Fluorine in PDB 6t57: Thrombin in Complex with A D-Phe-Pro-N-Amidinopiperidine Derivative

All present enzymatic activity of Thrombin in Complex with A D-Phe-Pro-N-Amidinopiperidine Derivative:
3.4.21.5;

The structure of Thrombin in Complex with A D-Phe-Pro-N-Amidinopiperidine Derivative, PDB code: 6t57 was solved by K.Ngo, N.Abazi, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.73 / 1.57
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.290, 71.660, 73.245, 90.00, 100.68, 90.00
R / Rfree (%)	19.3 / 21.3

The structure of Thrombin in Complex with A D-Phe-Pro-N-Amidinopiperidine Derivative also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Fluorine atom in the Thrombin in Complex with A D-Phe-Pro-N-Amidinopiperidine Derivative (pdb code 6t57). 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 in Complex with A D-Phe-Pro-N-Amidinopiperidine Derivative, PDB code: 6t57:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Thrombin in Complex with A D-Phe-Pro-N-Amidinopiperidine Derivative


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Thrombin in Complex with A D-Phe-Pro-N-Amidinopiperidine Derivative within 5.0Å range: probe atom residue distance (Å) B Occ H:F307 b:45.6 occ:0.94 F1 H:TFA307 0.0 45.6 0.9 C2 H:TFA307 1.4 48.1 0.9 F3 H:TFA307 2.2 51.2 0.9 F2 H:TFA307 2.2 52.8 0.9 C1 H:TFA307 2.3 42.1 0.9 OXT H:TFA307 2.9 36.9 0.9 O H:TFA307 3.2 33.1 0.9 CZ3 H:TRP60D 3.6 43.1 1.0 CH2 H:TRP60D 4.2 43.3 1.0 OE2 H:GLU192 4.5 66.0 1.0 CE3 H:TRP60D 4.6 43.3 1.0 CB H:GLU192 4.7 34.8 1.0 N H:GLY193 4.7 25.5 1.0 NZ H:LYS60F 4.9 44.2 1.0

Fluorine binding site 2 out of 3 in the Thrombin in Complex with A D-Phe-Pro-N-Amidinopiperidine Derivative


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Thrombin in Complex with A D-Phe-Pro-N-Amidinopiperidine Derivative within 5.0Å range: probe atom residue distance (Å) B Occ H:F307 b:52.8 occ:0.94 F2 H:TFA307 0.0 52.8 0.9 C2 H:TFA307 1.4 48.1 0.9 F1 H:TFA307 2.2 45.6 0.9 F3 H:TFA307 2.3 51.2 0.9 C1 H:TFA307 2.3 42.1 0.9 OXT H:TFA307 2.7 36.9 0.9 O H:TFA307 3.4 33.1 0.9 NZ H:LYS60F 3.5 44.2 1.0 O H:LEU41 3.6 34.6 1.0 O H:HOH427 3.6 37.2 1.0 SG H:CYS42 4.2 33.0 1.0 CE H:LYS60F 4.5 46.5 1.0 CZ3 H:TRP60D 4.6 43.1 1.0 C H:LEU41 4.8 32.7 1.0

Fluorine binding site 3 out of 3 in the Thrombin in Complex with A D-Phe-Pro-N-Amidinopiperidine Derivative


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Thrombin in Complex with A D-Phe-Pro-N-Amidinopiperidine Derivative within 5.0Å range: probe atom residue distance (Å) B Occ H:F307 b:51.2 occ:0.94 F3 H:TFA307 0.0 51.2 0.9 C2 H:TFA307 1.4 48.1 0.9 F1 H:TFA307 2.2 45.6 0.9 F2 H:TFA307 2.3 52.8 0.9 C1 H:TFA307 2.3 42.1 0.9 O H:TFA307 2.6 33.1 0.9 N H:GLY193 3.1 25.5 1.0 OXT H:TFA307 3.5 36.9 0.9 CA H:GLY193 3.5 29.3 1.0 O H:LEU41 3.9 34.6 1.0 C H:GLU192 4.0 27.4 1.0 CA H:GLU192 4.4 31.8 1.0 CB H:GLU192 4.4 34.8 1.0 C H:GLY193 4.7 28.3 1.0 O H:GLU192 5.0 31.8 1.0

K.Ngo, N.Abazi, A.Heine, G.Klebe. Thrombin in Complex with A D-Phe-Pro-N-Amidinopiperidine Derivative To Be Published.