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Fluorine in PDB 5q0h: Factor Xia in Complex with the Inhibitor Methyl [(4R,5E,8S)-11-Chloro- 8-[(2,6-Difluoro-4-Methylbenzene-1-Carbonyl)Amino]-4-Methyl-2-Oxo-1, 3,4,7,8,10-Hexahydro-2H-12,9-(Azeno)-1,10-Benzodiazacyclotetradecin- 15-Yl]Carbamate

Enzymatic activity of Factor Xia in Complex with the Inhibitor Methyl [(4R,5E,8S)-11-Chloro- 8-[(2,6-Difluoro-4-Methylbenzene-1-Carbonyl)Amino]-4-Methyl-2-Oxo-1, 3,4,7,8,10-Hexahydro-2H-12,9-(Azeno)-1,10-Benzodiazacyclotetradecin- 15-Yl]Carbamate

All present enzymatic activity of Factor Xia in Complex with the Inhibitor Methyl [(4R,5E,8S)-11-Chloro- 8-[(2,6-Difluoro-4-Methylbenzene-1-Carbonyl)Amino]-4-Methyl-2-Oxo-1, 3,4,7,8,10-Hexahydro-2H-12,9-(Azeno)-1,10-Benzodiazacyclotetradecin- 15-Yl]Carbamate:
3.4.21.27;

Protein crystallography data

The structure of Factor Xia in Complex with the Inhibitor Methyl [(4R,5E,8S)-11-Chloro- 8-[(2,6-Difluoro-4-Methylbenzene-1-Carbonyl)Amino]-4-Methyl-2-Oxo-1, 3,4,7,8,10-Hexahydro-2H-12,9-(Azeno)-1,10-Benzodiazacyclotetradecin- 15-Yl]Carbamate, PDB code: 5q0h was solved by S.Sheriff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.83 / 2.50
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 78.690, 78.690, 105.990, 90.00, 90.00, 120.00
R / Rfree (%) 16.8 / 21

Other elements in 5q0h:

The structure of Factor Xia in Complex with the Inhibitor Methyl [(4R,5E,8S)-11-Chloro- 8-[(2,6-Difluoro-4-Methylbenzene-1-Carbonyl)Amino]-4-Methyl-2-Oxo-1, 3,4,7,8,10-Hexahydro-2H-12,9-(Azeno)-1,10-Benzodiazacyclotetradecin- 15-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 [(4R,5E,8S)-11-Chloro- 8-[(2,6-Difluoro-4-Methylbenzene-1-Carbonyl)Amino]-4-Methyl-2-Oxo-1, 3,4,7,8,10-Hexahydro-2H-12,9-(Azeno)-1,10-Benzodiazacyclotetradecin- 15-Yl]Carbamate (pdb code 5q0h). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Factor Xia in Complex with the Inhibitor Methyl [(4R,5E,8S)-11-Chloro- 8-[(2,6-Difluoro-4-Methylbenzene-1-Carbonyl)Amino]-4-Methyl-2-Oxo-1, 3,4,7,8,10-Hexahydro-2H-12,9-(Azeno)-1,10-Benzodiazacyclotetradecin- 15-Yl]Carbamate, PDB code: 5q0h:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5q0h

Go back to Fluorine Binding Sites List in 5q0h
Fluorine binding site 1 out of 2 in the Factor Xia in Complex with the Inhibitor Methyl [(4R,5E,8S)-11-Chloro- 8-[(2,6-Difluoro-4-Methylbenzene-1-Carbonyl)Amino]-4-Methyl-2-Oxo-1, 3,4,7,8,10-Hexahydro-2H-12,9-(Azeno)-1,10-Benzodiazacyclotetradecin- 15-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 [(4R,5E,8S)-11-Chloro- 8-[(2,6-Difluoro-4-Methylbenzene-1-Carbonyl)Amino]-4-Methyl-2-Oxo-1, 3,4,7,8,10-Hexahydro-2H-12,9-(Azeno)-1,10-Benzodiazacyclotetradecin- 15-Yl]Carbamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:35.6
occ:1.00
 F34 A:9F1301 0.0 35.6 1.0
C33 A:9F1301 1.3 30.2 1.0
C32 A:9F1301 2.3 27.7 1.0
C28 A:9F1301 2.3 26.3 1.0
H60 A:9F1301 2.6 26.4 0.0
C35 A:9F1301 2.8 28.6 1.0
CB A:SER195 3.1 16.6 1.0
O38 A:9F1301 3.2 32.1 1.0
O A:SER214 3.2 20.6 1.0
CG2 A:THR213 3.2 14.6 1.0
CA A:SER195 3.4 15.5 1.0
C A:SER214 3.5 22.1 1.0
C31 A:9F1301 3.6 26.7 1.0
N37 A:9F1301 3.6 26.2 1.0
C29 A:9F1301 3.6 20.7 1.0
N A:SER195 3.7 16.4 1.0
N A:SER214 3.9 20.1 1.0
H62 A:9F1301 3.9 26.3 0.0
C A:THR213 4.0 20.9 1.0
C30 A:9F1301 4.1 20.8 1.0
N A:TRP215 4.1 19.8 1.0
CA A:SER214 4.1 19.6 1.0
O A:THR213 4.1 19.3 1.0
O A:HOH511 4.3 30.5 1.0
CB A:THR213 4.3 20.9 1.0
OG A:SER195 4.4 25.0 1.0
CA A:TRP215 4.4 18.8 1.0
H40 A:9F1301 4.4 24.4 0.0
C A:ASP194 4.5 18.6 1.0
C2 A:9F1301 4.6 24.3 1.0
O A:HOH425 4.6 21.0 1.0
CA A:THR213 4.7 16.7 1.0
F36 A:9F1301 4.7 30.7 1.0
O A:CYS191 4.8 24.8 1.0
CE1 A:HIS57 4.8 23.9 1.0
C39 A:9F1301 4.9 19.2 1.0
C A:SER195 4.9 17.5 1.0
CB A:ALA190 4.9 24.0 1.0
H65 A:9F1301 4.9 19.3 0.0
NE2 A:HIS57 5.0 24.7 1.0

Fluorine binding site 2 out of 2 in 5q0h

Go back to Fluorine Binding Sites List in 5q0h
Fluorine binding site 2 out of 2 in the Factor Xia in Complex with the Inhibitor Methyl [(4R,5E,8S)-11-Chloro- 8-[(2,6-Difluoro-4-Methylbenzene-1-Carbonyl)Amino]-4-Methyl-2-Oxo-1, 3,4,7,8,10-Hexahydro-2H-12,9-(Azeno)-1,10-Benzodiazacyclotetradecin- 15-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 [(4R,5E,8S)-11-Chloro- 8-[(2,6-Difluoro-4-Methylbenzene-1-Carbonyl)Amino]-4-Methyl-2-Oxo-1, 3,4,7,8,10-Hexahydro-2H-12,9-(Azeno)-1,10-Benzodiazacyclotetradecin- 15-Yl]Carbamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:30.7
occ:1.00
 F36 A:9F1301 0.0 30.7 1.0
C31 A:9F1301 1.4 26.7 1.0
C30 A:9F1301 2.3 20.8 1.0
C32 A:9F1301 2.3 27.7 1.0
H61 A:9F1301 2.6 20.9 0.0
C35 A:9F1301 2.8 28.6 1.0
H62 A:9F1301 3.0 26.3 0.0
N A:LYS192 3.0 21.7 1.0
N37 A:9F1301 3.2 26.2 1.0
CG A:LYS192 3.3 23.9 1.0
CA A:LYS192 3.3 20.1 1.0
C A:CYS191 3.5 25.6 1.0
C33 A:9F1301 3.6 30.2 1.0
O A:HOH514 3.6 25.7 1.0
C29 A:9F1301 3.6 20.7 1.0
O38 A:9F1301 3.6 32.1 1.0
CB A:LYS192 3.9 20.0 1.0
H46 A:9F1301 4.0 23.1 0.0
O A:CYS191 4.0 24.8 1.0
O A:HOH519 4.0 32.8 1.0
CA A:CYS191 4.1 23.8 1.0
C28 A:9F1301 4.1 26.3 1.0
SG A:CYS219 4.1 32.6 1.0
N11 A:9F1301 4.3 23.1 1.0
C2 A:9F1301 4.4 24.3 1.0
O A:HOH489 4.4 13.7 1.0
C3 A:9F1301 4.5 24.7 1.0
CD A:LYS192 4.5 32.9 1.0
C A:LYS192 4.6 24.2 1.0
F34 A:9F1301 4.7 35.6 1.0
O A:HOH511 4.7 30.5 1.0
SG A:CYS191 4.8 31.3 1.0
C39 A:9F1301 4.9 19.2 1.0
H64 A:9F1301 4.9 19.3 0.0
H42 A:9F1301 4.9 21.6 0.0
N A:GLY193 4.9 20.3 1.0
CE A:LYS192 5.0 35.1 1.0

Reference:

J.R.Corte, W.Yang, T.Fang, Y.Wang, H.Osuna, A.Lai, W.R.Ewing, K.A.Rossi, J.E.Myers, S.Sheriff, Z.Lou, J.J.Zheng, T.W.Harper, J.M.Bozarth, Y.Wu, J.M.Luettgen, D.A.Seiffert, M.L.Quan, R.R.Wexler, P.Y.S.Lam. Macrocyclic Inhibitors of Factor Xia: Discovery of Alkyl-Substituted Macrocyclic Amide Linkers with Improved Potency. Bioorg. Med. Chem. Lett. V. 27 3833 2017.
ISSN: ESSN 1464-3405
PubMed: 28687203
DOI: 10.1016/J.BMCL.2017.06.058
Page generated: Thu Aug 1 12:49:28 2024

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