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Chlorine in PDB 5lpd: Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (2-(Aminomethyl)-5-Chlorobenzyl) Pyrrolidine-2-Carboxamide

Enzymatic activity of Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (2-(Aminomethyl)-5-Chlorobenzyl) Pyrrolidine-2-Carboxamide

All present enzymatic activity of Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (2-(Aminomethyl)-5-Chlorobenzyl) Pyrrolidine-2-Carboxamide:
3.4.21.5;

Protein crystallography data

The structure of Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (2-(Aminomethyl)-5-Chlorobenzyl) Pyrrolidine-2-Carboxamide, PDB code: 5lpd was solved by A.Sandner, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.46 / 1.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.124, 70.994, 72.830, 90.00, 100.50, 90.00
R / Rfree (%) 14.9 / 17

Other elements in 5lpd:

The structure of Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (2-(Aminomethyl)-5-Chlorobenzyl) Pyrrolidine-2-Carboxamide also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (2-(Aminomethyl)-5-Chlorobenzyl) Pyrrolidine-2-Carboxamide (pdb code 5lpd). 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 (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (2-(Aminomethyl)-5-Chlorobenzyl) Pyrrolidine-2-Carboxamide, PDB code: 5lpd:

Chlorine binding site 1 out of 1 in 5lpd

Go back to Chlorine Binding Sites List in 5lpd
Chlorine binding site 1 out of 1 in the Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (2-(Aminomethyl)-5-Chlorobenzyl) Pyrrolidine-2-Carboxamide


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 (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (2-(Aminomethyl)-5-Chlorobenzyl) Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl307

b:13.9
occ:1.00
 CL H:71U307 0.0 13.9 1.0
C17 H:71U307 1.7 13.9 1.0
C16 H:71U307 2.7 14.3 1.0
C18 H:71U307 2.7 14.2 1.0
HG13 H:VAL213 2.9 14.6 1.0
HB3 H:ALA190 3.0 17.9 1.0
H H:PHE227 3.1 13.9 1.0
HA3 H:GLY226 3.2 15.5 1.0
H H:SER214 3.4 14.1 1.0
O H:PHE227 3.4 12.6 1.0
O H:TRP215 3.4 14.0 1.0
HA2 H:GLY226 3.4 15.5 1.0
H H:TRP215 3.5 15.5 1.0
N H:PHE227 3.6 11.6 1.0
CA H:GLY226 3.7 12.9 1.0
CG1 H:VAL213 3.8 12.2 1.0
HA H:VAL213 3.8 12.8 1.0
N H:TRP215 3.9 12.9 1.0
HG12 H:VAL213 3.9 14.6 1.0
C H:TRP215 3.9 14.5 1.0
CB H:ALA190 3.9 14.9 1.0
CZ H:TYR228 3.9 12.6 1.0
C H:GLY226 4.0 12.9 1.0
C19 H:71U307 4.0 15.4 1.0
C15 H:71U307 4.0 13.8 1.0
N H:SER214 4.0 11.7 1.0
OH H:TYR228 4.1 13.9 1.0
HB2 H:ALA190 4.1 17.9 1.0
C H:PHE227 4.2 11.9 1.0
HH H:TYR228 4.2 16.7 1.0
CE2 H:TYR228 4.2 12.4 1.0
CE1 H:TYR228 4.3 12.3 1.0
HB1 H:ALA190 4.3 17.9 1.0
HG11 H:VAL213 4.3 14.6 1.0
CA H:TRP215 4.3 14.0 1.0
OD1 H:ASP189 4.4 14.5 1.0
HE2 H:TYR228 4.4 14.9 1.0
H H:ALA190 4.4 16.4 1.0
HE1 H:TYR228 4.5 14.8 1.0
HA H:TRP215 4.5 16.8 1.0
C H:SER214 4.5 13.0 1.0
C20 H:71U307 4.5 15.7 1.0
CA H:PHE227 4.5 12.1 1.0
CA H:VAL213 4.5 10.6 1.0
HG22 H:VAL213 4.6 15.6 1.0
HA3 H:GLY216 4.6 16.6 1.0
N H:GLY216 4.6 14.5 1.0
C H:VAL213 4.7 11.6 1.0
CB H:VAL213 4.7 11.3 1.0
CD2 H:TYR228 4.7 10.8 1.0
CD1 H:TYR228 4.8 11.6 1.0
O H:HOH465 4.8 15.5 1.0
CA H:SER214 4.9 11.7 1.0
O H:GLY226 5.0 13.6 1.0

Reference:

A.Sandner, T.Hufner-Wulsdorf, A.Heine, T.Steinmetzer, G.Klebe. Strategies For Late-Stage Optimization: Profiling Thermodynamics By Preorganization and Salt Bridge Shielding. J.Med.Chem. V. 62 9753 2019.
ISSN: ISSN 0022-2623
PubMed: 31633354
DOI: 10.1021/ACS.JMEDCHEM.9B01196
Page generated: Fri Jul 26 12:04:32 2024

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