Receptor
PDB id Resolution Class Description Source Keywords
3GNP 1.8 Å EC: 3.2.1.21 CRYSTAL STRUCTURE OF A RICE OS3BGLU6 BETA-GLUCOSIDASE WITH O D-THIO-GLUCOSIDE ORYZA SATIVA SUBSP. JAPONICA BETA-ALPHA BARREL GLYCOSIDASE HYDROLASE
Ref.: STRUCTURAL AND ENZYMATIC CHARACTERIZATION OF OS3BGL RICE {BETA}-GLUCOSIDASE HYDROLYZING HYDROPHOBIC GLY AND (1->3)- AND (1->2)-LINKED DISACCHARIDES. PLANT PHYSIOL. 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:1002;
A:1003;
A:1004;
A:1005;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
SOG A:1001;
Valid;
none;
submit data
308.434 C14 H28 O5 S CCCCC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3GNP 1.8 Å EC: 3.2.1.21 CRYSTAL STRUCTURE OF A RICE OS3BGLU6 BETA-GLUCOSIDASE WITH O D-THIO-GLUCOSIDE ORYZA SATIVA SUBSP. JAPONICA BETA-ALPHA BARREL GLYCOSIDASE HYDROLASE
Ref.: STRUCTURAL AND ENZYMATIC CHARACTERIZATION OF OS3BGL RICE {BETA}-GLUCOSIDASE HYDROLYZING HYDROPHOBIC GLY AND (1->3)- AND (1->2)-LINKED DISACCHARIDES. PLANT PHYSIOL. 2009
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 23 families.
1 3GNP - SOG C14 H28 O5 S CCCCCCCCS[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 3GNP - SOG C14 H28 O5 S CCCCCCCCS[....
50% Homology Family (77)
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 1UYQ - NFG C12 H13 F N2 O9 c1cc(c(cc1....
12 1BGG - GCO C6 H12 O7 C([C@H]([C....
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 2ZOX - OLA C18 H34 O2 CCCCCCCCC=....
18 2E9M - OLA C18 H34 O2 CCCCCCCCC=....
19 2E9L - OLA C18 H34 O2 CCCCCCCCC=....
20 3AI0 - PNW C12 H15 N O8 c1cc(ccc1[....
21 4IPN - 1FT C12 H23 O13 P S C([C@@H]1[....
22 5N6T - 8P2 C7 H11 N2 O4 C([C@@H]1[....
23 2WBG Ki = 35.2 uM LGS C15 H28 N2 O5 CCCCCCCC/N....
24 2J7H Ki = 53 nM AZF C5 H12 N2 O3 C1[C@H]([C....
25 2J7D Ki = 160 nM GI1 C10 H17 N2 O6 CO[C@@H](c....
26 1W3J Kd = 484 nM OXZ C5 H11 N O4 C1[C@H]([C....
27 2J7C Ki = 10.7 nM IDE C15 H19 N3 O4 c1ccc(cc1)....
28 2J79 Ki = 640 nM GTL C6 H12 N2 O5 C([C@@H]1[....
29 2WC3 Ki = 0.83 uM AM3 C15 H28 N2 O5 CCCCCCCC/N....
30 2J75 - NOY C6 H13 N O4 C1[C@@H]([....
31 2VRJ Ki = 0.28 uM NCW C15 H28 N2 O4 S CCCCCCCCNC....
32 2J7F Ki = 361 nM GI3 C9 H13 N2 O6 c1c([nH]c2....
33 2J77 Ki = 4 uM NOJ C6 H13 N O4 C1[C@@H]([....
34 1UZ1 Ki = 130 nM IFL C6 H11 N O4 C1[C@@H]([....
35 2CBU Kd = 2.1 uM CTS C8 H15 N O4 C1C[N@]2C[....
36 2J7G Ki = 136 nM GI4 C10 H15 N2 O6 c1c([nH]c2....
37 5N6S - 8P5 C13 H23 N4 O5 C(CCN=[N+]....
38 2WC4 Ki = 9.1 uM AMF C15 H28 N2 O4 S CCCCCCCCN=....
39 2CBV Kd = 3.3 uM CGB C7 H13 N O4 C1C[C@]2([....
40 1OIF Kd = 0.019 uM IFM C6 H13 N O3 C1[C@@H]([....
41 2CES Ki = 138 nM GIM C8 H13 N2 O4 c1c[n+]2c(....
42 2J7E Ki = 114 nM GI2 C11 H17 N2 O6 COC(=O)Cc1....
43 2J78 Kd = 384 nM GOX C6 H12 N2 O5 C([C@@H]1[....
44 1OIM Kd = 4.762 uM NOJ C6 H13 N O4 C1[C@@H]([....
45 2CET Ki = 7.5 nM PGI C16 H21 N2 O4 c1ccc(cc1)....
46 2J7B Ki = 174 nM NTZ C6 H10 N4 O4 C([C@@H]1[....
47 4JIE - BMA C6 H12 O6 C([C@@H]1[....
48 3AIV - HBO C9 H9 N O5 COc1ccc2c(....
49 3AIQ - HBO C9 H9 N O5 COc1ccc2c(....
50 3AIR - DNF C6 H4 N2 O5 c1cc(c(cc1....
51 3AIS - HBK BGC n/a n/a
52 3AIW - DNF C6 H4 N2 O5 c1cc(c(cc1....
53 4PTX - BGC C6 H12 O6 C([C@@H]1[....
54 4PTV - TCB C12 H22 O10 S C([C@@H]1[....
55 3GNP - SOG C14 H28 O5 S CCCCCCCCS[....
56 5AYI - BGC C6 H12 O6 C([C@@H]1[....
57 1E56 - GLC HBO n/a n/a
58 1E55 Ki = 76 uM DHR C8 H7 N O2 c1cc(ccc1[....
59 1V08 Ki ~ 1 uM NTZ C6 H10 N4 O4 C([C@@H]1[....
60 1E4N - HBO C9 H9 N O5 COc1ccc2c(....
61 1H49 - HBO BGC n/a n/a
62 5GNX - BGC C6 H12 O6 C([C@@H]1[....
63 5GNY - BGC C6 H12 O6 C([C@@H]1[....
64 5GNZ - BGC C6 H12 O6 C([C@@H]1[....
65 2E40 - LGC C6 H10 O6 C([C@@H]1[....
66 3F5K Ki = 0.024 mM CE5 C30 H52 O26 C([C@@H]1[....
67 4QLL Ka = 2400 M^-1 CTT C24 H42 O21 C([C@@H]1[....
68 4QLJ - CTT C24 H42 O21 C([C@@H]1[....
69 3F5J Ki = 0.052 mM CTT C24 H42 O21 C([C@@H]1[....
70 4QLK Ka = 1800 M^-1 CTT C24 H42 O21 C([C@@H]1[....
71 3F5L Ki = 0.191 mM LB2 C12 H22 O11 C([C@@H]1[....
72 3PTQ - NFG C12 H13 F N2 O9 c1cc(c(cc1....
73 4PBG - BGP C6 H13 O9 P C([C@@H]1[....
74 3CMJ - SRT C4 H6 O6 [C@H]([C@H....
75 1V03 - BGC CCN IPH n/a n/a
76 2O9T - BGC C6 H12 O6 C([C@@H]1[....
77 2O9R Ki = 21 mM TCB C12 H22 O10 S C([C@@H]1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SOG; Similar ligands found: 20
No: Ligand ECFP6 Tc MDL keys Tc
1 SOG 1 1
2 HTG 0.977273 1
3 10M 0.634921 0.911111
4 G0S LYS PRO LEU NH2 0.5625 0.804878
5 PTQ 0.47541 0.744186
6 MSX MAN 0.457627 0.75
7 BNG 0.45 0.883721
8 HSJ 0.45 0.883721
9 BOG 0.45 0.883721
10 B7G 0.433333 0.883721
11 KGM 0.433333 0.883721
12 AFO 0.423729 0.8
13 HEX GLC 0.416667 0.860465
14 GLC HEX 0.416667 0.860465
15 BHG 0.416667 0.860465
16 JZR 0.416667 0.860465
17 IPT 0.415094 0.72093
18 1LL 0.411765 0.744186
19 TDG 0.411765 0.744186
20 YDR 0.409836 0.727273
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3GNP; Ligand: SOG; Similar sites found: 48
This union binding pocket(no: 1) in the query (biounit: 3gnp.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2VRQ XYP XYP AHR 0.00421 0.40856 1.02459
2 2W62 BGC BGC BGC BGC BGC 0.002045 0.45642 1.22951
3 4CD6 IFM BMA 0.01348 0.40836 1.5625
4 2Y24 XYP XYP GCV XYP 0.005606 0.42744 1.82768
5 3OGV PTQ 0.003011 0.41436 1.84426
6 5MGD GLC GAL GAL 0.001702 0.44326 2.04918
7 3AYS CT3 0.00004627 0.4802 2.12766
8 4YZT BGC BGC BGC BGC 0.00008119 0.50478 2.2541
9 4M82 NGB 0.0007141 0.45874 2.25564
10 1XC6 GAL 0.006082 0.41608 2.26571
11 1ECE BGC BGC BGC BGC 0.0004029 0.42 2.51397
12 5D9O BGC BGC BGC BGC 0.001814 0.46264 2.54958
13 4YHG CT3 0.0002729 0.46835 2.57069
14 3GFZ C2E 0.005345 0.42514 2.66344
15 1PX8 XYP 0.00005742 0.45062 2.66393
16 1UZ4 IFL 0.0006252 0.4744 2.72727
17 1X8D RNS 0.01926 0.40223 2.88462
18 3AXX CBI 0.0003016 0.40932 3.05677
19 4D1J DGJ 0.0006928 0.47636 3.07377
20 4LYQ MAN BMA BMA 0.009582 0.40671 3.07377
21 4W8B GLC BGC BGC XYS BGC XYS XYS GAL 0.000296 0.46676 3.10881
22 2NSX IFM 0.004349 0.40796 3.27869
23 3II1 BGC 0.000007758 0.60546 3.48361
24 2X05 X05 0.008323 0.40542 3.68852
25 5DG2 GAL GLC 0.007143 0.40532 3.7037
26 2VOT NHV 0.0007913 0.44754 3.89344
27 5NGL NOJ BGC 0.00537 0.42335 3.89344
28 5I79 CTT 0.002105 0.43073 4.27632
29 3ZQ9 NOY BGC 0.000337 0.42894 4.5082
30 2OYL IDC 0.003777 0.40033 4.71311
31 2JEQ GAL BGC BGC BGC XYS BGC XYS 0.0002433 0.46029 4.81013
32 4CU7 GIF 0.001536 0.44439 5.12295
33 1Y0G 8PP 0.02081 0.41508 5.2356
34 4MPO AMP 0.01332 0.41294 5.88235
35 4MNS 2AX 0.02541 0.41484 6.28931
36 1CEN BGC BGC 0.00002313 0.55273 7.28863
37 1KWK GAL 0.004933 0.43022 7.37705
38 4DSU BZI 0.02153 0.40485 7.93651
39 3ZMR GLO BGC BGC XYS BGC XYS XYS 0.0002278 0.46371 8.21053
40 5BVE 4VG 0.03174 0.41689 8.58726
41 1W6O LAT 0.007813 0.41542 8.95522
42 1GZW GAL BGC 0.00833 0.4131 8.95522
43 5A6M XYP XYP 0.002842 0.41735 9.04645
44 5A6M XYP XYP XYS 0.003701 0.41735 9.04645
45 4U5I BXP 0.0005947 0.48204 10.9181
46 5H4R CTT 0.00007449 0.50655 11.8687
47 3RJY GLC 0.00005212 0.40307 13.125
48 2CER PGI 0.00000000005712 0.81608 43.1493
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