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Chlorine in PDB 5tks: Factor Xia in Complex with the Inhibitor ((15S)-18-Chloro- 15-(((2E)- 3-(5-Chloro-2-(1H-Tetrazol-1-Yl)Phenyl)-2- Propenoyl)Amino)-17,19- Diazatricyclo[14.2.1.0~2,7~]Nonadeca-1(18),2,4,6,16(19)-Pentaen-5- Yl)Carbamate

Enzymatic activity of Factor Xia in Complex with the Inhibitor ((15S)-18-Chloro- 15-(((2E)- 3-(5-Chloro-2-(1H-Tetrazol-1-Yl)Phenyl)-2- Propenoyl)Amino)-17,19- Diazatricyclo[14.2.1.0~2,7~]Nonadeca-1(18),2,4,6,16(19)-Pentaen-5- Yl)Carbamate

All present enzymatic activity of Factor Xia in Complex with the Inhibitor ((15S)-18-Chloro- 15-(((2E)- 3-(5-Chloro-2-(1H-Tetrazol-1-Yl)Phenyl)-2- Propenoyl)Amino)-17,19- Diazatricyclo[14.2.1.0~2,7~]Nonadeca-1(18),2,4,6,16(19)-Pentaen-5- Yl)Carbamate:
3.4.21.27;

Protein crystallography data

The structure of Factor Xia in Complex with the Inhibitor ((15S)-18-Chloro- 15-(((2E)- 3-(5-Chloro-2-(1H-Tetrazol-1-Yl)Phenyl)-2- Propenoyl)Amino)-17,19- Diazatricyclo[14.2.1.0~2,7~]Nonadeca-1(18),2,4,6,16(19)-Pentaen-5- Yl)Carbamate, PDB code: 5tks was solved by S.Sheriff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.69 / 1.55
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 78.800, 78.800, 106.000, 90.00, 90.00, 120.00
R / Rfree (%) 16 / 17.6

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Factor Xia in Complex with the Inhibitor ((15S)-18-Chloro- 15-(((2E)- 3-(5-Chloro-2-(1H-Tetrazol-1-Yl)Phenyl)-2- Propenoyl)Amino)-17,19- Diazatricyclo[14.2.1.0~2,7~]Nonadeca-1(18),2,4,6,16(19)-Pentaen-5- Yl)Carbamate (pdb code 5tks). 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 ((15S)-18-Chloro- 15-(((2E)- 3-(5-Chloro-2-(1H-Tetrazol-1-Yl)Phenyl)-2- Propenoyl)Amino)-17,19- Diazatricyclo[14.2.1.0~2,7~]Nonadeca-1(18),2,4,6,16(19)-Pentaen-5- Yl)Carbamate, PDB code: 5tks:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 5tks

Go back to Chlorine Binding Sites List in 5tks
Chlorine binding site 1 out of 2 in the Factor Xia in Complex with the Inhibitor ((15S)-18-Chloro- 15-(((2E)- 3-(5-Chloro-2-(1H-Tetrazol-1-Yl)Phenyl)-2- Propenoyl)Amino)-17,19- Diazatricyclo[14.2.1.0~2,7~]Nonadeca-1(18),2,4,6,16(19)-Pentaen-5- Yl)Carbamate


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 ((15S)-18-Chloro- 15-(((2E)- 3-(5-Chloro-2-(1H-Tetrazol-1-Yl)Phenyl)-2- Propenoyl)Amino)-17,19- Diazatricyclo[14.2.1.0~2,7~]Nonadeca-1(18),2,4,6,16(19)-Pentaen-5- Yl)Carbamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:15.7
occ:1.00
 CL1 A:7DL301 0.0 15.7 1.0
C5 A:7DL301 1.7 15.7 1.0
C4 A:7DL301 2.7 16.6 1.0
C6 A:7DL301 2.7 14.5 1.0
H44 A:7DL301 2.8 16.9 1.0
H45 A:7DL301 2.8 13.4 1.0
HG23 A:THR213 2.9 15.0 1.0
HB3 A:ALA190 2.9 9.8 1.0
HA3 A:GLY226 3.0 12.6 1.0
H A:VAL227 3.1 14.6 1.0
H A:SER214 3.3 14.3 1.0
HH A:TYR228 3.4 14.6 1.0
HA2 A:GLY226 3.5 14.7 1.0
O A:TRP215 3.5 12.2 1.0
O A:VAL227 3.6 12.1 1.0
CA A:GLY226 3.6 12.7 1.0
N A:VAL227 3.7 11.8 1.0
H A:TRP215 3.7 10.0 1.0
HG22 A:THR213 3.8 10.5 1.0
CG2 A:THR213 3.8 12.4 1.0
CZ A:TYR228 3.9 13.2 1.0
CB A:ALA190 3.9 13.5 1.0
HA A:THR213 3.9 9.2 1.0
CE1 A:TYR228 4.0 12.2 1.0
C A:GLY226 4.0 13.8 1.0
C3 A:7DL301 4.0 14.9 1.0
N A:TRP215 4.0 11.5 1.0
C7 A:7DL301 4.0 14.1 1.0
C A:TRP215 4.0 13.3 1.0
HB2 A:ALA190 4.0 14.0 1.0
OH A:TYR228 4.1 15.8 1.0
N A:SER214 4.1 11.2 1.0
OD1 A:ASP189 4.1 19.8 1.0
HE1 A:TYR228 4.1 13.8 1.0
H A:ALA190 4.2 14.9 1.0
CE2 A:TYR228 4.2 13.1 1.0
C A:VAL227 4.3 13.0 1.0
HB1 A:ALA190 4.3 14.4 1.0
HG21 A:THR213 4.4 10.8 1.0
CA A:TRP215 4.4 12.1 1.0
C8 A:7DL301 4.5 14.2 1.0
CD1 A:TYR228 4.5 12.8 1.0
HA A:TRP215 4.5 11.8 1.0
C A:SER214 4.6 12.2 1.0
CA A:VAL227 4.6 11.3 1.0
CA A:THR213 4.7 9.9 1.0
HE2 A:TYR228 4.7 11.4 1.0
HA3 A:GLY216 4.7 12.6 1.0
CB A:THR213 4.8 12.9 1.0
CD2 A:TYR228 4.8 13.3 1.0
N A:GLY216 4.8 12.6 1.0
H43 A:7DL301 4.8 17.4 1.0
C A:THR213 4.8 13.1 1.0
O A:HOH415 4.8 22.0 1.0
CG A:TYR228 4.9 12.6 1.0
CA A:SER214 4.9 10.1 1.0
CA A:ALA190 5.0 13.4 1.0
N A:ALA190 5.0 14.1 1.0
O A:GLY226 5.0 13.8 1.0
N A:GLY226 5.0 13.6 1.0
HD1 A:TYR228 5.0 14.0 1.0

Chlorine binding site 2 out of 2 in 5tks

Go back to Chlorine Binding Sites List in 5tks
Chlorine binding site 2 out of 2 in the Factor Xia in Complex with the Inhibitor ((15S)-18-Chloro- 15-(((2E)- 3-(5-Chloro-2-(1H-Tetrazol-1-Yl)Phenyl)-2- Propenoyl)Amino)-17,19- Diazatricyclo[14.2.1.0~2,7~]Nonadeca-1(18),2,4,6,16(19)-Pentaen-5- Yl)Carbamate


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 ((15S)-18-Chloro- 15-(((2E)- 3-(5-Chloro-2-(1H-Tetrazol-1-Yl)Phenyl)-2- Propenoyl)Amino)-17,19- Diazatricyclo[14.2.1.0~2,7~]Nonadeca-1(18),2,4,6,16(19)-Pentaen-5- Yl)Carbamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:17.6
occ:1.00
 CL2 A:7DL301 0.0 17.6 1.0
C29 A:7DL301 1.7 14.9 1.0
N28 A:7DL301 2.7 14.7 1.0
C30 A:7DL301 2.8 14.5 1.0
HD3 A:LYS192 2.9 16.6 0.5
H56 A:7DL301 2.9 17.0 1.0
HD3 A:LYS192 3.0 21.9 0.5
HB3 A:LYS192 3.0 14.8 1.0
HZ3 A:LYS192 3.1 26.9 0.5
HG2 A:LYS192 3.1 15.8 0.5
HG2 A:LYS192 3.2 15.8 0.5
H53 A:7DL301 3.2 16.2 1.0
C22 A:7DL301 3.4 14.4 1.0
HZ2 A:LYS192 3.4 26.6 0.5
O A:HOH544 3.5 40.2 1.0
C23 A:7DL301 3.6 16.7 1.0
CD A:LYS192 3.7 16.7 0.5
NZ A:LYS192 3.7 26.7 0.5
CG A:LYS192 3.7 16.1 1.0
H68 A:7DL301 3.7 17.4 1.0
CD A:LYS192 3.7 21.9 0.5
O2 A:EDO303 3.8 23.2 1.0
CB A:LYS192 3.8 14.9 1.0
C20 A:7DL301 3.8 13.8 1.0
C1 A:EDO309 3.9 53.2 1.0
N31 A:7DL301 3.9 14.7 1.0
C2 A:EDO309 3.9 53.0 1.0
HE2 A:LYS192 3.9 15.4 0.5
O2 A:EDO310 4.1 56.3 1.0
O A:HOH454 4.2 39.2 1.0
HZ3 A:LYS192 4.3 19.4 0.5
CE A:LYS192 4.3 16.3 0.5
CE A:LYS192 4.4 23.3 0.5
O A:HOH470 4.5 40.7 1.0
C1 A:EDO310 4.5 57.4 1.0
HB2 A:LYS192 4.5 13.6 1.0
C27 A:7DL301 4.5 14.5 1.0
H67 A:7DL301 4.5 17.8 1.0
HZ1 A:LYS192 4.5 27.1 0.5
HD2 A:LYS192 4.5 17.3 0.5
OH A:TYR143 4.6 22.3 1.0
C37 A:7DL301 4.6 16.8 1.0
HD2 A:LYS192 4.6 22.4 0.5
O2 A:EDO309 4.7 53.1 1.0
HA A:LYS192 4.7 9.6 1.0
HH A:TYR143 4.7 23.4 1.0
H60 A:7DL301 4.7 15.2 1.0
C24 A:7DL301 4.7 19.2 1.0
HG3 A:LYS192 4.7 15.1 0.5
HG3 A:LYS192 4.8 15.2 0.5
CA A:LYS192 4.8 13.2 1.0
NZ A:LYS192 4.9 19.7 0.5
HE2 A:TYR143 4.9 18.6 1.0
CZ A:TYR143 4.9 20.9 1.0
C2 A:EDO310 4.9 55.1 1.0

Reference:

J.R.Corte, T.Fang, H.Osuna, D.J.Pinto, 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, C.P.Decicco, R.R.Wexler, M.L.Quan. Structure-Based Design of Macrocyclic Factor Xia Inhibitors: Discovery of the Macrocyclic Amide Linker. J. Med. Chem. V. 60 1060 2017.
ISSN: ISSN 1520-4804
PubMed: 28085275
DOI: 10.1021/ACS.JMEDCHEM.6B01460
Page generated: Fri Jul 26 17:30:32 2024

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