Receptor
PDB id Resolution Class Description Source Keywords
4QLK 1.83 Å EC: 3.2.1.21 CRYSTAL STRUCTURE OF RICE BGLU1 E176Q/Y341A MUTANT COMPLEXED CELLOTETRAOSE ORYZA SATIVA JAPONICA GROUP BETA-ALPHA-BARRELS OLIGOSACCHARIDE BINDING TRANSGLUCOSYLATHYDROLASE
Ref.: EFFECTS OF ACTIVE SITE CLEFT RESIDUES ON OLIGOSACCH BINDING, HYDROLYSIS, AND GLYCOSYNTHASE ACTIVITIES O BGLU1 AND ITS MUTANTS PROTEIN SCI. V. 23 1738 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:1003;
B:503;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
MES B:504;
A:1004;
Invalid;
Invalid;
none;
none;
submit data
195.237 C6 H13 N O4 S C1COC...
ZN A:1002;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
BGC BGC BGC BGC C:1;
D:1;
E:1;
Valid;
Valid;
Valid;
none;
none;
none;
Ka = 1800 M^-1
666.579 n/a O(CC1...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3F5K 1.8 Å EC: 3.2.1.21 SEMI-ACTIVE E176Q MUTANT OF RICE BGLU1, A PLANT EXOGLUCANASE GLUCOSIDASE ORYZA SATIVA JAPONICA GROUP BETA-ALPHA-BARRELS GLYCOSIDASE HYDROLASE
Ref.: THE STRUCTURAL BASIS OF OLIGOSACCHARIDE BINDING BY BGLU1 BETA-GLUCOSIDASE J.STRUCT.BIOL. V. 173 169 2011
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 25 families.
1 3F5K Ki = 0.024 mM BGC BGC BGC BGC BGC n/a n/a
2 7BZM - GIM C8 H13 N2 O4 c1c[n+]2c(....
3 4QLL Ka = 2400 M^-1 BGC BGC BGC BGC n/a n/a
4 4QLJ - BGC BGC BGC BGC n/a n/a
5 3F5J Ki = 0.052 mM BGC BGC BGC BGC n/a n/a
6 4QLK Ka = 1800 M^-1 BGC BGC BGC BGC n/a n/a
7 3F5L Ki = 0.191 mM BGC BGC n/a n/a
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 4JIE - BMA C6 H12 O6 C([C@@H]1[....
2 3F5K Ki = 0.024 mM BGC BGC BGC BGC BGC n/a n/a
3 7BZM - GIM C8 H13 N2 O4 c1c[n+]2c(....
4 4QLL Ka = 2400 M^-1 BGC BGC BGC BGC n/a n/a
5 4QLJ - BGC BGC BGC BGC n/a n/a
6 3F5J Ki = 0.052 mM BGC BGC BGC BGC n/a n/a
7 4QLK Ka = 1800 M^-1 BGC BGC BGC BGC n/a n/a
8 3F5L Ki = 0.191 mM BGC BGC n/a n/a
50% Homology Family (89)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1W9D ic50 = 0.58 mM SEH C10 H13 N O4 S2 CCS/C(=NOS....
2 1W9B ic50 = 0.99 mM CGT C15 H21 N O8 S2 c1ccc(cc1)....
3 1E6Q Ki = 0.7 mM NTZ C6 H10 N4 O4 C([C@@H]1[....
4 1E70 - G2F C6 H11 F O5 C([C@@H]1[....
5 1E71 - ASC C6 H8 O6 C([C@@H]([....
6 2WXD ic50 = 3.3 uM E18 C12 H18 N2 O4 S2 CN(C)CCS/C....
7 1E72 Ki = 0.6 mM GOX C6 H12 N2 O5 C([C@@H]1[....
8 1E6X - LGC C6 H10 O6 C([C@@H]1[....
9 1E73 - ASC C6 H8 O6 C([C@@H]([....
10 1E6S Ki = 0.6 mM GOX C6 H12 N2 O5 C([C@@H]1[....
11 1BGG - GCO C6 H12 O7 C([C@H]([C....
12 6R4K Ki = 51 uM JSK C17 H25 N7 O4 [H]/N=N/NC....
13 1E4I - NFG C12 H13 F N2 O9 c1cc(c(cc1....
14 4EK7 - BGC C6 H12 O6 C([C@@H]1[....
15 3U57 - DH8 C27 H34 N2 O8 C/C=C/1[C@....
16 3U5Y - SCG C17 H24 O10 COC(=O)C1=....
17 5OKK - BGP C6 H13 O9 P C([C@@H]1[....
18 5OKE - BG6 C6 H13 O9 P C([C@@H]1[....
19 5OKR - BG6 C6 H13 O9 P C([C@@H]1[....
20 5OKG - BG6 C6 H13 O9 P C([C@@H]1[....
21 5OKQ - BGP C6 H13 O9 P C([C@@H]1[....
22 5OKS - BG6 C6 H13 O9 P C([C@@H]1[....
23 2ZOX - OLA C18 H34 O2 CCCCCCCCC=....
24 2E9M - OLA C18 H34 O2 CCCCCCCCC=....
25 2E9L - OLA C18 H34 O2 CCCCCCCCC=....
26 3AI0 - PNW C12 H15 N O8 c1cc(ccc1[....
27 4IPN - SGC RTG n/a n/a
28 5N6T - 8P2 C7 H11 N2 O4 C([C@@H]1[....
29 2WBG Ki = 35.2 uM LGS C15 H28 N2 O5 CCCCCCCC/N....
30 2J7H Kd = 65 nM AZF C5 H12 N2 O3 C1[C@H]([C....
31 2J7D Kd = 74 nM GI1 C10 H17 N2 O6 CO[C@@H](c....
32 1W3J Kd = 484 nM OXZ C5 H11 N O4 C1[C@H]([C....
33 2J7C Ki = 10.7 nM IDE C15 H19 N3 O4 c1ccc(cc1)....
34 2J79 Kd = 1.1 uM GTL C6 H12 N2 O5 C([C@@H]1[....
35 2WC3 Ki = 0.83 uM AM3 C15 H28 N2 O5 CCCCCCCC/N....
36 2J75 - NOY C6 H13 N O4 C1[C@@H]([....
37 2VRJ Kd = 0.5 uM NCW C15 H28 N2 O4 S CCCCCCCCNC....
38 2J7F Kd = 445 nM GI3 C9 H13 N2 O6 c1c([nH]c2....
39 2J77 Kd = 12.9 uM NOJ C6 H13 N O4 C1[C@@H]([....
40 5OSS Kd = 28.3 uM AEZ C8 H12 N2 O4 c1[nH]c2c(....
41 1UZ1 Ki = 130 nM IFL C6 H11 N O4 C1[C@@H]([....
42 2CBU Kd = 2.1 uM CTS C8 H15 N O4 C1C[N@]2C[....
43 2J7G Kd = 100 nM GI4 C10 H15 N2 O6 c1c([nH]c2....
44 5N6S - 8P5 C13 H23 N4 O5 C(CCN=[N+]....
45 2WC4 Kd = 5.1 uM AMF C15 H28 N2 O4 S CCCCCCCCN=....
46 2CBV Kd = 3.3 uM CGB C7 H13 N O4 C1C[C@]2([....
47 1OIF Ka = 51450000 M^-1 IFM C6 H13 N O3 C1[C@@H]([....
48 2CES Kd = 56 nM GIM C8 H13 N2 O4 c1c[n+]2c(....
49 2J7E Kd = 48 nM GI2 C11 H17 N2 O6 COC(=O)Cc1....
50 2J78 Kd = 384 nM GOX C6 H12 N2 O5 C([C@@H]1[....
51 1OIM Ka = 210000 M^-1 NOJ C6 H13 N O4 C1[C@@H]([....
52 2CET Kd = 9.6 nM PGI C16 H21 N2 O4 c1ccc(cc1)....
53 2J7B Kd = 240 nM NTZ C6 H10 N4 O4 C([C@@H]1[....
54 4JIE - BMA C6 H12 O6 C([C@@H]1[....
55 3AIV - HBO C9 H9 N O5 COc1ccc2c(....
56 3AIQ - HBO C9 H9 N O5 COc1ccc2c(....
57 3AIR - DNF C6 H4 N2 O5 c1cc(c(cc1....
58 3AIS - HBK BGC n/a n/a
59 3AIW - DNF C6 H4 N2 O5 c1cc(c(cc1....
60 4PTX - BGC C6 H12 O6 C([C@@H]1[....
61 4PTV - SGC BGC n/a n/a
62 3GNP - SOG C14 H28 O5 S CCCCCCCCS[....
63 6RJM - GLC C6 H12 O6 C([C@@H]1[....
64 6RK2 - 6GR C13 H16 O8 c1ccc(c(c1....
65 6RJO - SA0 C13 H18 O7 c1ccc(c(c1....
66 5AYI - BGC C6 H12 O6 C([C@@H]1[....
67 1E56 - BGC HBO n/a n/a
68 1E55 Ki = 76 uM DHR C8 H7 N O2 c1cc(ccc1[....
69 1V08 Ki ~ 1 uM NTZ C6 H10 N4 O4 C([C@@H]1[....
70 1E4N - HBO C9 H9 N O5 COc1ccc2c(....
71 1H49 - HBO BGC n/a n/a
72 5GNX - BGC C6 H12 O6 C([C@@H]1[....
73 5GNY - BGC C6 H12 O6 C([C@@H]1[....
74 5GNZ - BGC C6 H12 O6 C([C@@H]1[....
75 2E40 - LGC C6 H10 O6 C([C@@H]1[....
76 3F5K Ki = 0.024 mM BGC BGC BGC BGC BGC n/a n/a
77 7BZM - GIM C8 H13 N2 O4 c1c[n+]2c(....
78 4QLL Ka = 2400 M^-1 BGC BGC BGC BGC n/a n/a
79 4QLJ - BGC BGC BGC BGC n/a n/a
80 3F5J Ki = 0.052 mM BGC BGC BGC BGC n/a n/a
81 4QLK Ka = 1800 M^-1 BGC BGC BGC BGC n/a n/a
82 3F5L Ki = 0.191 mM BGC BGC n/a n/a
83 3PTQ - NFG C12 H13 F N2 O9 c1cc(c(cc1....
84 4PBG - BGP C6 H13 O9 P C([C@@H]1[....
85 3CMJ - SRT C4 H6 O6 [C@H]([C@H....
86 5YIF - 8VR C9 H14 O8 C[C@]1(OC[....
87 1V03 - BGC CCN IPH n/a n/a
88 2O9T - BGC C6 H12 O6 C([C@@H]1[....
89 2O9R Ki = 21 mM SGC BGC n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: BGC BGC BGC BGC; Similar ligands found: 108
No: Ligand ECFP6 Tc MDL keys Tc
1 BGC BGC BGC BGC 1 1
2 BMA MAN MAN 0.774194 1
3 BGC BGC BGC BGC BGC BGC 0.762712 1
4 GLC BGC BGC BGC 0.762712 1
5 BGC BGC BGC 0.762712 1
6 BGC BGC BGC BGC BGC BGC BGC 0.762712 1
7 BGC BGC BGC BGC BGC 0.762712 1
8 GAL GLA 0.677966 1
9 MAN MAN M6P 0.671429 0.785714
10 BGC GLC GLC 0.623188 1
11 MMA MAN MAN 0.623188 0.942857
12 MAN MAN MAN 0.621622 0.970588
13 GLC GLC GLC GLC GLC 0.611111 1
14 BGC GLC GLC GLC 0.611111 1
15 MAN MAN MAN MAN MAN MAN MAN 0.607595 1
16 GLC GLC GLC 0.597222 0.942857
17 BGC GLC GLC GLC GLC GLC 0.59375 1
18 BGC GLC GLC GLC GLC 0.59375 1
19 1GN ACY GAL 1GN BGC ACY GAL BGC 0.581395 0.6875
20 BGC GAL GLA 0.565217 1
21 BGC BGC BGC BGC BGC BGC BGC BGC 0.555556 1
22 GAL SO4 GAL 0.555556 0.66
23 GAL NAG GAL NAG GAL 0.536585 0.6875
24 MAN MAN BMA 0.534247 0.942857
25 BMA MAN MAN MAN MAN 0.530864 0.942857
26 NAG NAG MAN MAN MAN 0.527473 0.6875
27 BMA NGT MAN MAN 0.522727 0.66
28 BMA BMA BMA BMA GLA 0.519481 1
29 BMA MAN MAN MAN 0.518987 0.916667
30 AHR AHR AHR AHR AHR AHR 0.507692 0.857143
31 AHR AHR AHR AHR 0.507692 0.857143
32 AHR AHR AHR AHR AHR 0.507692 0.857143
33 MMA MAN 0.507463 0.942857
34 MBG GAL 0.507463 0.942857
35 MAN MAN MAN GLC 0.506667 1
36 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.494737 0.733333
37 NAG BMA MAN MAN MAN MAN 0.494505 0.733333
38 H1M MAN MAN 0.493671 0.868421
39 AHR AHR 0.484375 0.857143
40 MAN BMA MAN MAN MAN MAN MAN 0.483146 0.942857
41 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.481013 1
42 NAG BMA MAN MAN MAN MAN MAN 0.476744 0.868421
43 GAL NAG GAL 0.47561 0.733333
44 NAG GAL GAL 0.475 0.733333
45 NDG BMA MAN MAN NAG MAN MAN 0.466019 0.6875
46 BQZ 0.453125 0.909091
47 BGC BGC BGC XYS XYS GAL GAL 0.450549 0.942857
48 GAL 1GN BGC ACY GAL 1GN BGC ACY GAL 6PZ 0.45 0.6
49 BGC GAL NAG NAG GAL GAL 0.447917 0.6875
50 BGC BGC BGC XYS 0.447059 0.942857
51 MAN MAN MAN MAN MAN MAN MAN MAN 0.446809 0.846154
52 GCU BGC 0.445946 0.914286
53 NAG BMA MAN MAN MAN MAN MAN MAN MAN MAN 0.444444 0.733333
54 BGC GAL NAG GAL 0.436782 0.733333
55 BMA MAN NAG 0.435294 0.733333
56 NAG NAG BMA MAN MAN MAN MAN 0.435185 0.634615
57 BGC BGC XYS XYS GAL 0.434783 0.942857
58 KDO MAN MAN MAN MAN MAN 0.433962 0.868421
59 GAL NAG FUC GAL 0.433333 0.717391
60 BGC GAL GLA NGA GAL 0.433333 0.733333
61 BGC BGC BGC XYS BGC XYS XYS 0.431818 0.942857
62 BGC BGC XYS BGC XYS XYS GAL 0.431579 0.942857
63 MAN BMA BMA BMA BMA BMA BMA 0.430556 1
64 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.430556 1
65 GLC GLC GLC GLC BGC GLC GLC 0.430556 1
66 BGC BGC GLC BGC XYS BGC XYS XYS 0.430233 0.916667
67 OPM MAN MAN 0.428571 0.804878
68 BGC BGC BGC XYS XYS GAL 0.425532 0.916667
69 NAG GAL BGC GAL 0.425287 0.733333
70 YZ0 MAN MAN NAG MAN 0.42268 0.702128
71 BGC BGC BGC XYS BGC XYS XYS GAL GAL 0.42268 0.942857
72 BGC BGC BGC XYS BGC XYS XYS GAL 0.42268 0.942857
73 GAL NGA A2G 0.421687 0.6875
74 NDG GLA GLC NAG GLC RAM 0.420561 0.673469
75 BGC BGC BGC XYS BGC XYS 0.420455 0.942857
76 FRU GLC GLA 0.419753 0.891892
77 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.416667 0.6875
78 MAN AML MAN MAN MAN MAN MAN MAN MAN 0.416667 0.825
79 GAL AAL GAL AAL 0.41573 0.891892
80 NAG GAL NAG GAL 0.41573 0.6875
81 GAL AAL GAL AAL GAL AAL 0.41573 0.891892
82 NAG GAL NAG GAL NAG GAL 0.41573 0.673469
83 AHR FUB 0.415385 0.857143
84 GLC FRU GLA GLA 0.414634 0.891892
85 GLC FRU GLA GLA GLA 0.414634 0.891892
86 GLC GLC XYS XYS 0.414634 0.914286
87 Z9N GLC 0.413333 0.842105
88 BMA MAN MAN NAG GAL NAG 0.411765 0.6875
89 BGC BGC BGC XYS BGC XYS BGC XYS BGC 0.411111 0.942857
90 BGC BGC BGC BGC XYS BGC XYS BGC BGC 0.411111 0.942857
91 BGC BGC BGC BGC BGC XYS 0.411111 0.942857
92 FUC GAL 0.410959 0.941176
93 C4W NAG FUC BMA MAN 0.409524 0.634615
94 NAG BMA MAN MAN NAG GAL NAG GAL 0.407767 0.673469
95 BGC BGC XYS GAL 0.406977 0.942857
96 BGC GAL GLA NGA 0.406593 0.733333
97 BMA BMA BMA BMA GLA BMA GLA 0.406593 0.916667
98 NDG GLA NAG GLC RAM 0.40566 0.673469
99 NDG NAG GLA NAG GLC RAM 0.40566 0.673469
100 GLC U8V 0.405405 0.916667
101 A2G GAL NAG 0.404494 0.6875
102 BGC FUC GAL NAG GAL 0.40404 0.717391
103 GLC BGC FUC GAL 0.4 0.970588
104 NAG NAG FUL BMA MAN MAN NAG GAL 0.4 0.622642
105 GLC EDO GLC 0.4 0.942857
106 BGC GLA GAL 0.4 1
107 NGB 0.4 0.622642
108 BGC FUC GAL 0.4 0.970588
Similar Ligands (3D)
Ligand no: 1; Ligand: BGC BGC BGC BGC; Similar ligands found: 10
No: Ligand Similarity coefficient
1 G3I 0.9467
2 MGL SGC BGC BGC 0.9414
3 GTM BGC BGC GDA 0.9190
4 GS1 SGC BGC SGC 0.9179
5 MGL SGC GLC GLC 0.9143
6 FRU BGC BGC BGC 0.9138
7 BMA BMA BMA BMA 0.8922
8 BEM BEM BEM MAW 0.8681
9 RCB 0.8669
10 XYP XYP XYP XYP 0.8602
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3F5K; Ligand: BGC BGC BGC BGC BGC; 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: 3f5k.bio3) has 29 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3F5K; Ligand: BGC BGC BGC BGC BGC; 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: 3f5k.bio3) has 24 residues
No: Leader PDB Ligand Sequence Similarity
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