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Chlorine in PDB 4x6m: Factor Xia in Complex with the Inhibitor 1-{(1S)-1-[4-(3-Amino-1H- Indazol-6-Yl)-5-Chloro-1H-Imidazol-2-Yl]-2-Phenylethyl}-3-[2- (Aminomethyl)-5-Chlorobenzyl]Urea

Enzymatic activity of Factor Xia in Complex with the Inhibitor 1-{(1S)-1-[4-(3-Amino-1H- Indazol-6-Yl)-5-Chloro-1H-Imidazol-2-Yl]-2-Phenylethyl}-3-[2- (Aminomethyl)-5-Chlorobenzyl]Urea

All present enzymatic activity of Factor Xia in Complex with the Inhibitor 1-{(1S)-1-[4-(3-Amino-1H- Indazol-6-Yl)-5-Chloro-1H-Imidazol-2-Yl]-2-Phenylethyl}-3-[2- (Aminomethyl)-5-Chlorobenzyl]Urea:
3.4.21.27;

Protein crystallography data

The structure of Factor Xia in Complex with the Inhibitor 1-{(1S)-1-[4-(3-Amino-1H- Indazol-6-Yl)-5-Chloro-1H-Imidazol-2-Yl]-2-Phenylethyl}-3-[2- (Aminomethyl)-5-Chlorobenzyl]Urea, PDB code: 4x6m was solved by A.Wei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.80 / 2.40
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 78.900, 78.900, 106.400, 90.00, 90.00, 120.00
R / Rfree (%) 19.1 / 23

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Factor Xia in Complex with the Inhibitor 1-{(1S)-1-[4-(3-Amino-1H- Indazol-6-Yl)-5-Chloro-1H-Imidazol-2-Yl]-2-Phenylethyl}-3-[2- (Aminomethyl)-5-Chlorobenzyl]Urea (pdb code 4x6m). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Factor Xia in Complex with the Inhibitor 1-{(1S)-1-[4-(3-Amino-1H- Indazol-6-Yl)-5-Chloro-1H-Imidazol-2-Yl]-2-Phenylethyl}-3-[2- (Aminomethyl)-5-Chlorobenzyl]Urea, PDB code: 4x6m:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4x6m

Go back to Chlorine Binding Sites List in 4x6m
Chlorine binding site 1 out of 2 in the Factor Xia in Complex with the Inhibitor 1-{(1S)-1-[4-(3-Amino-1H- Indazol-6-Yl)-5-Chloro-1H-Imidazol-2-Yl]-2-Phenylethyl}-3-[2- (Aminomethyl)-5-Chlorobenzyl]Urea


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Factor Xia in Complex with the Inhibitor 1-{(1S)-1-[4-(3-Amino-1H- Indazol-6-Yl)-5-Chloro-1H-Imidazol-2-Yl]-2-Phenylethyl}-3-[2- (Aminomethyl)-5-Chlorobenzyl]Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:23.4
occ:1.00
 CL A:3Y3301 0.0 23.4 1.0
C7 A:3Y3301 1.7 20.4 1.0
N6 A:3Y3301 2.7 18.9 1.0
H45 A:3Y3301 2.7 19.1 0.0
C8 A:3Y3301 2.8 18.4 1.0
H44 A:3Y3301 2.9 19.0 0.0
C12 A:3Y3301 3.4 18.9 1.0
C2 A:EDO310 3.4 46.6 1.0
C11 A:3Y3301 3.5 18.2 1.0
O2 A:EDO310 3.5 49.1 1.0
CG A:LYS192 3.6 20.8 1.0
CB A:LYS192 3.8 17.3 1.0
C5 A:3Y3301 3.8 19.6 1.0
N9 A:3Y3301 3.9 18.8 1.0
CD A:LYS192 4.0 30.6 1.0
C1 A:EDO310 4.2 44.8 1.0
CE A:LYS192 4.2 38.8 1.0
O1 A:EDO310 4.4 45.0 1.0
C16 A:3Y3301 4.6 20.9 1.0
OH A:TYR143 4.7 22.1 1.0
C14 A:3Y3301 4.8 17.8 1.0
CA A:LYS192 4.8 16.8 1.0

Chlorine binding site 2 out of 2 in 4x6m

Go back to Chlorine Binding Sites List in 4x6m
Chlorine binding site 2 out of 2 in the Factor Xia in Complex with the Inhibitor 1-{(1S)-1-[4-(3-Amino-1H- Indazol-6-Yl)-5-Chloro-1H-Imidazol-2-Yl]-2-Phenylethyl}-3-[2- (Aminomethyl)-5-Chlorobenzyl]Urea


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Factor Xia in Complex with the Inhibitor 1-{(1S)-1-[4-(3-Amino-1H- Indazol-6-Yl)-5-Chloro-1H-Imidazol-2-Yl]-2-Phenylethyl}-3-[2- (Aminomethyl)-5-Chlorobenzyl]Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:17.9
occ:1.00
 CL1 A:3Y3301 0.0 17.9 1.0
C34 A:3Y3301 1.7 17.2 1.0
C35 A:3Y3301 2.7 15.2 1.0
C33 A:3Y3301 2.7 16.5 1.0
H60 A:3Y3301 2.8 15.3 0.0
H59 A:3Y3301 2.8 16.7 0.0
O A:VAL227 3.4 17.0 1.0
CA A:GLY226 3.5 15.2 1.0
N A:VAL227 3.6 15.3 1.0
CZ A:TYR228 3.6 17.8 1.0
O A:TRP215 3.6 15.6 1.0
CG2 A:THR213 3.7 9.5 1.0
CE1 A:TYR228 3.7 14.3 1.0
C A:GLY226 3.7 17.8 1.0
OH A:TYR228 3.8 13.9 1.0
CB A:ALA190 3.9 16.1 1.0
CE2 A:TYR228 3.9 13.7 1.0
C32 A:3Y3301 4.0 12.6 1.0
C30 A:3Y3301 4.0 15.8 1.0
N A:SER214 4.1 16.0 1.0
C A:VAL227 4.1 17.1 1.0
CD1 A:TYR228 4.2 13.1 1.0
C A:TRP215 4.3 16.9 1.0
N A:TRP215 4.3 13.9 1.0
OD1 A:ASP189 4.3 23.9 1.0
CA A:THR213 4.4 16.0 1.0
CD2 A:TYR228 4.4 13.0 1.0
CA A:VAL227 4.5 13.7 1.0
C31 A:3Y3301 4.5 12.1 1.0
CB A:THR213 4.5 14.8 1.0
CG A:TYR228 4.5 12.4 1.0
O A:GLY226 4.6 15.7 1.0
C A:THR213 4.6 19.6 1.0
CA A:TRP215 4.8 14.2 1.0
C A:SER214 4.8 17.4 1.0
H58 A:3Y3301 4.8 12.8 0.0
O A:HOH548 4.9 26.6 1.0
N A:GLY226 4.9 15.2 1.0
OG1 A:THR213 4.9 11.4 1.0
CA A:SER214 5.0 15.2 1.0
N A:TYR228 5.0 13.1 1.0

Reference:

D.J.P.Pinto, J.M.Smallheer, J.R.Corte, E.J.D.Austin, C.Wang, T.Fang, L.M.Smith Ii, K.A.Rossi, A.R.Rendina, J.M.Bozarth, G.Zhang, A.Wei, V.Ramamurthy, S.Sheriff, J.E.Myers Jr., P.E.Morin, J.M.Luettgen, D.A.Seiffert, M.L.Quan, R.R.Wexler. Structure-Based Design of Inhibitors of Coagulation Factor Xia with Novel P1 Moieties Bioorg.Med.Chem.Lett. 2015.
ISSN: ESSN 1464-3405
Page generated: Fri Jul 26 03:15:05 2024

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