Iodine in PDB 4ue7: Thrombin in Complex with 1-Amidinopiperidine

All present enzymatic activity of Thrombin in Complex with 1-Amidinopiperidine:
3.4.21.5;

The structure of Thrombin in Complex with 1-Amidinopiperidine, PDB code: 4ue7 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)	19.56 / 1.13
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.262, 71.483, 72.440, 90.00, 100.30, 90.00
R / Rfree (%)	12.4 / 13.9

The structure of Thrombin in Complex with 1-Amidinopiperidine also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Iodine atom in the Thrombin in Complex with 1-Amidinopiperidine (pdb code 4ue7). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total only one binding site of Iodine was determined in the Thrombin in Complex with 1-Amidinopiperidine, PDB code: 4ue7:

Iodine binding site 1 out of 1 in the Thrombin in Complex with 1-Amidinopiperidine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Thrombin in Complex with 1-Amidinopiperidine within 5.0Å range: probe atom residue distance (Å) B Occ H:I1247 b:13.7 occ:0.46 HB2 H:TRP237 3.2 18.3 1.0 HA H:LEU234 3.3 14.0 1.0 H H:TRP237 3.3 19.8 1.0 HB2 H:LYS236 3.5 27.8 1.0 HD21 H:LEU234 3.5 19.4 1.0 NE2 H:HIS91 3.7 13.8 1.0 O H:HOH2285 3.8 51.1 1.0 HB3 H:TRP237 3.9 18.3 1.0 O H:HOH2280 3.9 19.1 1.0 N H:TRP237 3.9 16.5 1.0 CB H:TRP237 4.0 15.3 1.0 HD23 H:LEU234 4.1 19.4 1.0 CA H:LEU234 4.2 11.7 1.0 O H:ARG233 4.2 13.9 1.0 CD2 H:LEU234 4.2 16.2 1.0 O H:HOH2115 4.3 49.1 1.0 CB H:LYS236 4.4 23.2 1.0 H H:LYS236 4.4 20.5 1.0 O H:LEU234 4.4 13.9 1.0 CA H:TRP237 4.5 15.8 1.0 C H:LEU234 4.5 12.7 1.0 HE1 H:HIS91 4.6 15.1 1.0 HB3 H:LEU234 4.6 14.3 1.0 CE1 H:HIS91 4.6 12.6 1.0 HB3 H:LYS236 4.6 27.8 1.0 CD2 H:HIS91 4.7 12.9 1.0 HD2 H:HIS91 4.7 15.5 1.0 HA H:TRP237 4.7 18.9 1.0 C H:LYS236 4.8 17.8 1.0 N H:LYS236 4.8 17.1 1.0 CB H:LEU234 4.9 11.9 1.0 HD22 H:LEU234 4.9 19.4 1.0 CA H:LYS236 4.9 19.5 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