Fluorine in PDB 1mu8: Thrombin-HIRUGEN_L-378,650

All present enzymatic activity of Thrombin-HIRUGEN_L-378,650:
3.4.21.5;

The structure of Thrombin-HIRUGEN_L-378,650, PDB code: 1mu8 was solved by C.S.Burgey, K.A.Robinson, T.A.Lyle, P.E.Sanderson, S.D.Lewis, B.J.Lucas, J.A.Krueger, R.Singh, C.Miller-Stein, R.B.White, B.Wong, E.A.Lyle, P.D.Williams, C.A.Coburn, B.D.Dorsey, J.C.Barrow, M.T.Stranieri, M.A.Holahan, G.R.Sitko, J.J.Cook, D.R.Mcmasters, C.M.Mcdonough, W.M.Sanders, A.A.Wallace, F.C.Clayton, D.Bohn, Y.M.Leonard, T.J.Detwilerjr., J.J.Lynch Jr., Y.Yan, Z.Chen, L.Kuo, S.J.Gardell, J.A.Shafer, J.P.J.Vacca, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.120, 72.230, 73.030, 90.00, 100.80, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Fluorine atom in the Thrombin-HIRUGEN_L-378,650 (pdb code 1mu8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Thrombin-HIRUGEN_L-378,650, PDB code: 1mu8:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Thrombin-HIRUGEN_L-378,650


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Thrombin-HIRUGEN_L-378,650 within 5.0Å range: probe atom residue distance (Å) B Occ B:F248 b:48.0 occ:1.00 F13 B:CDB248 0.0 48.0 1.0 C11 B:CDB248 1.4 47.0 1.0 F1 B:CDB248 2.2 47.1 1.0 C12 B:CDB248 2.3 45.6 1.0 C2 B:CDB248 2.4 46.9 1.0 N18 B:CDB248 2.8 43.0 1.0 C3 B:CDB248 2.9 46.9 1.0 CE3 B:TRP215 3.4 25.1 1.0 CG B:GLU217 3.4 34.6 1.0 CZ3 B:TRP215 3.6 26.3 1.0 N1 B:CDB248 3.7 47.3 1.0 O B:GLY216 3.7 24.2 1.0 C21 B:CDB248 4.0 41.6 1.0 CD B:GLU217 4.1 36.6 1.0 CG1 B:ILE174 4.2 26.5 1.0 C B:GLY216 4.2 24.0 1.0 C4 B:CDB248 4.3 47.2 1.0 CD2 B:TRP215 4.4 24.7 1.0 CB B:GLU217 4.5 30.0 1.0 OE1 B:GLU217 4.5 39.4 1.0 CD1 B:ILE174 4.5 27.9 1.0 CA B:GLU217 4.6 28.6 1.0 N B:GLU217 4.6 25.9 1.0 N26 B:CDB248 4.7 40.9 1.0 CH2 B:TRP215 4.7 25.5 1.0 OE2 B:GLU217 4.8 36.6 1.0 O28 B:CDB248 4.8 38.9 1.0 C22 B:CDB248 4.8 40.6 1.0 C6 B:CDB248 4.9 47.1 1.0 N B:GLY216 4.9 21.8 1.0 CA B:GLY216 5.0 22.7 1.0

Fluorine binding site 2 out of 3 in the Thrombin-HIRUGEN_L-378,650


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Thrombin-HIRUGEN_L-378,650 within 5.0Å range: probe atom residue distance (Å) B Occ B:F248 b:47.1 occ:1.00 F1 B:CDB248 0.0 47.1 1.0 C11 B:CDB248 1.3 47.0 1.0 F13 B:CDB248 2.2 48.0 1.0 C12 B:CDB248 2.3 45.6 1.0 C2 B:CDB248 2.3 46.9 1.0 N1 B:CDB248 2.8 47.3 1.0 C3 B:CDB248 3.6 46.9 1.0 N18 B:CDB248 3.6 43.0 1.0 CD1 B:ILE174 3.9 27.9 1.0 C6 B:CDB248 4.1 47.1 1.0 CG1 B:ILE174 4.3 26.5 1.0 CG B:GLU217 4.6 34.6 1.0 C21 B:CDB248 4.6 41.6 1.0 C4 B:CDB248 4.7 47.2 1.0 OE1 B:GLU217 4.7 39.4 1.0 N26 B:CDB248 4.8 40.9 1.0 CD B:GLU217 4.9 36.6 1.0 C5 B:CDB248 5.0 46.5 1.0

Fluorine binding site 3 out of 3 in the Thrombin-HIRUGEN_L-378,650


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Thrombin-HIRUGEN_L-378,650 within 5.0Å range: probe atom residue distance (Å) B Occ B:F248 b:39.4 occ:1.00 F47 B:CDB248 0.0 39.4 1.0 C43 B:CDB248 1.3 38.4 1.0 C40 B:CDB248 2.4 38.6 1.0 C44 B:CDB248 2.4 38.8 1.0 N37 B:CDB248 2.8 41.0 1.0 C39 B:CDB248 2.8 39.4 1.0 C1 B:CDB248 2.9 40.0 1.0 CG1 B:VAL213 3.1 14.4 1.0 C B:SER214 3.2 18.6 1.0 O B:SER214 3.2 19.5 1.0 N B:TRP215 3.3 18.9 1.0 CA B:TRP215 3.4 21.1 1.0 N46 B:CDB248 3.6 38.5 1.0 C45 B:CDB248 3.7 38.5 1.0 N B:SER214 3.8 15.6 1.0 OG B:SER195 3.8 25.9 1.0 C B:TRP215 3.8 22.1 1.0 CA B:SER214 4.0 17.1 1.0 C B:VAL213 4.1 14.3 1.0 C34 B:CDB248 4.1 41.3 1.0 C50 B:CDB248 4.2 37.7 1.0 O B:TRP215 4.2 23.4 1.0 N B:GLY216 4.4 21.8 1.0 CB B:VAL213 4.4 16.0 1.0 O B:VAL213 4.5 11.7 1.0 CA B:VAL213 4.7 14.5 1.0 CA B:SER195 4.7 20.3 1.0 C33 B:CDB248 4.7 41.3 1.0 CB B:SER195 4.8 21.3 1.0 CB B:TRP215 4.8 21.4 1.0 O B:PHE227 4.9 14.5 1.0 CB B:ALA190 4.9 20.1 1.0 O28 B:CDB248 4.9 38.9 1.0 N B:SER195 5.0 20.3 1.0

C.S.Burgey, K.A.Robinson, T.A.Lyle, P.E.Sanderson, S.D.Lewis, B.J.Lucas, J.A.Krueger, R.Singh, C.Miller-Stein, R.B.White, B.Wong, E.A.Lyle, P.D.Williams, C.A.Coburn, B.D.Dorsey, J.C.Barrow, M.T.Stranieri, M.A.Holahan, G.R.Sitko, J.J.Cook, D.R.Mcmasters, C.M.Mcdonough, W.M.Sanders, A.A.Wallace, F.C.Clayton, D.Bohn, Y.M.Leonard, T.J.Detwiler Jr., J.J.Lynch Jr., Y.Yan, Z.Chen, L.Kuo, S.J.Gardell, J.A.Shafer, J.P.J.Vacca. Metabolism-Directed Optimization of 3-Aminopyrazinone Acetamide Thrombin Inhibitors. Development of An Orally Bioavailable Series Containing P1 and P3 Pyridines. J.Med.Chem. V. 46 461 2003.
ISSN: ISSN 0022-2623
PubMed: 12570369
DOI: 10.1021/JM020311F