Receptor
PDB id Resolution Class Description Source Keywords
5HC7 2.05 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF LAVANDULYL DIPHOSPHATE SYNTHASE FROM LA INTERMEDIA IN COMPLEX WITH S-THIOLO-ISOPENTENYLDIPHOSPHATE LAVANDULA LANATA SUBSTRATE BINDING TRANSFERASE LAVANDULYL INHIBITOR TRANSTRANSFERASE INHIBITOR COMPLEX
Ref.: STRUCTURE AND FUNCTION OF A "HEAD-TO-MIDDLE" PRENYLTRANSFERASE: LAVANDULYL DIPHOSPHATE SYNTHASE ANGEW.CHEM.INT.ED.ENGL. V. 55 4721 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:401;
 Part of Protein;
 none;
 submit data
24.305 Mg [Mg+2...
DST A:403;
A:402;
 Valid;
Valid;
 Atoms found LESS than expected: % Diff = 0.357;
none;
 submit data
262.158 C5 H12 O6 P2 S CC(=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5HC8 1.87 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF LAVANDULYL DIPHOSPHATE SYNTHASE FROM LA INTERMEDIA IN COMPLEX WITH DIMETHYLALLYL DIPHOSPHATE LAVANDULA LANATA SUBSTRATE BINDING PRENYLTRANSFERASE SUBSTRATE TRANSFERASE
Ref.: STRUCTURE AND FUNCTION OF A "HEAD-TO-MIDDLE" PRENYLTRANSFERASE: LAVANDULYL DIPHOSPHATE SYNTHASE ANGEW.CHEM.INT.ED.ENGL. V. 55 4721 2016
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 5HC8 - PIS H3 O6 P2 S OP(=O)(O)O....
2 5HC7 - DST C5 H12 O6 P2 S CC(=CCS[P@....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 5HC8 - PIS H3 O6 P2 S OP(=O)(O)O....
2 5HC7 - DST C5 H12 O6 P2 S CC(=CCS[P@....
50% Homology Family (28)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2E9D - B76 C20 H20 O8 P2 c1ccc(cc1)....
2 1X09 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
3 3TH8 - TH9 C19 H27 N O5 CCCCCCOc1c....
4 5CQJ ic50 = 15.4 uM 53Q C26 H28 Cl N O CCN(CC)CCO....
5 5ZHE - HJX C21 H34 O4 CCCCCCCCCC....
6 1V7U - FPP C15 H28 O7 P2 CC(=CCC/C(....
7 2E9C - B75 C24 H23 N O9 P2 S c1ccc2cc(c....
8 2E9A - B28 C20 H20 O7 P2 c1ccc(cc1)....
9 1X06 - FPS C15 H28 O6 P2 S CC(=CCC/C(....
10 1X07 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
11 2E98 - B29 C20 H18 O8 P2 c1ccc2c(c1....
12 3WYJ ic50 = 0.36 uM H78 C34 H36 N2 O18 P4 S2 c1cc(cc(c1....
13 1X08 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
14 2E99 - B08 C20 H20 O7 P2 c1ccc(cc1)....
15 2VG2 - IPE C5 H12 O7 P2 CC(=C)CCO[....
16 4ONC Kd = 410 nM 40B C19 H18 O7 P2 c1ccc(cc1)....
17 6IME - GST C10 H20 O6 P2 S CC(=CCCC(=....
18 2VG3 - GPP C10 H20 O7 P2 CC(=CCC/C(....
19 5HC8 - PIS H3 O6 P2 S OP(=O)(O)O....
20 5HC7 - DST C5 H12 O6 P2 S CC(=CCS[P@....
21 4Q9O Kd = 1.7 uM 2ZW C20 H19 Cl N2 O2 Cc1c(c(no1....
22 4Q9M Kd = 66 nM 2ZW C20 H19 Cl N2 O2 Cc1c(c(no1....
23 4U82 ic50 = 1.9 uM FPS C15 H28 O6 P2 S CC(=CCC/C(....
24 2VG1 - FPP C15 H28 O7 P2 CC(=CCC/C(....
25 2VG0 - GPP C10 H20 O7 P2 CC(=CCC/C(....
26 6SZG - M2K C8 H10 N2 O2 C1CCc2c(c(....
27 6ACS - CIT C6 H8 O7 C(C(=O)O)C....
28 6SZH - M2H C7 H8 N2 Cc1cc([nH]....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: DST; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 DST 1 1
2 GST 0.613636 0.871795
3 GGS 0.5625 0.85
4 FPS 0.5625 0.85
5 AG8 0.464286 0.693878
6 ISY 0.452381 0.820513
Similar Ligands (3D)
Ligand no: 1; Ligand: DST; Similar ligands found: 49
No: Ligand Similarity coefficient
1 DMA 0.9657
2 2JA 0.9477
3 IPE 0.9412
4 IPR 0.9256
5 0JX 0.9248
6 H6P 0.9227
7 0O3 0.9174
8 0CH 0.9123
9 0K2 0.9123
10 10G 0.9102
11 IS3 0.9099
12 P3S 0.9099
13 DED 0.9079
14 0CM 0.9075
15 0CJ 0.9040
16 EIP 0.9020
17 10D 0.9002
18 10E 0.8984
19 43Q 0.8981
20 3CX 0.8967
21 RGP 0.8966
22 2E6 0.8958
23 58X 0.8940
24 NFZ 0.8936
25 MGB 0.8912
26 ZZU 0.8899
27 2E5 0.8863
28 BHI 0.8849
29 6FR 0.8846
30 PUW 0.8833
31 PMV 0.8801
32 2E4 0.8784
33 M3L 0.8771
34 BOW 0.8770
35 HSA 0.8722
36 M28 0.8678
37 64Z 0.8655
38 HRG 0.8640
39 ARG 0.8636
40 M8O 0.8621
41 AHL 0.8595
42 OKP 0.8581
43 N8C 0.8576
44 5RP 0.8569
45 DAR 0.8561
46 VFM 0.8544
47 PML 0.8535
48 GGG 0.8524
49 4DI 0.8512
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5HC8; Ligand: 61G; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 5hc8.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 5XK9 GST 43.9655
Pocket No.: 2; Query (leader) PDB : 5HC8; Ligand: 61G; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5hc8.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5HC8; Ligand: PIS; Similar sites found with APoc: 3
This union binding pocket(no: 3) in the query (biounit: 5hc8.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 5XK9 GST 43.9655
2 5XK9 DMA 43.9655
3 5XK9 DMA 43.9655
Pocket No.: 4; Query (leader) PDB : 5HC8; Ligand: PIS; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5hc8.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5HC8; Ligand: ISY; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 5hc8.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 5HC8; Ligand: ISY; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5hc8.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
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