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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 (26)
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 5OSS Ki = 58 uM AEZ C8 H12 N2 O4 c1[nH]c2c(....
14 1UZ1 Ki = 130 nM IFL C6 H11 N O4 C1[C@@H]([....
15 2CBU Kd = 2.1 uM CTS C8 H15 N O4 C1C[N@]2C[....
16 2J7G Ki = 136 nM GI4 C10 H15 N2 O6 c1c([nH]c2....
17 5N6S - 8P5 C13 H23 N4 O5 C(CCN=[N+]....
18 2WC4 Ki = 9.1 uM AMF C15 H28 N2 O4 S CCCCCCCCN=....
19 2CBV Kd = 3.3 uM CGB C7 H13 N O4 C1C[C@]2([....
20 1OIF Kd = 0.019 uM IFM C6 H13 N O3 C1[C@@H]([....
21 2CES Ki = 138 nM GIM C8 H13 N2 O4 c1c[n+]2c(....
22 2J7E Ki = 114 nM GI2 C11 H17 N2 O6 COC(=O)Cc1....
23 2J78 Kd = 384 nM GOX C6 H12 N2 O5 C([C@@H]1[....
24 1OIM Kd = 4.762 uM NOJ C6 H13 N O4 C1[C@@H]([....
25 2CET Ki = 7.5 nM PGI C16 H21 N2 O4 c1ccc(cc1)....
26 2J7B Ki = 174 nM NTZ C6 H10 N4 O4 C([C@@H]1[....
70% Homology Family (26)
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 5OSS Ki = 58 uM AEZ C8 H12 N2 O4 c1[nH]c2c(....
14 1UZ1 Ki = 130 nM IFL C6 H11 N O4 C1[C@@H]([....
15 2CBU Kd = 2.1 uM CTS C8 H15 N O4 C1C[N@]2C[....
16 2J7G Ki = 136 nM GI4 C10 H15 N2 O6 c1c([nH]c2....
17 5N6S - 8P5 C13 H23 N4 O5 C(CCN=[N+]....
18 2WC4 Ki = 9.1 uM AMF C15 H28 N2 O4 S CCCCCCCCN=....
19 2CBV Kd = 3.3 uM CGB C7 H13 N O4 C1C[C@]2([....
20 1OIF Kd = 0.019 uM IFM C6 H13 N O3 C1[C@@H]([....
21 2CES Ki = 138 nM GIM C8 H13 N2 O4 c1c[n+]2c(....
22 2J7E Ki = 114 nM GI2 C11 H17 N2 O6 COC(=O)Cc1....
23 2J78 Kd = 384 nM GOX C6 H12 N2 O5 C([C@@H]1[....
24 1OIM Kd = 4.762 uM NOJ C6 H13 N O4 C1[C@@H]([....
25 2CET Ki = 7.5 nM PGI C16 H21 N2 O4 c1ccc(cc1)....
26 2J7B Ki = 174 nM NTZ C6 H10 N4 O4 C([C@@H]1[....
50% Homology Family (84)
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 1E4I - NFG C12 H13 F N2 O9 c1cc(c(cc1....
13 4EK7 - BGC C6 H12 O6 C([C@@H]1[....
14 3U57 - DH8 C27 H34 N2 O8 C/C=C/1[C@....
15 3U5Y - SCG C17 H24 O10 COC(=O)C1=....
16 5OKK - BGP C6 H13 O9 P C([C@@H]1[....
17 5OKE - BG6 C6 H13 O9 P C([C@@H]1[....
18 5OKR - BG6 C6 H13 O9 P C([C@@H]1[....
19 5OKG - BG6 C6 H13 O9 P C([C@@H]1[....
20 5OKQ - BGP C6 H13 O9 P C([C@@H]1[....
21 5OKS - BG6 C6 H13 O9 P C([C@@H]1[....
22 2ZOX - OLA C18 H34 O2 CCCCCCCCC=....
23 2E9M - OLA C18 H34 O2 CCCCCCCCC=....
24 2E9L - OLA C18 H34 O2 CCCCCCCCC=....
25 3AI0 - PNW C12 H15 N O8 c1cc(ccc1[....
26 4IPN - 1FT C12 H23 O13 P S C([C@@H]1[....
27 5N6T - 8P2 C7 H11 N2 O4 C([C@@H]1[....
28 2WBG Ki = 35.2 uM LGS C15 H28 N2 O5 CCCCCCCC/N....
29 2J7H Ki = 53 nM AZF C5 H12 N2 O3 C1[C@H]([C....
30 2J7D Ki = 160 nM GI1 C10 H17 N2 O6 CO[C@@H](c....
31 1W3J Kd = 484 nM OXZ C5 H11 N O4 C1[C@H]([C....
32 2J7C Ki = 10.7 nM IDE C15 H19 N3 O4 c1ccc(cc1)....
33 2J79 Ki = 640 nM GTL C6 H12 N2 O5 C([C@@H]1[....
34 2WC3 Ki = 0.83 uM AM3 C15 H28 N2 O5 CCCCCCCC/N....
35 2J75 - NOY C6 H13 N O4 C1[C@@H]([....
36 2VRJ Ki = 0.28 uM NCW C15 H28 N2 O4 S CCCCCCCCNC....
37 2J7F Ki = 361 nM GI3 C9 H13 N2 O6 c1c([nH]c2....
38 2J77 Ki = 4 uM NOJ C6 H13 N O4 C1[C@@H]([....
39 5OSS Ki = 58 uM AEZ C8 H12 N2 O4 c1[nH]c2c(....
40 1UZ1 Ki = 130 nM IFL C6 H11 N O4 C1[C@@H]([....
41 2CBU Kd = 2.1 uM CTS C8 H15 N O4 C1C[N@]2C[....
42 2J7G Ki = 136 nM GI4 C10 H15 N2 O6 c1c([nH]c2....
43 5N6S - 8P5 C13 H23 N4 O5 C(CCN=[N+]....
44 2WC4 Ki = 9.1 uM AMF C15 H28 N2 O4 S CCCCCCCCN=....
45 2CBV Kd = 3.3 uM CGB C7 H13 N O4 C1C[C@]2([....
46 1OIF Kd = 0.019 uM IFM C6 H13 N O3 C1[C@@H]([....
47 2CES Ki = 138 nM GIM C8 H13 N2 O4 c1c[n+]2c(....
48 2J7E Ki = 114 nM GI2 C11 H17 N2 O6 COC(=O)Cc1....
49 2J78 Kd = 384 nM GOX C6 H12 N2 O5 C([C@@H]1[....
50 1OIM Kd = 4.762 uM NOJ C6 H13 N O4 C1[C@@H]([....
51 2CET Ki = 7.5 nM PGI C16 H21 N2 O4 c1ccc(cc1)....
52 2J7B Ki = 174 nM NTZ C6 H10 N4 O4 C([C@@H]1[....
53 4JIE - BMA C6 H12 O6 C([C@@H]1[....
54 3AIV - HBO C9 H9 N O5 COc1ccc2c(....
55 3AIQ - HBO C9 H9 N O5 COc1ccc2c(....
56 3AIR - DNF C6 H4 N2 O5 c1cc(c(cc1....
57 3AIS - HBK BGC n/a n/a
58 3AIW - DNF C6 H4 N2 O5 c1cc(c(cc1....
59 4PTX - BGC C6 H12 O6 C([C@@H]1[....
60 4PTV - TCB C12 H22 O10 S C([C@@H]1[....
61 3GNP - SOG C14 H28 O5 S CCCCCCCCS[....
62 5AYI - BGC C6 H12 O6 C([C@@H]1[....
63 1E56 - GLC HBO n/a n/a
64 1E55 Ki = 76 uM DHR C8 H7 N O2 c1cc(ccc1[....
65 1V08 Ki ~ 1 uM NTZ C6 H10 N4 O4 C([C@@H]1[....
66 1E4N - HBO C9 H9 N O5 COc1ccc2c(....
67 1H49 - HBO BGC n/a n/a
68 5GNX - BGC C6 H12 O6 C([C@@H]1[....
69 5GNY - BGC C6 H12 O6 C([C@@H]1[....
70 5GNZ - BGC C6 H12 O6 C([C@@H]1[....
71 2E40 - LGC C6 H10 O6 C([C@@H]1[....
72 3F5K Ki = 0.024 mM CE5 C30 H52 O26 C([C@@H]1[....
73 4QLL Ka = 2400 M^-1 CTT C24 H42 O21 C([C@@H]1[....
74 4QLJ - CTT C24 H42 O21 C([C@@H]1[....
75 3F5J Ki = 0.052 mM CTT C24 H42 O21 C([C@@H]1[....
76 4QLK Ka = 1800 M^-1 CTT C24 H42 O21 C([C@@H]1[....
77 3F5L Ki = 0.191 mM LB2 C12 H22 O11 C([C@@H]1[....
78 3PTQ - NFG C12 H13 F N2 O9 c1cc(c(cc1....
79 4PBG - BGP C6 H13 O9 P C([C@@H]1[....
80 3CMJ - SRT C4 H6 O6 [C@H]([C@H....
81 5YIF - 8VR C9 H14 O8 C[C@]1(OC[....
82 1V03 - BGC CCN IPH n/a n/a
83 2O9T - BGC C6 H12 O6 C([C@@H]1[....
84 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 with APoc: 82
This union binding pocket(no: 1) in the query (biounit: 2cet.bio2) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 5MGD GLC GAL GAL 1.49573
2 5OA6 9PT 1.49573
3 2VOT NHV 1.7094
4 4YHG CT3 2.05656
5 5JIL 6KL 2.06186
6 4D1J DGJ 2.35043
7 4YZT BGC BGC BGC BGC 2.5641
8 1Q6I FK5 2.67857
9 3ZQ9 NOY BGC 2.77778
10 6I6R H62 2.77778
11 3WG3 A2G GAL NAG FUC 2.80899
12 3AXX CBI 2.83843
13 5I79 CTT 2.96053
14 3OGV PTQ 2.99145
15 2EPN NGT 2.99145
16 4W6Z ETF 3.17003
17 6D6W GCU 3.20513
18 4FFG 0U8 3.20513
19 4E8C GAL 3.20513
20 2Y24 XYP XYP GCV XYP 3.39426
21 4UFH GIF 3.4188
22 3DG6 MUC 3.54223
23 5WKR NAR 3.58744
24 4CU7 GIF 3.63248
25 3WUC GLC GAL 3.64964
26 1CEN BGC BGC 3.79009
27 5BXA MAN 3.84615
28 3LPF Z77 3.84615
29 4BPZ GLC BGC BGC 3.90625
30 1ULE GLA GAL NAG 4
31 1PX8 XYP 4.05983
32 6D50 GCB 4.05983
33 2E0P CTT 4.05983
34 1ZLQ EDT 4.05983
35 1QW9 KHP 4.05983
36 5TCI MLI 4.14634
37 2R0H CTO 4.26829
38 3M3E GAL A2G NPO 4.34783
39 2OVW CBI 4.37956
40 2D6M LBT 4.40252
41 1XC6 GAL 4.48718
42 2P7Q GG6 4.51128
43 1UZ4 IFL 4.54545
44 2VRQ XYP XYP AHR 4.70085
45 5A6B OAN 5.12821
46 5Z4T BMA BMA 5.17799
47 3II1 BGC 5.34188
48 5A6M XYP XYP XYS 5.62347
49 4CD6 IFM BMA 5.625
50 5K21 6QF 5.67376
51 4U5I BXP 5.7072
52 4YLZ LAT NAG GAL 5.88235
53 3TTY GLA 5.98291
54 1XZ3 ICF 6.32184
55 1KWK GAL 6.41026
56 4M82 NGB 6.51629
57 5L77 GUX 6.83761
58 4W8B GLC BGC BGC XYS BGC XYS XYS GAL 6.99482
59 2NSX IFM 7.26496
60 3I8T LBT 7.92683
61 6FOF LAT 8.67347
62 4FE2 ASP 9.01961
63 3ZMR GLO BGC BGC XYS BGC XYS XYS 9.18803
64 5NBP BGC BGC BGC 9.55882
65 5NFB 8VT 9.65909
66 1ECE BGC BGC BGC BGC 10.0559
67 3AYS CT3 11.1111
68 1A78 TDG 11.9403
69 3A76 SPD 12.5
70 2OYL IDC 12.8898
71 2JEQ GAL BGC BGC BGC XYS BGC XYS 12.9114
72 5NGL NOJ BGC 13.6752
73 5H4R CTT 13.8889
74 3NX2 FER 14.2857
75 5D9O BGC BGC BGC BGC 14.4476
76 6GL0 GLC BGC BGC 14.8036
77 3RJY GLC 15
78 4LYQ MAN BMA BMA 16.453
79 4UOZ GLA 21.1538
80 3UG4 AHR 22.8632
81 4CPB GAL CN8 28.9256
82 2CER PGI 48.7179
Pocket No.: 2; Query (leader) PDB : 2CET; Ligand: PGI; Similar sites found with APoc: 32
This union binding pocket(no: 2) in the query (biounit: 2cet.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 2X05 X05 1.49573
2 3X01 AMP 2.29008
3 3WN0 FUB 2.35043
4 5L9V OGA 2.38095
5 5L9B AKG 2.38095
6 1WKM MET 2.71186
7 4AZ6 OAN 2.75862
8 1GZW GAL BGC 2.98507
9 1SLT NDG GAL 3.73134
10 1OJK GLC BGC 3.9801
11 1OJJ GLC GAL 3.9801
12 4MJ0 SIA SIA 4
13 4EUO ABU 4.0625
14 3HQR OGA 4.06504
15 5DG2 GAL GLC 4.44444
16 2BS5 BGC GAL FUC 4.44444
17 6F7X MFU 4.44444
18 4D06 NAR 4.59364
19 1C9H RAP 4.6729
20 5GVR LMR 4.70085
21 2ZUX RAM 4.91453
22 3B00 16A 5.51471
23 5HV7 RBL 5.55556
24 2EA1 GPG 5.71429
25 3VV1 GAL FUC 6.25
26 3H22 B53 7.07071
27 4LAX FK5 8.17844
28 1LDN OXM 9.49367
29 4J25 OGA 10.917
30 4MPO AMP 11.1111
31 3ZF8 GDP 15.082
32 1NWW HPN 16.1074
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