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Chlorine in PDB 2bvx: Design and Discovery of Novel, Potent Thrombin Inhibitors with A Solubilizing Cationic P1-P2-Linker

Enzymatic activity of Design and Discovery of Novel, Potent Thrombin Inhibitors with A Solubilizing Cationic P1-P2-Linker

All present enzymatic activity of Design and Discovery of Novel, Potent Thrombin Inhibitors with A Solubilizing Cationic P1-P2-Linker:
3.4.21.5;

Protein crystallography data

The structure of Design and Discovery of Novel, Potent Thrombin Inhibitors with A Solubilizing Cationic P1-P2-Linker, PDB code: 2bvx was solved by S.Bulat, S.Bosio, E.Grabowski, M.A.Papadopoulos, S.Cerezo-Galvez, C.Rosenbaum, V.G.Matassa, I.Ott, G.Metz, J.Schamberger, R.Sekul, A.Feurer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 71.004, 71.711, 72.646, 90.00, 100.75, 90.00
R / Rfree (%) n/a / n/a

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Design and Discovery of Novel, Potent Thrombin Inhibitors with A Solubilizing Cationic P1-P2-Linker (pdb code 2bvx). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Design and Discovery of Novel, Potent Thrombin Inhibitors with A Solubilizing Cationic P1-P2-Linker, PDB code: 2bvx:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 2bvx

Go back to Chlorine Binding Sites List in 2bvx
Chlorine binding site 1 out of 2 in the Design and Discovery of Novel, Potent Thrombin Inhibitors with A Solubilizing Cationic P1-P2-Linker


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Design and Discovery of Novel, Potent Thrombin Inhibitors with A Solubilizing Cationic P1-P2-Linker within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl1246

b:74.1
occ:1.00
CL2 H:5CB1246 0.0 74.1 1.0
C6 H:5CB1246 1.7 74.1 1.0
C4 H:5CB1246 2.7 74.1 1.0
C8 H:5CB1246 2.7 74.1 1.0
O H:PHE227 3.4 36.4 1.0
CG1 H:VAL213 3.6 25.1 1.0
O H:TRP215 3.6 36.7 1.0
N H:PHE227 3.6 36.4 1.0
N H:SER214 3.8 32.8 1.0
CB H:ALA190 3.9 15.5 1.0
CA H:GLY226 4.0 25.9 1.0
C9 H:5CB1246 4.0 74.1 1.0
C5 H:5CB1246 4.0 74.1 1.0
CE2 H:TYR228 4.1 44.1 1.0
C H:PHE227 4.1 36.4 1.0
C H:GLY226 4.1 25.9 1.0
C H:TRP215 4.1 36.7 1.0
CA H:VAL213 4.2 23.3 1.0
N H:TRP215 4.3 36.7 1.0
CB H:VAL213 4.4 25.1 1.0
CD2 H:TYR228 4.4 44.1 1.0
CZ H:TYR228 4.4 44.1 1.0
C H:VAL213 4.4 23.3 1.0
C H:SER214 4.4 32.8 1.0
CA H:PHE227 4.5 36.4 1.0
C7 H:5CB1246 4.5 74.1 1.0
CA H:TRP215 4.7 36.7 1.0
CA H:SER214 4.7 32.8 1.0
OH H:TYR228 4.7 44.1 1.0
CG2 H:VAL213 4.8 25.1 1.0
N H:GLY216 4.8 33.0 1.0
O H:SER214 4.9 32.8 1.0
CG H:TYR228 4.9 44.1 1.0
CE1 H:TYR228 5.0 44.1 1.0

Chlorine binding site 2 out of 2 in 2bvx

Go back to Chlorine Binding Sites List in 2bvx
Chlorine binding site 2 out of 2 in the Design and Discovery of Novel, Potent Thrombin Inhibitors with A Solubilizing Cationic P1-P2-Linker


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Design and Discovery of Novel, Potent Thrombin Inhibitors with A Solubilizing Cationic P1-P2-Linker within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl1246

b:74.1
occ:1.00
CL3 H:5CB1246 0.0 74.1 1.0
C17 H:5CB1246 1.7 74.1 1.0
C19 H:5CB1246 2.7 74.1 1.0
N18 H:5CB1246 2.8 74.1 1.0
C16 H:5CB1246 3.1 74.1 1.0
O H:HOH2037 3.3 38.2 1.0
CE2 H:TYR60A 3.4 26.6 1.0
CZ H:TYR60A 3.6 26.6 1.0
CD2 H:HIS57 3.6 41.0 1.0
CD2 H:TYR60A 3.7 26.6 1.0
CZ3 H:TRP60D 3.8 28.9 1.0
CH2 H:TRP60D 3.9 28.9 1.0
CE1 H:TYR60A 4.0 26.6 1.0
OH H:TYR60A 4.0 26.6 1.0
N21 H:5CB1246 4.1 74.1 1.0
C20 H:5CB1246 4.1 74.1 1.0
CG H:TYR60A 4.1 26.6 1.0
C15 H:5CB1246 4.2 74.1 1.0
O32 H:5CB1246 4.2 74.1 1.0
CD1 H:TYR60A 4.3 26.6 1.0
CG H:HIS57 4.3 41.0 1.0
CD1 H:LEU99 4.3 35.7 1.0
CE3 H:TRP60D 4.5 28.9 1.0
CB H:HIS57 4.5 41.0 1.0
NE2 H:HIS57 4.6 41.0 1.0
C22 H:5CB1246 4.6 74.1 1.0
CZ2 H:TRP60D 4.6 28.9 1.0

Reference:

S.Bulat, S.Bosio, M.A.Papadopoulos, S.Cerezo-Galvez, E.Grabowski, C.Rosenbaum, V.G.Matassa, I.Ott, G.Metz, J.Schamberger, R.Sekul, A.Feurer. Design and Discovery of Novel, Potent Pyrazinone-Based Thrombin Inhibitors with A Solubilizing P1-P2-Linker Lett.Drug Des.Discovery V. 3 289 2006.
ISSN: ISSN 1570-1808
DOI: 10.2174/157018006777574203
Page generated: Sat Dec 12 09:01:02 2020

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