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Chlorine in PDB 4udw: Thrombin in Complex with 1-(2R)-2-Amino-3-Phenyl-Propanoyl-N-(2, 5DICHLOROPHENYL)Methylpyrrolidine-2-Carboxamide

Enzymatic activity of Thrombin in Complex with 1-(2R)-2-Amino-3-Phenyl-Propanoyl-N-(2, 5DICHLOROPHENYL)Methylpyrrolidine-2-Carboxamide

All present enzymatic activity of Thrombin in Complex with 1-(2R)-2-Amino-3-Phenyl-Propanoyl-N-(2, 5DICHLOROPHENYL)Methylpyrrolidine-2-Carboxamide:
3.4.21.5;

Protein crystallography data

The structure of Thrombin in Complex with 1-(2R)-2-Amino-3-Phenyl-Propanoyl-N-(2, 5DICHLOROPHENYL)Methylpyrrolidine-2-Carboxamide, PDB code: 4udw 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) 71.13 / 1.16
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 69.640, 71.106, 72.327, 90.00, 100.44, 90.00
R / Rfree (%) 12.4 / 14.1

Other elements in 4udw:

The structure of Thrombin in Complex with 1-(2R)-2-Amino-3-Phenyl-Propanoyl-N-(2, 5DICHLOROPHENYL)Methylpyrrolidine-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 1-(2R)-2-Amino-3-Phenyl-Propanoyl-N-(2, 5DICHLOROPHENYL)Methylpyrrolidine-2-Carboxamide (pdb code 4udw). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Thrombin in Complex with 1-(2R)-2-Amino-3-Phenyl-Propanoyl-N-(2, 5DICHLOROPHENYL)Methylpyrrolidine-2-Carboxamide, PDB code: 4udw:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4udw

Go back to Chlorine Binding Sites List in 4udw
Chlorine binding site 1 out of 2 in the Thrombin in Complex with 1-(2R)-2-Amino-3-Phenyl-Propanoyl-N-(2, 5DICHLOROPHENYL)Methylpyrrolidine-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 1-(2R)-2-Amino-3-Phenyl-Propanoyl-N-(2, 5DICHLOROPHENYL)Methylpyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl1249

b:17.6
occ:1.00
 CL H:N6L1249 0.0 17.6 1.0
C H:N6L1249 1.8 14.6 1.0
C6 H:N6L1249 2.7 14.5 1.0
C1 H:N6L1249 2.7 13.3 1.0
C2 H:N6L1249 3.1 14.3 1.0
HA H:CYS191 3.2 18.5 1.0
O H:N6L1249 3.5 16.8 1.0
HG3 H:GLU192 3.6 30.7 0.5
HG2 H:GLU192 3.6 30.7 0.5
N H:GLU192 3.6 16.9 0.5
N H:GLU192 3.6 17.0 0.5
H H:GLU192 3.7 20.3 0.5
H H:GLU192 3.7 20.4 0.5
HA H:GLU192 3.7 21.2 0.5
HA H:GLU192 3.7 21.2 0.5
C H:CYS191 3.8 15.9 1.0
SG H:CYS220 3.9 17.9 1.0
N2 H:N6L1249 3.9 13.8 1.0
CA H:CYS191 4.0 15.4 1.0
C3 H:N6L1249 4.0 12.8 1.0
C5 H:N6L1249 4.0 13.8 1.0
O H:HOH2271 4.0 26.5 1.0
CG H:GLU192 4.0 25.6 0.5
HB2 H:GLU192 4.0 24.5 0.5
C7 H:N6L1249 4.1 15.5 1.0
CA H:GLU192 4.1 17.7 0.5
CA H:GLU192 4.1 17.7 0.5
O H:GLY219 4.2 18.2 1.0
O H:CYS191 4.3 15.6 1.0
O H:HOH2272 4.3 26.8 1.0
C4 H:N6L1249 4.4 12.8 1.0
O H:GLY216 4.5 17.7 0.6
O1 H:N6L1249 4.6 15.5 1.0
H H:GLY216 4.6 16.2 0.4
H H:GLY216 4.6 16.7 0.6
CB H:GLU192 4.6 20.4 0.5
CB H:GLU192 4.7 20.6 0.5
SG H:CYS191 4.8 18.4 1.0
N H:CYS191 4.9 13.5 1.0
HA3 H:GLY216 4.9 16.6 0.4
HA3 H:GLY216 4.9 17.3 0.6
CB H:CYS191 5.0 15.8 1.0

Chlorine binding site 2 out of 2 in 4udw

Go back to Chlorine Binding Sites List in 4udw
Chlorine binding site 2 out of 2 in the Thrombin in Complex with 1-(2R)-2-Amino-3-Phenyl-Propanoyl-N-(2, 5DICHLOROPHENYL)Methylpyrrolidine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Thrombin in Complex with 1-(2R)-2-Amino-3-Phenyl-Propanoyl-N-(2, 5DICHLOROPHENYL)Methylpyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl1249

b:13.1
occ:1.00
 CL1 H:N6L1249 0.0 13.1 1.0
C4 H:N6L1249 1.8 12.8 1.0
C3 H:N6L1249 2.7 12.8 1.0
C5 H:N6L1249 2.7 13.8 1.0
HG11 H:VAL213 2.9 14.3 1.0
HB1 H:ALA190 3.0 16.0 1.0
H H:PHE227 3.1 14.1 1.0
HA3 H:GLY226 3.2 15.2 1.0
O H:TRP215 3.3 12.6 1.0
HA2 H:GLY226 3.4 15.2 1.0
H H:SER214 3.4 12.5 1.0
H H:TRP215 3.4 13.5 1.0
O H:PHE227 3.5 11.6 1.0
N H:PHE227 3.6 11.7 1.0
CA H:GLY226 3.7 12.7 1.0
CG1 H:VAL213 3.7 11.9 1.0
C H:TRP215 3.8 12.6 1.0
N H:TRP215 3.8 11.3 1.0
HG13 H:VAL213 3.8 14.3 1.0
CB H:ALA190 3.9 13.3 1.0
HA H:VAL213 3.9 12.3 1.0
C6 H:N6L1249 4.0 14.5 1.0
C H:GLY226 4.0 12.1 1.0
C1 H:N6L1249 4.0 13.3 1.0
N H:SER214 4.1 10.4 1.0
HB3 H:ALA190 4.1 16.0 1.0
CZ H:TYR228 4.1 11.1 1.0
OH H:TYR228 4.2 12.7 1.0
HB2 H:ALA190 4.2 16.0 1.0
C H:PHE227 4.2 10.9 1.0
HG12 H:VAL213 4.3 14.3 1.0
CA H:TRP215 4.3 12.2 1.0
HH H:TYR228 4.3 15.2 1.0
HA3 H:GLY216 4.3 17.3 0.6
OD1 H:ASP189 4.4 13.8 1.0
CE2 H:TYR228 4.4 10.7 1.0
CE1 H:TYR228 4.4 11.3 1.0
HA H:TRP215 4.4 14.6 1.0
C H:N6L1249 4.4 14.6 1.0
H H:ALA190 4.5 15.6 1.0
C H:SER214 4.5 11.3 1.0
N H:GLY216 4.5 13.9 0.6
N H:GLY216 4.5 13.5 0.4
CA H:PHE227 4.6 11.3 1.0
HA3 H:GLY216 4.6 16.6 0.4
HE2 H:TYR228 4.6 12.9 1.0
CA H:VAL213 4.6 10.3 1.0
HE1 H:TYR228 4.6 13.6 1.0
HG23 H:VAL213 4.7 14.1 1.0
C H:VAL213 4.7 10.1 1.0
CB H:VAL213 4.7 10.9 1.0
O H:HOH2223 4.8 13.4 1.0
CA H:SER214 4.9 10.7 1.0
CA H:GLY216 4.9 14.4 0.6
CA H:GLY216 4.9 13.8 0.4
HA2 H:GLY216 4.9 16.6 0.4
CD2 H:TYR228 4.9 10.5 1.0
CD1 H:TYR228 4.9 10.9 1.0
CA H:ALA190 5.0 13.5 1.0

Reference:

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
Page generated: Fri Jul 26 02:12:24 2024

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