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Chlorine in PDB 2vip: Fragment-Based Discovery of Mexiletine Derivatives As Orally Bioavailable Inhibitors of Urokinase-Type Plasminogen Activator

Enzymatic activity of Fragment-Based Discovery of Mexiletine Derivatives As Orally Bioavailable Inhibitors of Urokinase-Type Plasminogen Activator

All present enzymatic activity of Fragment-Based Discovery of Mexiletine Derivatives As Orally Bioavailable Inhibitors of Urokinase-Type Plasminogen Activator:
3.4.21.73;

Protein crystallography data

The structure of Fragment-Based Discovery of Mexiletine Derivatives As Orally Bioavailable Inhibitors of Urokinase-Type Plasminogen Activator, PDB code: 2vip was solved by M.Frederickson, O.Callaghan, G.Chessari, M.Congreve, S.R.Cowan, J.E.Matthews, R.Mcmenamin, D.Smith, M.Vinkovic, N.G.Wallis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.62 / 1.72
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.488, 54.382, 81.029, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 23.8

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Fragment-Based Discovery of Mexiletine Derivatives As Orally Bioavailable Inhibitors of Urokinase-Type Plasminogen Activator (pdb code 2vip). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Fragment-Based Discovery of Mexiletine Derivatives As Orally Bioavailable Inhibitors of Urokinase-Type Plasminogen Activator, PDB code: 2vip:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 2vip

Go back to Chlorine Binding Sites List in 2vip
Chlorine binding site 1 out of 4 in the Fragment-Based Discovery of Mexiletine Derivatives As Orally Bioavailable Inhibitors of Urokinase-Type Plasminogen Activator


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Fragment-Based Discovery of Mexiletine Derivatives As Orally Bioavailable Inhibitors of Urokinase-Type Plasminogen Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1247

b:15.3
occ:0.50
 CL1 A:L1R1247 0.0 15.3 0.5
CL1 A:L1R1247 0.5 22.5 0.5
C15 A:L1R1247 1.7 8.7 0.5
C15 A:L1R1247 1.8 22.2 0.5
C14 A:L1R1247 2.7 24.2 0.5
C14 A:L1R1247 2.7 9.8 0.5
C17 A:L1R1247 2.7 12.6 0.5
C17 A:L1R1247 2.8 21.6 0.5
O18 A:L1R1247 3.1 12.6 0.5
O18 A:L1R1247 3.1 17.3 0.5
O A:HOH2266 3.2 38.1 1.0
SG A:CYS220 3.3 14.6 1.0
N A:GLN192 3.3 12.2 1.0
O A:HOH2335 3.7 25.2 1.0
CB A:GLN192 3.8 12.9 1.0
C19 A:L1R1247 3.8 18.6 0.5
CA A:GLN192 3.9 11.5 1.0
C19 A:L1R1247 3.9 18.0 0.5
SG A:CYS191 3.9 15.1 1.0
C13 A:L1R1247 4.0 23.5 0.5
C13 A:L1R1247 4.0 8.8 0.5
C22 A:L1R1247 4.0 14.9 0.5
C22 A:L1R1247 4.1 22.1 0.5
O A:HOH2334 4.1 44.6 1.0
C A:CYS191 4.2 15.2 1.0
O A:GLY219 4.3 12.9 1.0
CA A:CYS191 4.4 10.2 1.0
C24 A:L1R1247 4.5 22.4 0.5
C24 A:L1R1247 4.5 6.1 0.5
C A:GLY219 4.6 15.9 1.0
O A:HOH2349 4.7 38.9 1.0
CG A:GLN192 4.8 17.9 1.0
CB A:CYS191 4.9 10.3 1.0
CA A:GLY219 4.9 11.9 1.0
N21 A:L1R1247 5.0 10.4 0.5

Chlorine binding site 2 out of 4 in 2vip

Go back to Chlorine Binding Sites List in 2vip
Chlorine binding site 2 out of 4 in the Fragment-Based Discovery of Mexiletine Derivatives As Orally Bioavailable Inhibitors of Urokinase-Type Plasminogen Activator


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Fragment-Based Discovery of Mexiletine Derivatives As Orally Bioavailable Inhibitors of Urokinase-Type Plasminogen Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1247

b:22.5
occ:0.50
 CL1 A:L1R1247 0.0 22.5 0.5
CL1 A:L1R1247 0.5 15.3 0.5
C15 A:L1R1247 1.7 22.2 0.5
C15 A:L1R1247 1.8 8.7 0.5
C17 A:L1R1247 2.7 12.6 0.5
C14 A:L1R1247 2.7 24.2 0.5
C17 A:L1R1247 2.7 21.6 0.5
C14 A:L1R1247 2.8 9.8 0.5
O18 A:L1R1247 2.9 12.6 0.5
O18 A:L1R1247 3.0 17.3 0.5
O A:HOH2266 3.3 38.1 1.0
SG A:CYS220 3.4 14.6 1.0
C19 A:L1R1247 3.5 18.6 0.5
C19 A:L1R1247 3.6 18.0 0.5
N A:GLN192 3.7 12.2 1.0
O A:GLY219 4.0 12.9 1.0
C22 A:L1R1247 4.0 14.9 0.5
C13 A:L1R1247 4.0 23.5 0.5
C22 A:L1R1247 4.0 22.1 0.5
C13 A:L1R1247 4.1 8.8 0.5
O A:HOH2335 4.1 25.2 1.0
O A:HOH2349 4.2 38.9 1.0
CB A:GLN192 4.3 12.9 1.0
O A:HOH2334 4.3 44.6 1.0
SG A:CYS191 4.3 15.1 1.0
C A:GLY219 4.3 15.9 1.0
CA A:GLN192 4.3 11.5 1.0
C24 A:L1R1247 4.5 6.1 0.5
C24 A:L1R1247 4.5 22.4 0.5
C A:CYS191 4.5 15.2 1.0
CA A:GLY219 4.6 11.9 1.0
CA A:CYS191 4.6 10.2 1.0
N A:GLY219 4.7 12.9 1.0
N21 A:L1R1247 4.7 10.4 0.5
C20 A:L1R1247 4.8 16.1 0.5
C20 A:L1R1247 4.8 17.6 0.5
O A:HOH2347 4.9 21.6 1.0
N A:CYS220 5.0 12.6 1.0

Chlorine binding site 3 out of 4 in 2vip

Go back to Chlorine Binding Sites List in 2vip
Chlorine binding site 3 out of 4 in the Fragment-Based Discovery of Mexiletine Derivatives As Orally Bioavailable Inhibitors of Urokinase-Type Plasminogen Activator


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Fragment-Based Discovery of Mexiletine Derivatives As Orally Bioavailable Inhibitors of Urokinase-Type Plasminogen Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1247

b:17.6
occ:0.50
 CL2 A:L1R1247 0.0 17.6 0.5
CL2 A:L1R1247 0.5 17.6 0.5
C22 A:L1R1247 1.7 22.1 0.5
C22 A:L1R1247 1.7 14.9 0.5
C17 A:L1R1247 2.6 21.6 0.5
C17 A:L1R1247 2.7 12.6 0.5
C24 A:L1R1247 2.7 6.1 0.5
C24 A:L1R1247 2.7 22.4 0.5
O18 A:L1R1247 2.9 17.3 0.5
O18 A:L1R1247 2.9 12.6 0.5
C19 A:L1R1247 3.1 18.0 0.5
C19 A:L1R1247 3.4 18.6 0.5
CG1 A:VAL213 3.6 8.9 1.0
N A:TRP215 3.6 11.8 1.0
CA A:TRP215 3.6 12.3 1.0
OG A:SER195 3.7 12.4 1.0
C A:SER214 3.7 13.7 1.0
O A:SER214 3.7 12.4 1.0
C20 A:L1R1247 3.7 16.1 0.5
C20 A:L1R1247 3.8 17.6 0.5
O A:HOH2331 3.9 19.1 1.0
C A:TRP215 3.9 14.3 1.0
C15 A:L1R1247 3.9 22.2 0.5
C13 A:L1R1247 4.0 23.5 0.5
C13 A:L1R1247 4.0 8.8 0.5
C15 A:L1R1247 4.0 8.7 0.5
O A:TRP215 4.0 10.9 1.0
N A:SER214 4.4 9.9 1.0
OG A:SER190 4.4 16.2 1.0
C14 A:L1R1247 4.5 24.2 0.5
C14 A:L1R1247 4.5 9.8 0.5
O A:HOH2191 4.5 16.8 1.0
CA A:SER214 4.6 9.0 1.0
N A:GLY216 4.6 11.1 1.0
O A:CYS191 4.6 13.2 1.0
O A:HOH2347 4.6 21.6 1.0
C A:VAL213 4.9 10.7 1.0
CB A:SER195 4.9 7.6 1.0
N A:SER195 4.9 9.8 1.0
CA A:SER195 5.0 9.6 1.0
C A:CYS191 5.0 15.2 1.0
N21 A:L1R1247 5.0 14.9 0.5

Chlorine binding site 4 out of 4 in 2vip

Go back to Chlorine Binding Sites List in 2vip
Chlorine binding site 4 out of 4 in the Fragment-Based Discovery of Mexiletine Derivatives As Orally Bioavailable Inhibitors of Urokinase-Type Plasminogen Activator


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Fragment-Based Discovery of Mexiletine Derivatives As Orally Bioavailable Inhibitors of Urokinase-Type Plasminogen Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1247

b:17.6
occ:0.50
 CL2 A:L1R1247 0.0 17.6 0.5
CL2 A:L1R1247 0.5 17.6 0.5
C22 A:L1R1247 1.7 22.1 0.5
C22 A:L1R1247 1.8 14.9 0.5
C24 A:L1R1247 2.7 22.4 0.5
C17 A:L1R1247 2.7 21.6 0.5
C24 A:L1R1247 2.7 6.1 0.5
C17 A:L1R1247 2.8 12.6 0.5
O18 A:L1R1247 2.9 17.3 0.5
O18 A:L1R1247 3.0 12.6 0.5
CG1 A:VAL213 3.3 8.9 1.0
C19 A:L1R1247 3.3 18.0 0.5
OG A:SER195 3.4 12.4 1.0
C19 A:L1R1247 3.6 18.6 0.5
C20 A:L1R1247 3.9 16.1 0.5
C A:SER214 3.9 13.7 1.0
N A:TRP215 3.9 11.8 1.0
O A:SER214 4.0 12.4 1.0
C20 A:L1R1247 4.0 17.6 0.5
C13 A:L1R1247 4.0 23.5 0.5
O A:HOH2331 4.0 19.1 1.0
C15 A:L1R1247 4.0 22.2 0.5
C13 A:L1R1247 4.0 8.8 0.5
C15 A:L1R1247 4.1 8.7 0.5
CA A:TRP215 4.1 12.3 1.0
O A:CYS191 4.2 13.2 1.0
OG A:SER190 4.3 16.2 1.0
C A:TRP215 4.4 14.3 1.0
N A:SER214 4.4 9.9 1.0
O A:TRP215 4.4 10.9 1.0
N A:SER195 4.5 9.8 1.0
C14 A:L1R1247 4.5 24.2 0.5
C14 A:L1R1247 4.5 9.8 0.5
CB A:SER195 4.6 7.6 1.0
CA A:SER195 4.6 9.6 1.0
C A:CYS191 4.7 15.2 1.0
CA A:SER214 4.7 9.0 1.0
CB A:VAL213 4.8 11.9 1.0
O A:HOH2191 4.8 16.8 1.0
C A:VAL213 4.8 10.7 1.0
CB A:SER190 4.8 11.1 1.0
O A:ACT1245 4.8 13.9 1.0
O A:HOH2347 5.0 21.6 1.0

Reference:

M.Frederickson, O.Callaghan, G.Chessari, M.Congreve, S.R.Cowan, J.E.Matthews, R.Mcmenamin, D.Smith, M.Vinkovic, N.G.Wallis. Fragment-Based Discovery of Mexiletine Derivatives As Orally Bioavailable Inhibitors of Urokinase-Type Plasminogen Activator J.Med.Chem. V. 51 183 2008.
ISSN: ISSN 0022-2623
PubMed: 18163548
DOI: 10.1021/JM701359Z
Page generated: Sat Jul 20 11:53:01 2024

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