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Fluorine in PDB 5qtv: Factor Xia in Complex with the Inhibitor Methyl [(2R,7S)-7-({(2E)-3- [5-Chloro-2-(1H-Tetrazol-1-Yl)Phenyl]Prop-2-Enoyl}Amino)-2- (Trifluoromethyl)-2,3,4,5,6,7-Hexahydro-1H-8,11-Epimino-1,9- Benzodiazacyclotridecin-14-Yl]Carbamate

Enzymatic activity of Factor Xia in Complex with the Inhibitor Methyl [(2R,7S)-7-({(2E)-3- [5-Chloro-2-(1H-Tetrazol-1-Yl)Phenyl]Prop-2-Enoyl}Amino)-2- (Trifluoromethyl)-2,3,4,5,6,7-Hexahydro-1H-8,11-Epimino-1,9- Benzodiazacyclotridecin-14-Yl]Carbamate

All present enzymatic activity of Factor Xia in Complex with the Inhibitor Methyl [(2R,7S)-7-({(2E)-3- [5-Chloro-2-(1H-Tetrazol-1-Yl)Phenyl]Prop-2-Enoyl}Amino)-2- (Trifluoromethyl)-2,3,4,5,6,7-Hexahydro-1H-8,11-Epimino-1,9- Benzodiazacyclotridecin-14-Yl]Carbamate:
3.4.21.27;

Protein crystallography data

The structure of Factor Xia in Complex with the Inhibitor Methyl [(2R,7S)-7-({(2E)-3- [5-Chloro-2-(1H-Tetrazol-1-Yl)Phenyl]Prop-2-Enoyl}Amino)-2- (Trifluoromethyl)-2,3,4,5,6,7-Hexahydro-1H-8,11-Epimino-1,9- Benzodiazacyclotridecin-14-Yl]Carbamate, PDB code: 5qtv was solved by S.Sheriff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.70 / 2.20
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 78.800, 78.800, 106.100, 90.00, 90.00, 120.00
R / Rfree (%) 17.4 / 20.2

Other elements in 5qtv:

The structure of Factor Xia in Complex with the Inhibitor Methyl [(2R,7S)-7-({(2E)-3- [5-Chloro-2-(1H-Tetrazol-1-Yl)Phenyl]Prop-2-Enoyl}Amino)-2- (Trifluoromethyl)-2,3,4,5,6,7-Hexahydro-1H-8,11-Epimino-1,9- Benzodiazacyclotridecin-14-Yl]Carbamate also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Factor Xia in Complex with the Inhibitor Methyl [(2R,7S)-7-({(2E)-3- [5-Chloro-2-(1H-Tetrazol-1-Yl)Phenyl]Prop-2-Enoyl}Amino)-2- (Trifluoromethyl)-2,3,4,5,6,7-Hexahydro-1H-8,11-Epimino-1,9- Benzodiazacyclotridecin-14-Yl]Carbamate (pdb code 5qtv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Factor Xia in Complex with the Inhibitor Methyl [(2R,7S)-7-({(2E)-3- [5-Chloro-2-(1H-Tetrazol-1-Yl)Phenyl]Prop-2-Enoyl}Amino)-2- (Trifluoromethyl)-2,3,4,5,6,7-Hexahydro-1H-8,11-Epimino-1,9- Benzodiazacyclotridecin-14-Yl]Carbamate, PDB code: 5qtv:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5qtv

Go back to Fluorine Binding Sites List in 5qtv
Fluorine binding site 1 out of 3 in the Factor Xia in Complex with the Inhibitor Methyl [(2R,7S)-7-({(2E)-3- [5-Chloro-2-(1H-Tetrazol-1-Yl)Phenyl]Prop-2-Enoyl}Amino)-2- (Trifluoromethyl)-2,3,4,5,6,7-Hexahydro-1H-8,11-Epimino-1,9- Benzodiazacyclotridecin-14-Yl]Carbamate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Factor Xia in Complex with the Inhibitor Methyl [(2R,7S)-7-({(2E)-3- [5-Chloro-2-(1H-Tetrazol-1-Yl)Phenyl]Prop-2-Enoyl}Amino)-2- (Trifluoromethyl)-2,3,4,5,6,7-Hexahydro-1H-8,11-Epimino-1,9- Benzodiazacyclotridecin-14-Yl]Carbamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:16.4
occ:1.00
 F42 A:QLS301 0.0 16.4 1.0
C41 A:QLS301 1.3 18.3 1.0
F44 A:QLS301 2.1 17.2 1.0
F43 A:QLS301 2.1 18.0 1.0
C39 A:QLS301 2.4 16.1 1.0
H67 A:QLS301 2.9 14.1 0.0
N40 A:QLS301 2.9 16.0 1.0
C38 A:QLS301 2.9 14.0 1.0
H68 A:QLS301 3.0 14.1 0.0
H69 A:QLS301 3.2 16.1 0.0
H71 A:QLS301 3.3 16.1 0.0
CD1 A:LEU41 3.3 20.2 1.0
H62 A:QLS301 3.4 15.2 0.0
NH2 A:ARG39 3.6 54.9 1.0
C32 A:QLS301 3.6 16.5 1.0
C31 A:QLS301 3.8 15.1 1.0
O A:HOH595 4.0 38.3 1.0
O A:HOH581 4.2 34.6 1.0
O A:HOH439 4.3 25.5 1.0
CZ A:ARG39 4.5 66.4 1.0
C20 A:QLS301 4.5 13.8 1.0
O A:LEU41 4.5 19.4 1.0
CG A:LEU41 4.7 19.4 1.0
C27 A:QLS301 4.7 16.4 1.0
CA A:LEU41 4.7 14.6 1.0
H56 A:QLS301 4.8 13.8 0.0
NE A:ARG39 4.8 57.9 1.0
H54 A:QLS301 5.0 14.5 0.0
C30 A:QLS301 5.0 16.9 1.0

Fluorine binding site 2 out of 3 in 5qtv

Go back to Fluorine Binding Sites List in 5qtv
Fluorine binding site 2 out of 3 in the Factor Xia in Complex with the Inhibitor Methyl [(2R,7S)-7-({(2E)-3- [5-Chloro-2-(1H-Tetrazol-1-Yl)Phenyl]Prop-2-Enoyl}Amino)-2- (Trifluoromethyl)-2,3,4,5,6,7-Hexahydro-1H-8,11-Epimino-1,9- Benzodiazacyclotridecin-14-Yl]Carbamate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Factor Xia in Complex with the Inhibitor Methyl [(2R,7S)-7-({(2E)-3- [5-Chloro-2-(1H-Tetrazol-1-Yl)Phenyl]Prop-2-Enoyl}Amino)-2- (Trifluoromethyl)-2,3,4,5,6,7-Hexahydro-1H-8,11-Epimino-1,9- Benzodiazacyclotridecin-14-Yl]Carbamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:18.0
occ:1.00
 F43 A:QLS301 0.0 18.0 1.0
C41 A:QLS301 1.3 18.3 1.0
F42 A:QLS301 2.1 16.4 1.0
F44 A:QLS301 2.1 17.2 1.0
C39 A:QLS301 2.4 16.1 1.0
H69 A:QLS301 2.6 16.1 0.0
N40 A:QLS301 2.8 16.0 1.0
C32 A:QLS301 2.9 16.5 1.0
NH2 A:ARG39 3.0 54.9 1.0
C31 A:QLS301 3.2 15.1 1.0
H62 A:QLS301 3.4 15.2 0.0
C27 A:QLS301 3.4 16.4 1.0
C38 A:QLS301 3.7 14.0 1.0
H71 A:QLS301 3.7 16.1 0.0
CZ A:ARG39 3.9 66.4 1.0
H68 A:QLS301 3.9 14.1 0.0
C30 A:QLS301 4.0 16.9 1.0
C25 A:QLS301 4.1 14.8 1.0
H67 A:QLS301 4.1 14.1 0.0
C28 A:QLS301 4.2 17.7 1.0
NH1 A:ARG39 4.3 39.9 1.0
C29 A:QLS301 4.4 16.4 1.0
C2 A:EDO316 4.5 53.9 1.0
C24 A:QLS301 4.6 14.2 1.0
H54 A:QLS301 4.6 14.5 0.0
H59 A:QLS301 4.7 14.2 0.0
NE A:ARG39 4.7 57.9 1.0
O2 A:EDO316 4.7 53.1 1.0
N26 A:QLS301 4.8 14.4 1.0
C20 A:QLS301 4.9 13.8 1.0
H60 A:QLS301 4.9 17.8 0.0
N33 A:QLS301 5.0 17.6 1.0

Fluorine binding site 3 out of 3 in 5qtv

Go back to Fluorine Binding Sites List in 5qtv
Fluorine binding site 3 out of 3 in the Factor Xia in Complex with the Inhibitor Methyl [(2R,7S)-7-({(2E)-3- [5-Chloro-2-(1H-Tetrazol-1-Yl)Phenyl]Prop-2-Enoyl}Amino)-2- (Trifluoromethyl)-2,3,4,5,6,7-Hexahydro-1H-8,11-Epimino-1,9- Benzodiazacyclotridecin-14-Yl]Carbamate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Factor Xia in Complex with the Inhibitor Methyl [(2R,7S)-7-({(2E)-3- [5-Chloro-2-(1H-Tetrazol-1-Yl)Phenyl]Prop-2-Enoyl}Amino)-2- (Trifluoromethyl)-2,3,4,5,6,7-Hexahydro-1H-8,11-Epimino-1,9- Benzodiazacyclotridecin-14-Yl]Carbamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:17.2
occ:1.00
 F44 A:QLS301 0.0 17.2 1.0
C41 A:QLS301 1.3 18.3 1.0
F42 A:QLS301 2.1 16.4 1.0
F43 A:QLS301 2.1 18.0 1.0
C39 A:QLS301 2.4 16.1 1.0
H68 A:QLS301 2.5 14.1 0.0
H69 A:QLS301 2.6 16.1 0.0
C38 A:QLS301 2.9 14.0 1.0
O A:HOH581 3.1 34.6 1.0
H67 A:QLS301 3.5 14.1 0.0
C2 A:EDO316 3.5 53.9 1.0
N40 A:QLS301 3.6 16.0 1.0
H54 A:QLS301 3.8 14.5 0.0
C20 A:QLS301 4.2 13.8 1.0
NH2 A:ARG39 4.2 54.9 1.0
H71 A:QLS301 4.3 16.1 0.0
C32 A:QLS301 4.4 16.5 1.0
C19 A:QLS301 4.4 14.4 1.0
O2 A:EDO316 4.4 53.1 1.0
H55 A:QLS301 4.5 14.5 0.0
O A:HOH439 4.5 25.5 1.0
C1 A:EDO316 4.7 55.5 1.0
H56 A:QLS301 4.8 13.8 0.0
O A:HOH595 4.8 38.3 1.0
H57 A:QLS301 4.9 13.8 0.0
C27 A:QLS301 4.9 16.4 1.0
H62 A:QLS301 5.0 15.2 0.0
C31 A:QLS301 5.0 15.1 1.0

Reference:

T.Fang, J.R.Corte, P.J.Gilligan, Y.Jeon, H.Osuna, K.A.Rossi, J.E.Myers Jr., S.Sheriff, Z.Lou, J.J.Zheng, T.W.Harper, J.M.Bozarth, Y.Wu, J.M.Luettgen, D.A.Seiffert, R.R.Wexler, P.Y.S.Lam. Orally Bioavailable Amine-Linked Macrocyclic Inhibitors of Factor Xia. Bioorg.Med.Chem.Lett. 26949 2020.
ISSN: ESSN 1464-3405
PubMed: 31932224
DOI: 10.1016/J.BMCL.2020.126949
Page generated: Thu Aug 1 13:30:12 2024

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