Receptor
PDB id Resolution Class Description Source Keywords
2CET 1.97 Å EC: 3.2.1.21 BETA-GLUCOSIDASE FROM THERMOTOGA MARITIMA IN COMPLEX WITH PHENETHYL-SUBSTITUTED GLUCOIMIDAZOLE THERMOTOGA MARITIMA GLYCOSIDE HYDROLASE INHIBITOR TRANSITION STATE MIMIC FAMILY 1 PHENETHYL-SUBSTITUTED GLUCOIMIDAZOLE HYDROLASE
Ref.: STRUCTURAL, KINETIC, AND THERMODYNAMIC ANALYSIS OF GLUCOIMIDAZOLE-DERIVED GLYCOSIDASE INHIBITORS. BIOCHEMISTRY V. 45 11879 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT A:1446;
Invalid;
none;
submit data
59.044 C2 H3 O2 CC(=O...
CA B:1446;
Part of Protein;
none;
submit data
40.078 Ca [Ca+2...
PGI A:1447;
B:1447;
Valid;
Valid;
none;
none;
Ki = 7.5 nM
305.349 C16 H21 N2 O4 c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2CET 1.97 Å EC: 3.2.1.21 BETA-GLUCOSIDASE FROM THERMOTOGA MARITIMA IN COMPLEX WITH PHENETHYL-SUBSTITUTED GLUCOIMIDAZOLE THERMOTOGA MARITIMA GLYCOSIDE HYDROLASE INHIBITOR TRANSITION STATE MIMIC FAMILY 1 PHENETHYL-SUBSTITUTED GLUCOIMIDAZOLE HYDROLASE
Ref.: STRUCTURAL, KINETIC, AND THERMODYNAMIC ANALYSIS OF GLUCOIMIDAZOLE-DERIVED GLYCOSIDASE INHIBITORS. BIOCHEMISTRY V. 45 11879 2006
Members (25)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 23 families.
1 5N6T - 8P2 C7 H11 N2 O4 C([C@@H]1[....
2 2WBG Ki = 35.2 uM LGS C15 H28 N2 O5 CCCCCCCC/N....
3 2J7H Ki = 53 nM AZF C5 H12 N2 O3 C1[C@H]([C....
4 2J7D Ki = 160 nM GI1 C10 H17 N2 O6 CO[C@@H](c....
5 1W3J Kd = 484 nM OXZ C5 H11 N O4 C1[C@H]([C....
6 2J7C Ki = 10.7 nM IDE C15 H19 N3 O4 c1ccc(cc1)....
7 2J79 Ki = 640 nM GTL C6 H12 N2 O5 C([C@@H]1[....
8 2WC3 Ki = 0.83 uM AM3 C15 H28 N2 O5 CCCCCCCC/N....
9 2J75 - NOY C6 H13 N O4 C1[C@@H]([....
10 2VRJ Ki = 0.28 uM NCW C15 H28 N2 O4 S CCCCCCCCNC....
11 2J7F Ki = 361 nM GI3 C9 H13 N2 O6 c1c([nH]c2....
12 2J77 Ki = 4 uM NOJ C6 H13 N O4 C1[C@@H]([....
13 1UZ1 Ki = 130 nM IFL C6 H11 N O4 C1[C@@H]([....
14 2CBU Kd = 2.1 uM CTS C8 H15 N O4 C1C[N@]2C[....
15 2J7G Ki = 136 nM GI4 C10 H15 N2 O6 c1c([nH]c2....
16 5N6S - 8P5 C13 H23 N4 O5 C(CCN=[N+]....
17 2WC4 Ki = 9.1 uM AMF C15 H28 N2 O4 S CCCCCCCCN=....
18 2CBV Kd = 3.3 uM CGB C7 H13 N O4 C1C[C@]2([....
19 1OIF Kd = 0.019 uM IFM C6 H13 N O3 C1[C@@H]([....
20 2CES Ki = 138 nM GIM C8 H13 N2 O4 c1c[n+]2c(....
21 2J7E Ki = 114 nM GI2 C11 H17 N2 O6 COC(=O)Cc1....
22 2J78 Kd = 384 nM GOX C6 H12 N2 O5 C([C@@H]1[....
23 1OIM Kd = 4.762 uM NOJ C6 H13 N O4 C1[C@@H]([....
24 2CET Ki = 7.5 nM PGI C16 H21 N2 O4 c1ccc(cc1)....
25 2J7B Ki = 174 nM NTZ C6 H10 N4 O4 C([C@@H]1[....
70% Homology Family (25)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 5N6T - 8P2 C7 H11 N2 O4 C([C@@H]1[....
2 2WBG Ki = 35.2 uM LGS C15 H28 N2 O5 CCCCCCCC/N....
3 2J7H Ki = 53 nM AZF C5 H12 N2 O3 C1[C@H]([C....
4 2J7D Ki = 160 nM GI1 C10 H17 N2 O6 CO[C@@H](c....
5 1W3J Kd = 484 nM OXZ C5 H11 N O4 C1[C@H]([C....
6 2J7C Ki = 10.7 nM IDE C15 H19 N3 O4 c1ccc(cc1)....
7 2J79 Ki = 640 nM GTL C6 H12 N2 O5 C([C@@H]1[....
8 2WC3 Ki = 0.83 uM AM3 C15 H28 N2 O5 CCCCCCCC/N....
9 2J75 - NOY C6 H13 N O4 C1[C@@H]([....
10 2VRJ Ki = 0.28 uM NCW C15 H28 N2 O4 S CCCCCCCCNC....
11 2J7F Ki = 361 nM GI3 C9 H13 N2 O6 c1c([nH]c2....
12 2J77 Ki = 4 uM NOJ C6 H13 N O4 C1[C@@H]([....
13 1UZ1 Ki = 130 nM IFL C6 H11 N O4 C1[C@@H]([....
14 2CBU Kd = 2.1 uM CTS C8 H15 N O4 C1C[N@]2C[....
15 2J7G Ki = 136 nM GI4 C10 H15 N2 O6 c1c([nH]c2....
16 5N6S - 8P5 C13 H23 N4 O5 C(CCN=[N+]....
17 2WC4 Ki = 9.1 uM AMF C15 H28 N2 O4 S CCCCCCCCN=....
18 2CBV Kd = 3.3 uM CGB C7 H13 N O4 C1C[C@]2([....
19 1OIF Kd = 0.019 uM IFM C6 H13 N O3 C1[C@@H]([....
20 2CES Ki = 138 nM GIM C8 H13 N2 O4 c1c[n+]2c(....
21 2J7E Ki = 114 nM GI2 C11 H17 N2 O6 COC(=O)Cc1....
22 2J78 Kd = 384 nM GOX C6 H12 N2 O5 C([C@@H]1[....
23 1OIM Kd = 4.762 uM NOJ C6 H13 N O4 C1[C@@H]([....
24 2CET Ki = 7.5 nM PGI C16 H21 N2 O4 c1ccc(cc1)....
25 2J7B Ki = 174 nM NTZ C6 H10 N4 O4 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: PGI; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 PGI 1 1
2 VGB 0.555556 0.857143
3 NHV 0.552239 0.898305
4 GSZ 0.547945 0.857143
5 GI4 0.507937 0.87931
6 GI2 0.470588 0.809524
7 GI3 0.421875 0.877193
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2CET; Ligand: PGI; Similar sites found: 46
This union binding pocket(no: 1) in the query (biounit: 2cet.bio2) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5MGD GLC GAL GAL 0.002766 0.41942 1.49573
2 4YHG CT3 0.0001445 0.49909 2.05656
3 4YZT BGC BGC BGC BGC 0.000127 0.51403 2.5641
4 3ZQ9 NOY BGC 0.0002754 0.46625 2.77778
5 3AXX CBI 0.001888 0.40614 2.83843
6 5I79 CTT 0.002334 0.43781 2.96053
7 3OGV PTQ 0.00268 0.43505 2.99145
8 2EPN NGT 0.02397 0.40701 2.99145
9 4FFG 0U8 0.01535 0.41954 3.20513
10 4XBT FLC 0.0108 0.41069 3.87097
11 4BPZ GLC BGC BGC 0.01681 0.41311 3.90625
12 1ZLQ EDT 0.02567 0.40781 4.05983
13 5TCI MLI 0.03454 0.40198 4.14634
14 2OVW CBI 0.01737 0.41673 4.37956
15 2D6M LBT 0.01194 0.42155 4.40252
16 1XC6 GAL 0.006714 0.42882 4.48718
17 1UZ4 IFL 0.0002127 0.5188 4.54545
18 2VRQ XYP XYP AHR 0.002521 0.43627 4.70085
19 1QKQ MAN 0.003733 0.41634 4.92958
20 3II1 BGC 0.000005939 0.64192 5.34188
21 2VUZ NAG BMA NAG MAN MAN NAG NAG 0.03596 0.40066 5.42636
22 5A6M XYP XYP 0.01586 0.40641 5.62347
23 5A6M XYP XYP XYS 0.01772 0.40049 5.62347
24 4CD6 IFM BMA 0.0288 0.40518 5.625
25 4U5I BXP 0.0006083 0.49941 5.7072
26 1XZ3 ICF 0.01104 0.40496 6.32184
27 4M82 NGB 0.001781 0.40073 6.51629
28 5L77 GUX 0.009827 0.40218 6.83761
29 4W8B GLC BGC BGC XYS BGC XYS XYS GAL 0.001186 0.45601 6.99482
30 2NSX IFM 0.01453 0.40826 7.26496
31 4FE2 ASP 0.01951 0.41398 9.01961
32 3ZMR GLO BGC BGC XYS BGC XYS XYS 0.0007213 0.47131 9.18803
33 1ECE BGC BGC BGC BGC 0.001678 0.42863 10.0559
34 3AYS CT3 0.00006832 0.5344 11.1111
35 1A78 TDG 0.01069 0.43062 11.9403
36 3A76 SPD 0.02929 0.40573 12.5
37 2OYL IDC 0.002768 0.40978 12.8898
38 2JEQ GAL BGC BGC BGC XYS BGC XYS 0.0007784 0.4598 12.9114
39 5NGL NOJ BGC 0.00557 0.43753 13.6752
40 5H4R CTT 0.0000996 0.51924 13.8889
41 3NX2 FER 0.01568 0.40492 14.2857
42 3RJY GLC 0.00002792 0.56759 15
43 4LYQ MAN BMA BMA 0.00855 0.42362 16.453
44 4UOZ GLA 0.02955 0.40056 21.1538
45 4CPB GAL CN8 0.04079 0.40073 28.9256
46 2CER PGI 0.0000000003462 0.62217 48.7179
Pocket No.: 2; Query (leader) PDB : 2CET; Ligand: PGI; Similar sites found: 22
This union binding pocket(no: 2) in the query (biounit: 2cet.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2X05 X05 0.01793 0.40794 1.49573
2 3WN0 FUB 0.01028 0.40244 2.35043
3 5L9V OGA 0.009953 0.42463 2.38095
4 5L9B AKG 0.01073 0.42298 2.38095
5 1WKM MET 0.03693 0.40407 2.71186
6 1GZW GAL BGC 0.0036 0.45776 2.98507
7 1OJJ GLC GAL 0.02695 0.40662 3.9801
8 4MJ0 SIA SIA 0.03992 0.40301 4
9 4EUO ABU 0.01083 0.41423 4.0625
10 3HQR OGA 0.02181 0.40375 4.06504
11 2R0H CTO 0.04072 0.40141 4.26829
12 5DG2 GAL GLC 0.004569 0.44502 4.44444
13 3K8L CEY 0.03392 0.40032 4.48718
14 1C9H RAP 0.0125 0.42842 4.6729
15 5GVR LMR 0.002428 0.47027 4.70085
16 3B00 16A 0.02529 0.40419 5.51471
17 3TTY GLA 0.01414 0.42113 5.98291
18 3VV1 GAL FUC 0.01089 0.43602 6.25
19 2B4B B33 0.03662 0.40064 7.60234
20 4LAX FK5 0.04242 0.40016 8.17844
21 4J25 OGA 0.0268 0.40674 10.917
22 4MPO AMP 0.01718 0.41367 11.1111
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