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Fluorine in PDB 7mbo: Factor Xia (Pichia Pastoris; C500S [C122S]) in Complex with the Inhibitor Milvexian (Bms-986177), Iupac Name:(6R,10S)-10-{4-[5- Chloro-2-(4-Chloro-1H-1,2,3-Triazol-1-Yl)Phenyl]-6- Oxopyrimidin- 1(6H)-Yl}-1-(Difluoromethyl)-6-Methyl-1,4,7,8,9,10-Hexahydro-15,11- (Metheno)Pyrazolo[4,3-B][1,7]Diazacyclotetradecin-5(6H)-One

Enzymatic activity of Factor Xia (Pichia Pastoris; C500S [C122S]) in Complex with the Inhibitor Milvexian (Bms-986177), Iupac Name:(6R,10S)-10-{4-[5- Chloro-2-(4-Chloro-1H-1,2,3-Triazol-1-Yl)Phenyl]-6- Oxopyrimidin- 1(6H)-Yl}-1-(Difluoromethyl)-6-Methyl-1,4,7,8,9,10-Hexahydro-15,11- (Metheno)Pyrazolo[4,3-B][1,7]Diazacyclotetradecin-5(6H)-One

All present enzymatic activity of Factor Xia (Pichia Pastoris; C500S [C122S]) in Complex with the Inhibitor Milvexian (Bms-986177), Iupac Name:(6R,10S)-10-{4-[5- Chloro-2-(4-Chloro-1H-1,2,3-Triazol-1-Yl)Phenyl]-6- Oxopyrimidin- 1(6H)-Yl}-1-(Difluoromethyl)-6-Methyl-1,4,7,8,9,10-Hexahydro-15,11- (Metheno)Pyrazolo[4,3-B][1,7]Diazacyclotetradecin-5(6H)-One:
3.4.21.27;

Protein crystallography data

The structure of Factor Xia (Pichia Pastoris; C500S [C122S]) in Complex with the Inhibitor Milvexian (Bms-986177), Iupac Name:(6R,10S)-10-{4-[5- Chloro-2-(4-Chloro-1H-1,2,3-Triazol-1-Yl)Phenyl]-6- Oxopyrimidin- 1(6H)-Yl}-1-(Difluoromethyl)-6-Methyl-1,4,7,8,9,10-Hexahydro-15,11- (Metheno)Pyrazolo[4,3-B][1,7]Diazacyclotetradecin-5(6H)-One, PDB code: 7mbo was solved by S.Sheriff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.88 / 0.92
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.025, 69.588, 85.127, 90, 90, 90
R / Rfree (%) 16.2 / 16.8

Other elements in 7mbo:

The structure of Factor Xia (Pichia Pastoris; C500S [C122S]) in Complex with the Inhibitor Milvexian (Bms-986177), Iupac Name:(6R,10S)-10-{4-[5- Chloro-2-(4-Chloro-1H-1,2,3-Triazol-1-Yl)Phenyl]-6- Oxopyrimidin- 1(6H)-Yl}-1-(Difluoromethyl)-6-Methyl-1,4,7,8,9,10-Hexahydro-15,11- (Metheno)Pyrazolo[4,3-B][1,7]Diazacyclotetradecin-5(6H)-One also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Factor Xia (Pichia Pastoris; C500S [C122S]) in Complex with the Inhibitor Milvexian (Bms-986177), Iupac Name:(6R,10S)-10-{4-[5- Chloro-2-(4-Chloro-1H-1,2,3-Triazol-1-Yl)Phenyl]-6- Oxopyrimidin- 1(6H)-Yl}-1-(Difluoromethyl)-6-Methyl-1,4,7,8,9,10-Hexahydro-15,11- (Metheno)Pyrazolo[4,3-B][1,7]Diazacyclotetradecin-5(6H)-One (pdb code 7mbo). 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 (Pichia Pastoris; C500S [C122S]) in Complex with the Inhibitor Milvexian (Bms-986177), Iupac Name:(6R,10S)-10-{4-[5- Chloro-2-(4-Chloro-1H-1,2,3-Triazol-1-Yl)Phenyl]-6- Oxopyrimidin- 1(6H)-Yl}-1-(Difluoromethyl)-6-Methyl-1,4,7,8,9,10-Hexahydro-15,11- (Metheno)Pyrazolo[4,3-B][1,7]Diazacyclotetradecin-5(6H)-One, PDB code: 7mbo:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7mbo

Go back to Fluorine Binding Sites List in 7mbo
Fluorine binding site 1 out of 2 in the Factor Xia (Pichia Pastoris; C500S [C122S]) in Complex with the Inhibitor Milvexian (Bms-986177), Iupac Name:(6R,10S)-10-{4-[5- Chloro-2-(4-Chloro-1H-1,2,3-Triazol-1-Yl)Phenyl]-6- Oxopyrimidin- 1(6H)-Yl}-1-(Difluoromethyl)-6-Methyl-1,4,7,8,9,10-Hexahydro-15,11- (Metheno)Pyrazolo[4,3-B][1,7]Diazacyclotetradecin-5(6H)-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Factor Xia (Pichia Pastoris; C500S [C122S]) in Complex with the Inhibitor Milvexian (Bms-986177), Iupac Name:(6R,10S)-10-{4-[5- Chloro-2-(4-Chloro-1H-1,2,3-Triazol-1-Yl)Phenyl]-6- Oxopyrimidin- 1(6H)-Yl}-1-(Difluoromethyl)-6-Methyl-1,4,7,8,9,10-Hexahydro-15,11- (Metheno)Pyrazolo[4,3-B][1,7]Diazacyclotetradecin-5(6H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:14.1
occ:1.00
 F42 A:YXG302 0.0 14.1 1.0
C30 A:YXG302 1.3 11.5 1.0
H65 A:YXG302 1.9 11.5 1.0
F43 A:YXG302 2.2 14.0 1.0
N37 A:YXG302 2.3 10.2 1.0
HB3 A:LYS192 2.5 8.9 1.0
C16 A:YXG302 2.9 9.1 1.0
C11 A:YXG302 3.1 8.6 1.0
HE1 A:TYR143 3.1 10.0 1.0
CE1 A:TYR143 3.2 10.0 1.0
H46 A:YXG302 3.2 9.0 1.0
HD11 A:ILE151 3.2 11.2 1.0
HB2 A:LYS192 3.2 8.8 1.0
CB A:LYS192 3.3 8.8 1.0
N32 A:YXG302 3.3 10.5 1.0
C5 A:YXG302 3.3 9.0 1.0
C A:LYS192 3.4 7.2 1.0
HD13 A:ILE151 3.4 11.2 1.0
O A:LYS192 3.5 7.8 1.0
CZ A:TYR143 3.5 10.6 1.0
HH A:TYR143 3.6 12.0 1.0
N A:GLY193 3.7 6.9 1.0
CD1 A:TYR143 3.7 9.3 1.0
HA3 A:GLY193 3.8 6.8 1.0
CD1 A:ILE151 3.8 11.2 1.0
OH A:TYR143 3.8 12.0 1.0
CA A:LYS192 3.9 7.8 1.0
HD1 A:TYR143 4.0 9.3 1.0
HD3 A:LYS192 4.0 12.2 1.0
H A:GLY193 4.0 6.9 1.0
C6 A:YXG302 4.0 8.1 1.0
HA2 A:GLY193 4.0 6.8 1.0
CA A:GLY193 4.1 6.8 1.0
C14 A:YXG302 4.1 8.9 1.0
CE2 A:TYR143 4.2 10.7 1.0
HG12 A:ILE151 4.2 11.8 1.0
C9 A:YXG302 4.2 9.6 1.0
H47 A:YXG302 4.3 8.1 1.0
HA A:LYS192 4.3 7.9 1.0
C8 A:YXG302 4.4 8.9 1.0
CG A:TYR143 4.4 9.2 1.0
CG A:LYS192 4.5 10.2 1.0
HD12 A:ILE151 4.5 11.2 1.0
CG1 A:ILE151 4.6 11.8 1.0
CD A:LYS192 4.6 12.2 1.0
CD2 A:TYR143 4.6 9.9 1.0
HE2 A:TYR143 4.7 10.7 1.0
H A:TYR143 4.8 7.8 1.0
HD2 A:LYS192 4.8 12.2 1.0
HG2 A:LYS192 4.8 10.2 1.0
H49 A:YXG302 4.9 8.9 1.0
C17 A:YXG302 5.0 7.9 1.0
HG13 A:ILE151 5.0 11.8 1.0

Fluorine binding site 2 out of 2 in 7mbo

Go back to Fluorine Binding Sites List in 7mbo
Fluorine binding site 2 out of 2 in the Factor Xia (Pichia Pastoris; C500S [C122S]) in Complex with the Inhibitor Milvexian (Bms-986177), Iupac Name:(6R,10S)-10-{4-[5- Chloro-2-(4-Chloro-1H-1,2,3-Triazol-1-Yl)Phenyl]-6- Oxopyrimidin- 1(6H)-Yl}-1-(Difluoromethyl)-6-Methyl-1,4,7,8,9,10-Hexahydro-15,11- (Metheno)Pyrazolo[4,3-B][1,7]Diazacyclotetradecin-5(6H)-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Factor Xia (Pichia Pastoris; C500S [C122S]) in Complex with the Inhibitor Milvexian (Bms-986177), Iupac Name:(6R,10S)-10-{4-[5- Chloro-2-(4-Chloro-1H-1,2,3-Triazol-1-Yl)Phenyl]-6- Oxopyrimidin- 1(6H)-Yl}-1-(Difluoromethyl)-6-Methyl-1,4,7,8,9,10-Hexahydro-15,11- (Metheno)Pyrazolo[4,3-B][1,7]Diazacyclotetradecin-5(6H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:14.0
occ:1.00
 F43 A:YXG302 0.0 14.0 1.0
C30 A:YXG302 1.3 11.5 1.0
H65 A:YXG302 1.9 11.5 1.0
F42 A:YXG302 2.2 14.1 1.0
N37 A:YXG302 2.3 10.2 1.0
H46 A:YXG302 2.3 9.0 1.0
HH A:TYR143 3.0 12.0 1.0
C16 A:YXG302 3.0 9.1 1.0
C5 A:YXG302 3.1 9.0 1.0
OH A:TYR143 3.2 12.0 1.0
N32 A:YXG302 3.3 10.5 1.0
C11 A:YXG302 3.4 8.6 1.0
O A:HOH486 3.7 20.1 1.0
HB3 A:LYS192 3.7 8.9 1.0
CZ A:TYR143 3.7 10.6 1.0
HD3 A:LYS192 3.9 12.2 1.0
HE1 A:TYR143 4.0 10.0 1.0
CE1 A:TYR143 4.1 10.0 1.0
C14 A:YXG302 4.2 8.9 1.0
C9 A:YXG302 4.3 9.6 1.0
C8 A:YXG302 4.3 8.9 1.0
CE2 A:TYR143 4.5 10.7 1.0
O A:HOH489 4.5 16.0 1.0
CB A:LYS192 4.6 8.8 1.0
H49 A:YXG302 4.6 8.9 1.0
HB2 A:LYS192 4.6 8.8 1.0
HD11 A:ILE151 4.7 11.2 1.0
C6 A:YXG302 4.7 8.1 1.0
HE2 A:TYR143 4.7 10.7 1.0
CD A:LYS192 4.8 12.2 1.0

Reference:

A.K.Dilger, K.B.Pabbisetty, J.R.Corte, T.Fang, W.Yang, D.J.P.Pinto, Y.Wang, Y.Zhu, A.Mathur, J.Li, X.Hou, D.Smith, D.Sun, H.Zhang, S.Krishnananthan, D.R.Wu, J.E.Myers, S.Sheriff, K.A.Rossi, S.Chacko, J.J.Zheng, M.A.Galella, T.Ziemba, E.A.Dierks, J.M.Bozarth, Y.Wu, E.Crain, P.C.Wong, J.M.Luettgen, R.R.Wexler, W.R.Ewing. Discovery of Milvexian, A High-Affinity, Orally Bioavailable Inhibitor of Factor Xia in Clinical Studies For Antithrombotic Therapy Journal of Medicinal 2021CHEMISTRY.
DOI: 10.1021/ACS.JMEDCHEM.1C00613
Page generated: Tue Jul 15 21:37:47 2025

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