Receptor
PDB id Resolution Class Description Source Keywords
3PTQ 2.45 Å EC: 3.2.1.21 THE CRYSTAL STRUCTURE OF RICE (ORYZA SATIVA L.) OS4BGLU12 WI DINITROPHENYL 2-DEOXY-2-FLUORO-BETA-D-GLUCOPYRANOSIDE ORYZA SATIVA BETA-ALPHA BARREL GLYCOSIDASE HYDROLASE
Ref.: THE CRYSTAL STRUCTURE OF RICE (ORYZA SATIVA L.) OS4 AN OLIGOSACCHARIDE AND TUBERONIC ACID GLUCOSIDE-HYD BETA-GLUCOSIDASE WITH SIGNIFICANT THIOGLUCOHYDROLAS ACTIVITY ARCH.BIOCHEM.BIOPHYS. V. 510 62 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:3966;
A:3968;
A:3969;
A:3970;
B:3967;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NFG A:1001;
B:1002;
Valid;
Valid;
none;
none;
submit data
348.238 C12 H13 F N2 O9 c1cc(...
ZN A:487;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3PTQ 2.45 Å EC: 3.2.1.21 THE CRYSTAL STRUCTURE OF RICE (ORYZA SATIVA L.) OS4BGLU12 WI DINITROPHENYL 2-DEOXY-2-FLUORO-BETA-D-GLUCOPYRANOSIDE ORYZA SATIVA BETA-ALPHA BARREL GLYCOSIDASE HYDROLASE
Ref.: THE CRYSTAL STRUCTURE OF RICE (ORYZA SATIVA L.) OS4 AN OLIGOSACCHARIDE AND TUBERONIC ACID GLUCOSIDE-HYD BETA-GLUCOSIDASE WITH SIGNIFICANT THIOGLUCOHYDROLAS ACTIVITY ARCH.BIOCHEM.BIOPHYS. V. 510 62 2011
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 23 families.
1 3PTQ - NFG C12 H13 F N2 O9 c1cc(c(cc1....
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 3PTQ - NFG C12 H13 F N2 O9 c1cc(c(cc1....
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: NFG; Similar ligands found: 15
No: Ligand ECFP6 Tc MDL keys Tc
1 NFG 1 1
2 M2F 1 1
3 DCB 0.702703 0.983871
4 NIN MBF BMA BMA 0.658228 0.983871
5 KHP 0.463768 0.777778
6 145 0.44 0.868852
7 147 0.424658 0.836066
8 MBE 0.424658 0.836066
9 GLA NPO 0.424658 0.836066
10 NBZ GLA 0.424658 0.836066
11 PNW 0.424658 0.836066
12 PNA 0.424658 0.836066
13 PNG 0.424658 0.836066
14 GAL NPO 0.424658 0.836066
15 PNJ 0.407895 0.828125
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3PTQ; Ligand: NFG; Similar sites found: 43
This union binding pocket(no: 1) in the query (biounit: 3ptq.bio2) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2VRQ XYP XYP AHR 0.001285 0.43585 1.20968
2 4BQ4 AAL GAL AAL GAL 0.003136 0.43189 1.38614
3 3VDB 149 0.007112 0.41226 1.58416
4 1CEN BGC BGC 0.00009857 0.43461 1.74927
5 4YZT BGC BGC BGC BGC 0.00008538 0.50651 1.78218
6 3OGV PTQ 0.0009715 0.44124 1.78218
7 4YHG CT3 0.0003503 0.46604 1.79949
8 5A95 BGC BGC BGC 0.04971 0.41142 1.91781
9 5N0F 7K2 0.007244 0.42497 1.9337
10 2VOT NHV 0.0007572 0.44076 1.9802
11 3II1 BGC 0.000008308 0.40478 1.9802
12 5MGD GLC GAL GAL 0.001175 0.40893 2.17822
13 3AXX CBI 0.0005668 0.46959 2.18341
14 1IHU AF3 0.00958 0.40466 2.20713
15 4LYQ MAN BMA BMA 0.004149 0.42619 2.22717
16 4UFH GIF 0.003559 0.40011 2.37624
17 2OYL IDC 0.0004338 0.4096 2.4948
18 1YKJ FAD 0.0489 0.40646 2.79188
19 3AYS CT3 0.0001233 0.45277 2.92553
20 1UZ4 IFL 0.0002999 0.41338 2.95455
21 4M82 NGB 0.0007 0.45427 3.00752
22 1OC7 MA3 0.01772 0.40609 3.02198
23 2JEQ GAL BGC BGC BGC XYS BGC XYS 0.0002896 0.46452 3.03797
24 3ZMR GLO BGC BGC XYS BGC XYS XYS 0.000287 0.45004 3.57895
25 5WUU 7UU 0.01754 0.40718 3.59712
26 4CD5 BMA MVL 0.006936 0.41105 4.75248
27 5M67 3D1 0.03194 0.40814 4.80167
28 5M67 NAD 0.03906 0.40371 4.80167
29 5A6M XYP XYP 0.006427 0.4128 4.88998
30 5A6M XYP XYP XYS 0.006343 0.40898 4.88998
31 1PX8 XYP 0.00009748 0.43314 4.9505
32 4D1J DGJ 0.002002 0.40073 4.9505
33 5T7I LAT NAG GAL 0.007156 0.42553 5.16129
34 2NSX IFM 0.001327 0.43524 5.83501
35 3ZQ9 NOY BGC 0.0009183 0.41995 6.33663
36 5D9O BGC BGC BGC BGC 0.001656 0.46011 6.93069
37 5I79 CTT 0.001738 0.43004 8.22368
38 4CU7 GIF 0.0003191 0.43963 8.31683
39 5NGL NOJ BGC 0.001126 0.45874 9.90099
40 4W8B GLC BGC BGC XYS BGC XYS XYS GAL 0.0003059 0.46871 10.8808
41 4U5I BXP 0.0006365 0.48216 11.1663
42 5H4R CTT 0.0001509 0.49474 11.8687
43 2CER PGI 0.0000000001358 0.56662 41.7178
Pocket No.: 2; Query (leader) PDB : 3PTQ; Ligand: NFG; Similar sites found: 10
This union binding pocket(no: 2) in the query (biounit: 3ptq.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2E0P CTT 0.00351 0.41176 1.78218
2 1XC6 GAL 0.003968 0.40536 2.37624
3 2EVL GAL SPH EIC 0.01875 0.42466 2.39234
4 4XZ6 TMO 0.01707 0.41443 2.94985
5 4MPO AMP 0.007363 0.42108 3.26797
6 2Y24 XYP XYP GCV XYP 0.001911 0.40295 4.69974
7 5DG2 GAL GLC 0.005003 0.42983 5.18518
8 4DRI RAP 0.01585 0.40422 6.25
9 2YMZ LAT 0.002124 0.4677 6.92308
10 3RJY GLC 0.00003757 0.40385 17.5
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