ 0.444444 0.666667
161 MAN 7D1 0.442623 0.888889
162 G2F BGC BGC BGC BGC BGC 0.441176 0.868421
163 NLC 0.439394 0.733333
164 NDG GAL 0.439394 0.733333
165 GAL NDG 0.439394 0.733333
166 GAL MGC 0.439394 0.702128
167 WZ3 0.438356 0.916667
168 FMO 0.4375 0.868421
169 GAL NGA A2G 0.43662 0.673469
170 NAG GAL NAG 0.434211 0.6875
171 NAG BMA MAN MAN MAN MAN 0.433735 0.733333
172 BMA BMA GLA BMA BMA 0.430556 1
173 AAL GAL AAL GAL AAL GAL AAL GAL 0.430233 0.825
174 GLC GLC XYP 0.428571 1
175 FRU GAL 0.428571 0.842105
176 BMA FRU 0.428571 0.842105
177 GLA MAN RAM RAM ABE MAN GLA 0.425532 0.868421
178 BGC BGC ZZ1 0.425 0.767442
179 4MU MAN MAN 0.425 0.767442
180 BGC GLA GAL FUC 0.421053 0.970588
181 NAG BMA 0.42029 0.653061
182 1GN ACY GAL ACY 1GN BGC GAL BGC 0.418605 0.6875
183 ACY 1GN GAL 1GN BGC ACY GAL BGC 0.418605 0.6875
184 GLA GAL BGC 5VQ 0.41791 0.891892
185 GLA GAL NAG FUC GAL GLC 0.417582 0.717391
186 GLC GLC GLC BGC 0.416667 1
187 FUC GAL NAG GAL FUC 0.416667 0.702128
188 BGC BGC G2F SHG 0.415584 0.846154
189 NAG BMA MAN MAN MAN MAN MAN 0.4125 0.868421
190 KHO 0.409836 0.888889
191 MAN BMA 0.409836 1
192 BGC GLA 0.409836 1
193 BMA GLA 0.409836 1
194 GLA BGC 0.409836 1
195 GLA BMA 0.409836 1
196 GLA GLC 0.409836 1
197 MLB 0.409836 1
198 LAK 0.409836 1
199 GAL GAL 0.409836 1
200 MVP 0.409091 0.733333
201 ABL 0.409091 0.702128
202 FUC GAL NAG GAL BGC 0.409091 0.717391
203 SGA BGC 0.409091 0.702128
204 G2I 0.408451 0.767442
205 G3I 0.408451 0.767442
206 OXZ BGC BGC 0.408451 0.6875
207 WOO 0.408163 0.848485
208 BGC 0.408163 0.848485
209 GXL 0.408163 0.848485
210 GAL 0.408163 0.848485
211 GLC 0.408163 0.848485
212 ALL 0.408163 0.848485
213 MAN 0.408163 0.848485
214 GLA 0.408163 0.848485
215 BMA 0.408163 0.848485
216 GIV 0.408163 0.848485
217 GAL BGC BGC XYS 0.407895 0.942857
218 MAN DGO 0.40625 0.914286
219 GLA MMA ABE 0.405405 0.868421
220 GLC GLC BGC XYS BGC XYS 0.405063 0.942857
221 MAN MAN MAN BMA MAN MAN MAN 0.404762 0.942857
222 MAN MAN NAG MAN NAG 0.404494 0.6875
223 NAG MAN GAL MAN MAN NAG GAL 0.404494 0.6875
224 NAG NAG BMA MAN MAN 0.404494 0.6875
225 3MG 0.403846 0.857143
226 SOR GLC GLC 0.402778 0.970588
227 GLA GAL GLC NBU 0.4 0.846154
228 2M8 0.4 0.911765
229 ISX 0.4 0.761905
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3GD9; Ligand: GLC BGC BGC BGC; Similar sites found: 69
This union binding pocket(no: 1) in the query (biounit: 3gd9.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5CLO NS8 0.01963 0.40082 None
2 3A16 PXO 0.006121 0.42858 1.3624
3 4KBA 1QM 0.008157 0.41224 1.51057
4 3E9I XAH 0.004202 0.44029 1.63488
5 1WUB OTP 0.02823 0.41175 1.68539
6 1M15 ADP 0.004693 0.44307 1.96078
7 1M15 ARG 0.004693 0.44307 1.96078
8 3R96 AMP 0.007846 0.43529 2.12766
9 3R96 ACO 0.007846 0.43529 2.12766
10 5D9G GLU ASN LEU TYR PHE GLN 0.009874 0.40822 2.43902
11 3OV6 MK0 0.009357 0.42447 2.45232
12 4GCZ FMN 0.007553 0.41352 2.45232
13 3NZ1 3NY 0.002355 0.44688 2.68199
14 4MKF AP5 0.03702 0.4039 2.76498
15 4QRH 0O2 0.004925 0.42228 2.85714
16 2F3R G5P 0.01015 0.42396 2.89855
17 3A5Y KAA 0.007063 0.42346 2.89855
18 4WOE ADP 0.0009762 0.4662 2.99728
19 3G1Z AMP 0.009386 0.40489 3.06748
20 3SAO DBH 0.0004681 0.49316 3.125
21 1REQ DCA 0.006733 0.44468 3.26975
22 5MRH Q9Z 0.002332 0.43851 3.26975
23 1M5W DXP 0.01532 0.40339 3.29218
24 2GQS C2R 0.004419 0.40706 3.37553
25 3KYF 5GP 5GP 0.004551 0.4197 3.4632
26 1LSH PLD 0.006182 0.43204 3.54223
27 1RYD GLC 0.006667 0.42701 3.54223
28 4MOB ADP 0.004305 0.43402 3.61446
29 4I53 1C1 0.01582 0.40012 3.63128
30 4CS4 AXZ 0.03457 0.40887 3.64964
31 4CS4 ANP 0.0308 0.40615 3.64964
32 4I54 1C1 0.01889 0.40934 3.68272
33 4DSU BZI 0.006834 0.42514 3.7037
34 2YKL NLD 0.004959 0.41348 3.77358
35 4FE2 AIR 0.01117 0.40132 3.92157
36 4K55 H6P 0.00003739 0.42599 4.03226
37 3A5Z KAA 0.007024 0.42509 4.18848
38 4DQ2 BTX 0.02305 0.40382 4.26829
39 3CBC DBS 0.0002384 0.41191 5.05051
40 3FW4 CAQ 0.002001 0.44992 5.05618
41 5XDT ZI7 0.008703 0.422 5.19481
42 5UIU 8CG 0.01005 0.42164 5.57276
43 3LVW GSH 0.01944 0.41433 5.99455
44 4WVW SLT 0.009136 0.40608 6.25
45 2OBD PCW 0.0123 0.41859 6.53951
46 5D3X 4IP 0.01982 0.41066 6.58683
47 4HIA FMN 0.02382 0.40882 6.81818
48 4FFG 0U8 0.01858 0.41779 7.08447
49 1Y7P RIP 0.001362 0.41024 7.62332
50 4RYV ZEA 0.007919 0.40837 7.74194
51 5DYO FLU 0.0007986 0.47306 8.01887
52 3HCH RSM 0.009434 0.42358 8.21918
53 4NS0 PIO 0.01568 0.40381 8.27068
54 2VDF OCT 0.0004362 0.43387 8.3004
55 2G30 ALA ALA PHE 0.000006741 0.53207 8.52713
56 1ULE GLA GAL NAG 0.01641 0.4056 8.66667
57 3DZ6 PUT 0.00566 0.43788 8.95522
58 1QKQ MAN 0.00001929 0.51927 9.15493
59 5HWV MBN 0.001862 0.41055 9.23077
60 4R38 RBF 0.0008733 0.40713 9.28571
61 1UYY BGC BGC 0.01717 0.40091 9.92366
62 3G08 FEE 0.03543 0.41433 12.1212
63 3IES M24 0.03205 0.40229 13.079
64 1NCQ W11 0.004494 0.42415 13.2353
65 5F6U 5VK 0.002461 0.4471 13.3758
66 2BVE PH5 0.03164 0.40156 13.4454
67 5H9Q TD2 0.001177 0.4656 18.0645
68 3H0L ADP 0.01132 0.40534 18.8011
69 3QRC SCR 0.001216 0.44042 21.6561
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