Fluorine in PDB 5qcm: Factor Xia in Complex with the Inhibitor Methyl ~{N}-[4-[[(1~{S})-2- [(~{E})-3-[3-Chloranyl-2-Fluoranyl-6-(1,2,3,4-Tetrazol-1-Yl) Phenyl]Prop-2-Enoyl]-3,4-Dihydro-1~{H}-Isoquinolin-1- Yl]Carbonylamino]Phenyl]Carbamate

Enzymatic activity of Factor Xia in Complex with the Inhibitor Methyl ~{N}-[4-[[(1~{S})-2- [(~{E})-3-[3-Chloranyl-2-Fluoranyl-6-(1,2,3,4-Tetrazol-1-Yl) Phenyl]Prop-2-Enoyl]-3,4-Dihydro-1~{H}-Isoquinolin-1- Yl]Carbonylamino]Phenyl]Carbamate

All present enzymatic activity of Factor Xia in Complex with the Inhibitor Methyl ~{N}-[4-[[(1~{S})-2- [(~{E})-3-[3-Chloranyl-2-Fluoranyl-6-(1,2,3,4-Tetrazol-1-Yl) Phenyl]Prop-2-Enoyl]-3,4-Dihydro-1~{H}-Isoquinolin-1- Yl]Carbonylamino]Phenyl]Carbamate:
3.4.21.27;

Protein crystallography data

The structure of Factor Xia in Complex with the Inhibitor Methyl ~{N}-[4-[[(1~{S})-2- [(~{E})-3-[3-Chloranyl-2-Fluoranyl-6-(1,2,3,4-Tetrazol-1-Yl) Phenyl]Prop-2-Enoyl]-3,4-Dihydro-1~{H}-Isoquinolin-1- Yl]Carbonylamino]Phenyl]Carbamate, PDB code: 5qcm was solved by S.Sheriff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	22.83 / 2.20
*Space group*	P 3₂ 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	79.100, 79.100, 106.300, 90.00, 90.00, 120.00
*R / R_free (%)*	21.5 / 24.4

Other elements in 5qcm:

The structure of Factor Xia in Complex with the Inhibitor Methyl ~{N}-[4-[[(1~{S})-2- [(~{E})-3-[3-Chloranyl-2-Fluoranyl-6-(1,2,3,4-Tetrazol-1-Yl) Phenyl]Prop-2-Enoyl]-3,4-Dihydro-1~{H}-Isoquinolin-1- Yl]Carbonylamino]Phenyl]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 ~{N}-[4-[[(1~{S})-2- [(~{E})-3-[3-Chloranyl-2-Fluoranyl-6-(1,2,3,4-Tetrazol-1-Yl) Phenyl]Prop-2-Enoyl]-3,4-Dihydro-1~{H}-Isoquinolin-1- Yl]Carbonylamino]Phenyl]Carbamate (pdb code 5qcm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Factor Xia in Complex with the Inhibitor Methyl ~{N}-[4-[[(1~{S})-2- [(~{E})-3-[3-Chloranyl-2-Fluoranyl-6-(1,2,3,4-Tetrazol-1-Yl) Phenyl]Prop-2-Enoyl]-3,4-Dihydro-1~{H}-Isoquinolin-1- Yl]Carbonylamino]Phenyl]Carbamate, PDB code: 5qcm:

Fluorine binding site 1 out of 1 in 5qcm

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Fluorine Binding Sites List in 5qcm

Fluorine binding site 1 out of 1 in the Factor Xia in Complex with the Inhibitor Methyl ~{N}-[4-[[(1~{S})-2- [(~{E})-3-[3-Chloranyl-2-Fluoranyl-6-(1,2,3,4-Tetrazol-1-Yl) Phenyl]Prop-2-Enoyl]-3,4-Dihydro-1~{H}-Isoquinolin-1- Yl]Carbonylamino]Phenyl]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 ~{N}-[4-[[(1~{S})-2- [(~{E})-3-[3-Chloranyl-2-Fluoranyl-6-(1,2,3,4-Tetrazol-1-Yl) Phenyl]Prop-2-Enoyl]-3,4-Dihydro-1~{H}-Isoquinolin-1- Yl]Carbonylamino]Phenyl]Carbamate within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:F301 b:39.2 occ:1.00	F17	A:BVJ301	0.0	39.2	1.0
	C5	A:BVJ301	1.3	35.5	1.0
	C4	A:BVJ301	2.3	37.4	1.0
	C6	A:BVJ301	2.4	36.1	1.0
	H46	A:BVJ301	2.7	40.4	0.0
	C13	A:BVJ301	2.9	37.0	1.0
	CL1	A:BVJ301	2.9	37.9	1.0
	C14	A:BVJ301	3.0	40.5	1.0
	CG2	A:THR213	3.2	17.6	1.0
	C	A:SER214	3.3	25.0	1.0
	O	A:SER214	3.3	23.1	1.0
	N	A:TRP215	3.6	21.9	1.0
	C3	A:BVJ301	3.6	37.9	1.0
	C7	A:BVJ301	3.6	36.1	1.0
	N	A:SER214	3.7	23.1	1.0
	CA	A:TRP215	3.9	21.7	1.0
	CB	A:SER195	3.9	23.8	1.0
	H45	A:BVJ301	3.9	37.1	0.0
	C	A:THR213	4.0	25.8	1.0
	CA	A:SER214	4.0	22.5	1.0
	C2	A:BVJ301	4.1	36.2	1.0
	C15	A:BVJ301	4.2	39.8	1.0
	CA	A:SER195	4.3	21.6	1.0
	C	A:TRP215	4.3	24.9	1.0
	CB	A:THR213	4.4	26.3	1.0
	CB	A:ALA190	4.4	21.6	1.0
	O	A:THR213	4.4	25.4	1.0
	H43	A:BVJ301	4.5	37.9	0.0
	CA	A:THR213	4.6	21.1	1.0
	O	A:HOH436	4.6	32.0	1.0
	O	A:TRP215	4.6	22.5	1.0
	N	A:SER195	4.6	21.2	1.0
	O16	A:BVJ301	4.6	40.3	1.0
	N8	A:BVJ301	4.8	39.2	1.0

Reference:

D.J.P.Pinto, M.J.Orwat, L.M.Smith, M.L.Quan, P.Y.S.Lam, K.A.Rossi, A.Apedo, J.M.Bozarth, Y.Wu, J.J.Zheng, B.Xin, N.Toussaint, P.Stetsko, O.Gudmundsson, B.Maxwell, E.J.Crain, P.C.Wong, Z.Lou, T.W.Harper, S.A.Chacko, J.E.Myers, S.Sheriff, H.Zhang, X.Hou, A.Mathur, D.A.Seiffert, R.R.Wexler, J.M.Luettgen, W.R.Ewing. Discovery of A Parenteral Small Molecule Coagulation Factor Xia Inhibitor Clinical Candidate (Bms-962212). J. Med. Chem. V. 60 9703 2017.
ISSN: ISSN 1520-4804
PubMed: 29077405
DOI: 10.1021/ACS.JMEDCHEM.7B01171

Page generated: Tue Jul 15 06:17:24 2025

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