Chlorine in PDB 5afy: Thrombin in Complex with 3-Chloro-Benzamide

All present enzymatic activity of Thrombin in Complex with 3-Chloro-Benzamide:
3.4.21.5;

The structure of Thrombin in Complex with 3-Chloro-Benzamide, PDB code: 5afy was solved by E.Ruehmann, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.45 / 1.12
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.373, 71.500, 72.636, 90.00, 100.53, 90.00
R / Rfree (%)	12.2 / 13.8

The structure of Thrombin in Complex with 3-Chloro-Benzamide also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Chlorine atom in the Thrombin in Complex with 3-Chloro-Benzamide (pdb code 5afy). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total only one binding site of Chlorine was determined in the Thrombin in Complex with 3-Chloro-Benzamide, PDB code: 5afy:

Chlorine binding site 1 out of 1 in the Thrombin in Complex with 3-Chloro-Benzamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Thrombin in Complex with 3-Chloro-Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl1248 b:13.5 occ:0.80 CL H:WCE1248 0.0 13.5 0.8 C1 H:WCE1248 1.7 13.6 0.8 C6 H:WCE1248 2.7 14.1 0.8 C2 H:WCE1248 2.7 15.1 0.8 HG11 H:VAL213 2.7 12.9 1.0 H H:PHE227 3.1 10.5 1.0 HA3 H:GLY226 3.2 11.9 1.0 O H:PHE227 3.2 9.1 1.0 HB1 H:ALA190 3.3 14.6 1.0 H H:SER214 3.3 10.3 1.0 O H:TRP215 3.3 10.4 1.0 H H:TRP215 3.4 11.0 1.0 HA2 H:GLY226 3.5 11.9 1.0 N H:PHE227 3.5 8.7 1.0 CG1 H:VAL213 3.6 10.7 1.0 HG13 H:VAL213 3.6 12.9 1.0 CA H:GLY226 3.7 9.9 1.0 HA H:VAL213 3.8 10.1 1.0 N H:TRP215 3.8 9.1 1.0 C H:TRP215 3.9 10.2 1.0 C H:GLY226 3.9 8.9 1.0 C5 H:WCE1248 4.0 16.7 0.8 CZ H:TYR228 4.0 9.0 1.0 N H:SER214 4.0 8.6 1.0 C3 H:WCE1248 4.0 16.4 0.8 C H:PHE227 4.1 8.5 1.0 CB H:ALA190 4.1 12.2 1.0 HG12 H:VAL213 4.1 12.9 1.0 OH H:TYR228 4.1 10.5 1.0 HB3 H:ALA190 4.2 14.6 1.0 CE2 H:TYR228 4.2 8.9 1.0 CE1 H:TYR228 4.2 9.1 1.0 HH H:TYR228 4.3 12.6 1.0 CA H:TRP215 4.4 10.0 1.0 CA H:VAL213 4.4 8.4 1.0 HB2 H:ALA190 4.4 14.6 1.0 CA H:PHE227 4.4 9.3 1.0 HE2 H:TYR228 4.4 10.7 1.0 C4 H:WCE1248 4.5 16.7 0.8 HE1 H:TYR228 4.5 10.9 1.0 HA H:TRP215 4.5 12.0 1.0 HG23 H:VAL213 4.6 12.6 1.0 C H:VAL213 4.6 8.7 1.0 CB H:VAL213 4.6 9.4 1.0 C H:SER214 4.6 9.2 1.0 N H:GLY216 4.6 11.0 1.0 HA3 H:GLY216 4.6 14.6 1.0 OD1 H:ASP189 4.6 11.7 1.0 CD2 H:TYR228 4.7 8.4 1.0 CD1 H:TYR228 4.7 8.8 1.0 H H:ALA190 4.7 13.7 1.0 CA H:SER214 4.9 8.8 1.0 O H:HOH2227 4.9 11.1 1.0 O H:GLY226 4.9 9.4 1.0 CG H:TYR228 5.0 8.0 1.0

E.Ruehmann, M.Betz, A.Heine, G.Klebe. Fragments Can Bind Either More Enthalpy or Entropy-Driven: Crystal Structures and Residual Hydration Pattern Suggest Why. J.Med.Chem. V. 58 6960 2015.
ISSN: ISSN 0022-2623
PubMed: 26270568
DOI: 10.1021/ACS.JMEDCHEM.5B00812