Chlorine in PDB 6gbw: Thrombin in Complex with MI2100 ((S)-N-(2-(Aminomethyl)-5- Chlorobenzyl)-1-((Benzylsulfonyl)-L-Arginyl)Pyrrolidine-2- Carboxamide)

Enzymatic activity of Thrombin in Complex with MI2100 ((S)-N-(2-(Aminomethyl)-5- Chlorobenzyl)-1-((Benzylsulfonyl)-L-Arginyl)Pyrrolidine-2- Carboxamide)

All present enzymatic activity of Thrombin in Complex with MI2100 ((S)-N-(2-(Aminomethyl)-5- Chlorobenzyl)-1-((Benzylsulfonyl)-L-Arginyl)Pyrrolidine-2- Carboxamide):
3.4.21.5;

Protein crystallography data

The structure of Thrombin in Complex with MI2100 ((S)-N-(2-(Aminomethyl)-5- Chlorobenzyl)-1-((Benzylsulfonyl)-L-Arginyl)Pyrrolidine-2- Carboxamide), PDB code: 6gbw 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) 21.78 / 1.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 69.840, 71.119, 72.858, 90.00, 100.58, 90.00
R / Rfree (%) 13.2 / 16.5

Other elements in 6gbw:

The structure of Thrombin in Complex with MI2100 ((S)-N-(2-(Aminomethyl)-5- Chlorobenzyl)-1-((Benzylsulfonyl)-L-Arginyl)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 MI2100 ((S)-N-(2-(Aminomethyl)-5- Chlorobenzyl)-1-((Benzylsulfonyl)-L-Arginyl)Pyrrolidine-2- Carboxamide) (pdb code 6gbw). 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 MI2100 ((S)-N-(2-(Aminomethyl)-5- Chlorobenzyl)-1-((Benzylsulfonyl)-L-Arginyl)Pyrrolidine-2- Carboxamide), PDB code: 6gbw:

Chlorine binding site 1 out of 1 in 6gbw

Go back to Chlorine Binding Sites List in 6gbw
Chlorine binding site 1 out of 1 in the Thrombin in Complex with MI2100 ((S)-N-(2-(Aminomethyl)-5- Chlorobenzyl)-1-((Benzylsulfonyl)-L-Arginyl)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 MI2100 ((S)-N-(2-(Aminomethyl)-5- Chlorobenzyl)-1-((Benzylsulfonyl)-L-Arginyl)Pyrrolidine-2- Carboxamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl306

b:14.6
occ:1.00
CL H:EU5306 0.0 14.6 1.0
C21 H:EU5306 1.7 14.5 1.0
C20 H:EU5306 2.7 15.1 1.0
C22 H:EU5306 2.7 16.0 1.0
HG13 H:VAL213 2.9 16.7 1.0
HB3 H:ALA190 3.0 20.3 1.0
H H:PHE227 3.1 16.2 1.0
HA3 H:GLY226 3.2 17.9 1.0
H H:SER214 3.4 15.6 1.0
O H:PHE227 3.4 13.1 1.0
O H:TRP215 3.4 15.5 1.0
HA2 H:GLY226 3.4 17.9 1.0
H H:TRP215 3.5 16.9 1.0
N H:PHE227 3.6 13.5 1.0
CA H:GLY226 3.7 14.9 1.0
CG1 H:VAL213 3.8 13.9 1.0
HA H:VAL213 3.9 14.4 1.0
CB H:ALA190 3.9 16.9 1.0
N H:TRP215 3.9 14.1 1.0
HG12 H:VAL213 3.9 16.7 1.0
C H:TRP215 3.9 15.3 1.0
CZ H:TYR228 4.0 13.3 1.0
C H:GLY226 4.0 14.3 1.0
C23 H:EU5306 4.0 16.3 1.0
C19 H:EU5306 4.0 15.1 1.0
N H:SER214 4.0 13.0 1.0
HB2 H:ALA190 4.1 20.3 1.0
OH H:TYR228 4.1 14.6 1.0
C H:PHE227 4.2 12.5 1.0
HB1 H:ALA190 4.2 20.3 1.0
HH H:TYR228 4.2 17.5 1.0
CE2 H:TYR228 4.2 13.1 1.0
CE1 H:TYR228 4.3 13.0 1.0
HG11 H:VAL213 4.3 16.7 1.0
OD1 H:ASP189 4.4 15.2 1.0
CA H:TRP215 4.4 14.8 1.0
HE2 H:TYR228 4.4 15.7 1.0
H H:ALA190 4.4 18.5 1.0
C H:SER214 4.5 13.8 1.0
HG22 H:VAL213 4.5 17.0 1.0
HE1 H:TYR228 4.5 15.6 1.0
C24 H:EU5306 4.5 16.6 1.0
CA H:PHE227 4.5 12.9 1.0
HA H:TRP215 4.5 17.7 1.0
CA H:VAL213 4.5 12.0 1.0
HA3 H:GLY216 4.6 19.6 1.0
C H:VAL213 4.7 12.7 1.0
CB H:VAL213 4.7 12.8 1.0
N H:GLY216 4.7 15.9 1.0
CD2 H:TYR228 4.7 12.7 1.0
CD1 H:TYR228 4.8 12.7 1.0
O H:HOH450 4.8 16.1 1.0
CA H:SER214 4.8 13.1 1.0
CA H:ALA190 5.0 16.3 1.0
O H:GLY226 5.0 14.9 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: Sat Dec 12 13:01:33 2020

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