Receptor
PDB id Resolution Class Description Source Keywords
2O9R 2.3 Å EC: 3.2.1.21 BETA-GLUCOSIDASE B COMPLEXED WITH THIOCELLOBIOSE PAENIBACILLUS POLYMYXA BETA-GLUCOSIDASE GLYCOSYL HYDROLASE FAMILY 1 THIOCELLOBIOSE INHIBITOR
Ref.: CRYSTAL STRUCTURES OF PAENIBACILLUS POLYMYXA BETA-GLUCOSIDASE B COMPLEXES REVEAL THE MOLECULAR BASIS OF SUBSTRATE SPECIFICITY AND GIVE NEW INSIGHTS INTO THE CATALYTIC MACHINERY OF FAMILY I GLYCOSIDASES J.MOL.BIOL. V. 371 1204 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
TCB A:500;
Valid;
none;
Ki = 21 mM
358.362 C12 H22 O10 S C([C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2O9R 2.3 Å EC: 3.2.1.21 BETA-GLUCOSIDASE B COMPLEXED WITH THIOCELLOBIOSE PAENIBACILLUS POLYMYXA BETA-GLUCOSIDASE GLYCOSYL HYDROLASE FAMILY 1 THIOCELLOBIOSE INHIBITOR
Ref.: CRYSTAL STRUCTURES OF PAENIBACILLUS POLYMYXA BETA-GLUCOSIDASE B COMPLEXES REVEAL THE MOLECULAR BASIS OF SUBSTRATE SPECIFICITY AND GIVE NEW INSIGHTS INTO THE CATALYTIC MACHINERY OF FAMILY I GLYCOSIDASES J.MOL.BIOL. V. 371 1204 2007
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 23 families.
1 2O9T - BGC C6 H12 O6 C([C@@H]1[....
2 2O9R Ki = 21 mM TCB C12 H22 O10 S C([C@@H]1[....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 2O9T - BGC C6 H12 O6 C([C@@H]1[....
2 2O9R Ki = 21 mM TCB C12 H22 O10 S C([C@@H]1[....
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: TCB; Similar ligands found: 32
No: Ligand ECFP6 Tc MDL keys Tc
1 TCB 1 1
2 GLC SGC 1 1
3 SGC SGC BGC 0.911111 1
4 TM6 0.672131 0.972222
5 BGC SGC BGC SGC BGC SGC BGC SGC 0.672131 0.972222
6 1FT 0.660714 0.76087
7 GLC MA1 0.615385 0.971429
8 GLC SSG SSG SGC 0.571429 0.971429
9 TDG 0.568182 0.971429
10 1LL 0.568182 0.971429
11 GLC SSG SGC SGC MA3 0.542373 0.921053
12 BGC SGC SGC GTM 0.542373 0.921053
13 BGC SSG SSG SGC MA3 0.542373 0.921053
14 SMD 0.508772 0.921053
15 BGC SGC BGC SGC BGC SGC BGC SGC SGC 0.478873 0.972222
16 WZ1 0.474576 0.921053
17 TM5 0.464789 0.972222
18 GLC SGC SGC MGL 0.464789 0.921053
19 YDR 0.45614 1
20 GLC 0.444444 0.8
21 WOO 0.444444 0.8
22 BMA 0.444444 0.8
23 GIV 0.444444 0.8
24 GAL 0.444444 0.8
25 MAN 0.444444 0.8
26 GXL 0.444444 0.8
27 ALL 0.444444 0.8
28 BGC 0.444444 0.8
29 GLA 0.444444 0.8
30 G0S LYS PRO LEU NH2 0.411765 0.837838
31 IPT 0.411765 0.789474
32 GTM BGC BGC 0.408451 0.921053
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2O9R; Ligand: TCB; Similar sites found: 37
This union binding pocket(no: 1) in the query (biounit: 2o9r.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3II1 BGC 0.00003768 0.54842 2.43363
2 1PX8 XYP 0.0002423 0.42092 2.65487
3 3PQB VGP 0.007999 0.40823 2.65487
4 5I79 CTT 0.005032 0.40957 2.96053
5 2VOT NHV 0.002508 0.42728 3.09735
6 3AYS CT3 0.0001082 0.45658 3.19149
7 4M82 NGB 0.002188 0.43192 3.25815
8 4MPO AMP 0.008083 0.40777 3.26797
9 3ZQ9 NOY BGC 0.001412 0.41365 3.62595
10 1XSE NDP 0.01167 0.42319 3.72881
11 3CH6 NAP 0.01541 0.43178 4.1958
12 3CH6 311 0.01541 0.43178 4.1958
13 2J62 GSZ 0.01362 0.40239 4.20354
14 4CD6 IFM BMA 0.003814 0.43805 4.375
15 4LYQ MAN BMA BMA 0.01009 0.40776 4.45434
16 4W8B GLC BGC BGC XYS BGC XYS XYS GAL 0.001334 0.43972 4.66321
17 3RJY GLC 0.000005049 0.41661 4.6875
18 3B00 16A 0.005861 0.41466 4.77941
19 2OVW CBI 0.01845 0.40354 4.86618
20 4CU7 GIF 0.009331 0.40939 5.0885
21 1UZ4 IFL 0.0003284 0.49143 5.68182
22 1W6P NDG GAL 0.007786 0.42144 5.97015
23 3ZMR GLO BGC BGC XYS BGC XYS XYS 0.0007557 0.45601 5.97345
24 2JEQ GAL BGC BGC BGC XYS BGC XYS 0.001004 0.44061 6.32911
25 1GZW GAL BGC 0.007246 0.42466 6.71642
26 2NSX IFM 0.01148 0.40105 6.85841
27 1KWK GAL 0.01077 0.41534 7.07965
28 2Y24 XYP XYP GCV XYP 0.01445 0.4089 8.094
29 5NGL NOJ BGC 0.003518 0.43454 8.84956
30 4BPZ GLC BGC BGC 0.01101 0.41025 8.98438
31 1CEN BGC BGC 0.0001149 0.43334 9.91254
32 4YZT BGC BGC BGC BGC 0.000226 0.48639 9.95575
33 4YHG CT3 0.0005342 0.45773 10.0257
34 2YMZ LAT 0.006529 0.42002 10.7692
35 5H4R CTT 0.00009866 0.50352 12.6263
36 4U5I BXP 0.0003428 0.50094 14.6402
37 2CER PGI 0.0000000002823 0.56162 46.4602
Feedback