Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:1004;
B:1004;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
MES A:1003;
B:1003;
Invalid;
Invalid;
none;
none;
submit data
195.237 C6 H13 N O4 S C1COC...
SO4 A:1002;
B:1002;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
ZN A:1001;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
BGC BGC BGC BGC BGC D:1;
C:1;
Valid;
Valid;
none;
none;
Ki = 0.024 mM
828.72 n/a O(C1C...
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 BGC; Similar ligands found: 134
No: Ligand ECFP6 Tc MDL keys Tc
1 GLC BGC BGC BGC 1 1
2 BGC BGC BGC BGC BGC BGC 1 1
3 BGC BGC BGC BGC BGC BGC BGC 1 1
4 BGC BGC BGC BGC BGC 1 1
5 BGC BGC BGC 1 1
6 GAL GLA 0.888889 1
7 BGC BGC BGC BGC 0.762712 1
8 MAN MAN M6P 0.716667 0.785714
9 BGC GAL GLA 0.709091 1
10 BGC BGC BGC BGC BGC BGC BGC BGC 0.689655 1
11 GAL NAG GAL NAG GAL 0.647059 0.6875
12 MBG GAL 0.641509 0.942857
13 BMA MAN MAN 0.627119 1
14 MAN MAN MAN GLC 0.622951 1
15 GAL SO4 GAL 0.606557 0.66
16 BQZ 0.58 0.909091
17 NAG GAL GAL 0.575758 0.733333
18 GAL NAG GAL 0.573529 0.733333
19 GCU BGC 0.55 0.914286
20 MAN MAN MAN 0.536232 0.970588
21 MAN BMA BMA BMA BMA BMA BMA 0.534483 1
22 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.534483 1
23 GLC GLC GLC GLC BGC GLC GLC 0.534483 1
24 AHR FUB 0.529412 0.857143
25 BMA MAN NAG 0.521127 0.733333
26 BGC GAL NAG GAL 0.520548 0.733333
27 GAL NAG FUC GAL 0.513158 0.717391
28 BGC GAL GLA NGA GAL 0.513158 0.733333
29 FUC GAL 0.508475 0.941176
30 BGC GLA GAL 0.5 1
31 GAL AAL GAL AAL GAL AAL 0.493333 0.891892
32 NAG GAL NAG GAL NAG GAL 0.493333 0.673469
33 NAG GAL NAG GAL 0.493333 0.6875
34 GAL AAL GAL AAL 0.493333 0.891892
35 GAL NGA A2G 0.485714 0.6875
36 BGC FUC GAL 0.484848 0.970588
37 GLC BGC FUC GAL 0.484848 0.970588
38 MMA MAN MAN 0.484848 0.942857
39 MAN BMA BMA 0.484375 0.942857
40 A2G GAL 0.484375 0.733333
41 BGC GAL GLA NGA 0.480519 0.733333
42 MGL GAL 0.474576 0.942857
43 MBG GLA 0.473684 0.942857
44 BGC GAL NAG 0.472973 0.733333
45 BGC FUC GAL NAG GAL 0.470588 0.717391
46 GAL FUC GAL 0.469697 0.970588
47 47N 0.46875 0.891892
48 GAL AAL 0.46875 0.891892
49 MAN MAN MAN MAN MAN MAN MAN 0.467532 1
50 RR7 GLC 0.466667 0.942857
51 NAG NAG BMA MAN 0.463415 0.634615
52 G2F SHG BGC BGC 0.461538 0.891892
53 NOY BGC 0.460317 0.702128
54 MAN MAN 0.457627 0.941176
55 GLA NAG GAL FUC 0.455696 0.717391
56 RAM MAN GLA ABE RAM MAN GLA ABE 0.454545 0.868421
57 MAN MAN MAN MAN MAN MAN MAN MAN 0.452381 0.846154
58 OPM MAN MAN 0.452055 0.804878
59 5QP 0.451613 0.885714
60 BGC FUC GAL NAG 0.451219 0.717391
61 RZM 0.45 0.688889
62 BGC OXZ 0.444444 0.666667
63 IFM BGC 0.444444 0.711111
64 MAN GLA ABE 0.444444 0.916667
65 9MR 0.444444 0.744186
66 GLC EDO GLC 0.444444 0.942857
67 7D1 MAN 0.442623 0.888889
68 G2F BGC BGC BGC BGC BGC 0.441176 0.868421
69 MAN MAN BMA 0.441176 0.942857
70 MGC GAL 0.439394 0.702128
71 NAG GAL 0.439394 0.733333
72 NOJ GLC 0.4375 0.695652
73 GLC DMJ 0.4375 0.695652
74 MAN MNM 0.4375 0.702128
75 NAG GAL NAG 0.434211 0.6875
76 BGC GAL NGA GAL 0.434211 0.733333
77 BGC XGP 0.430769 0.785714
78 CJX 0.430769 0.717391
79 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.430556 1
80 BMA BMA BMA BMA GLA 0.430556 1
81 FRU BMA 0.428571 0.842105
82 MAN IPD MAN 0.428571 0.785714
83 RAM MAN GLA ABE RAM MAN GLA 0.425532 0.868421
84 BGC ZZ1 BGC 0.425 0.767442
85 GDQ GLC 0.424242 0.666667
86 MAN G63 0.424242 0.653061
87 IPD MAN 0.421875 0.738095
88 BGC GAL FUC GLA 0.421053 0.970588
89 NAG BMA 0.42029 0.653061
90 BGC GLC GLC 0.42029 1
91 1GN ACY GAL 1GN BGC ACY GAL BGC 0.418605 0.6875
92 NAG BMA MAN MAN MAN MAN 0.418605 0.733333
93 BGC 5VQ GAL GLA 0.41791 0.891892
94 GLC GAL NAG GAL FUC GLA 0.417582 0.717391
95 GAL NAG GAL FUC FUC 0.416667 0.702128
96 BGC GLC GLC GLC 0.416667 1
97 GLC GLC GLC GLC GLC 0.416667 1
98 NAG BMA MAN MAN MAN MAN MAN 0.4125 0.868421
99 GLC BGC BGC 0.410959 0.942857
100 BMA MAN MAN MAN MAN 0.410256 0.942857
101 ABL 0.409091 0.702128
102 BGC GAL NAG GAL FUC 0.409091 0.717391
103 G3I 0.408451 0.767442
104 G2I 0.408451 0.767442
105 BGC OXZ BGC 0.408451 0.6875
106 GLC 0.408163 0.848485
107 GLA 0.408163 0.848485
108 BGC 0.408163 0.848485
109 MAN 0.408163 0.848485
110 BMA 0.408163 0.848485
111 GAL 0.408163 0.848485
112 ALL 0.408163 0.848485
113 GXL 0.408163 0.848485
114 GLC GLC 0.408163 0.848485
115 BGC GAL 0.408163 0.848485
116 GIV 0.408163 0.848485
117 GAL GAL 0.408163 0.848485
118 WOO 0.408163 0.848485
119 BGC BGC XYS GAL 0.407895 0.942857
120 GLC U8V 0.40625 0.916667
121 DGO MAN 0.40625 0.914286
122 MMA GLA ABE 0.405405 0.868421
123 BGC BGC BGC XYS BGC XYS 0.405063 0.942857
124 MAN BMA MAN MAN MAN MAN MAN 0.404762 0.942857
125 BGC GAL NAG NAG GAL GAL 0.404494 0.6875
126 NAG NAG MAN MAN MAN 0.404494 0.6875
127 3MG 0.403846 0.857143
128 ZB1 0.403846 0.857143
129 GPM GLC 0.402985 0.767442
130 GLC GLC GLC 0.402778 0.942857
131 SOR GLC GLC 0.402778 0.970588
132 GLC NBU GAL GLA 0.4 0.846154
133 2M8 0.4 0.911765
134 ISX 0.4 0.761905
Similar Ligands (3D)
Ligand no: 1; Ligand: BGC BGC BGC BGC BGC; Similar ligands found: 3
No: Ligand Similarity coefficient
1 GLC BGC BGC BGC BGC 0.9945
2 BMA BMA BMA BMA BMA 0.8824
3 MAN BMA BMA BMA BMA 0.8756
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
APoc FAQ
Feedback