Fluorine in PDB 5qtt: Factor Xia in Complex with the Inhibitor Methyl [(3R,7S)-7-{[5-Amino- 1-(3-Chloro-2-Fluorophenyl)-1H-Pyrazole-4-Carbonyl]Amino}-3-Methyl-2- Oxo-2,3,4,5,6,7-Hexahydro-1H-12,8-(Metheno)-1,9- Benzodiazacyclotetradecin-15-Yl]Carbamate

Enzymatic activity of Factor Xia in Complex with the Inhibitor Methyl [(3R,7S)-7-{[5-Amino- 1-(3-Chloro-2-Fluorophenyl)-1H-Pyrazole-4-Carbonyl]Amino}-3-Methyl-2- Oxo-2,3,4,5,6,7-Hexahydro-1H-12,8-(Metheno)-1,9- Benzodiazacyclotetradecin-15-Yl]Carbamate

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

Protein crystallography data

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

*Resolution Low / High (Å)*	41.80 / 2.23
*Space group*	P 3₂ 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	79.040, 79.040, 105.570, 90.00, 90.00, 120.00
*R / R_free (%)*	18.5 / 22.6

Other elements in 5qtt:

The structure of Factor Xia in Complex with the Inhibitor Methyl [(3R,7S)-7-{[5-Amino- 1-(3-Chloro-2-Fluorophenyl)-1H-Pyrazole-4-Carbonyl]Amino}-3-Methyl-2- Oxo-2,3,4,5,6,7-Hexahydro-1H-12,8-(Metheno)-1,9- 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 [(3R,7S)-7-{[5-Amino- 1-(3-Chloro-2-Fluorophenyl)-1H-Pyrazole-4-Carbonyl]Amino}-3-Methyl-2- Oxo-2,3,4,5,6,7-Hexahydro-1H-12,8-(Metheno)-1,9- Benzodiazacyclotetradecin-15-Yl]Carbamate (pdb code 5qtt). 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 [(3R,7S)-7-{[5-Amino- 1-(3-Chloro-2-Fluorophenyl)-1H-Pyrazole-4-Carbonyl]Amino}-3-Methyl-2- Oxo-2,3,4,5,6,7-Hexahydro-1H-12,8-(Metheno)-1,9- Benzodiazacyclotetradecin-15-Yl]Carbamate, PDB code: 5qtt:

Fluorine binding site 1 out of 1 in 5qtt

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Fluorine Binding Sites List in 5qtt

Fluorine binding site 1 out of 1 in the Factor Xia in Complex with the Inhibitor Methyl [(3R,7S)-7-{[5-Amino- 1-(3-Chloro-2-Fluorophenyl)-1H-Pyrazole-4-Carbonyl]Amino}-3-Methyl-2- Oxo-2,3,4,5,6,7-Hexahydro-1H-12,8-(Metheno)-1,9- 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 [(3R,7S)-7-{[5-Amino- 1-(3-Chloro-2-Fluorophenyl)-1H-Pyrazole-4-Carbonyl]Amino}-3-Methyl-2- Oxo-2,3,4,5,6,7-Hexahydro-1H-12,8-(Metheno)-1,9- Benzodiazacyclotetradecin-15-Yl]Carbamate within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:F301 b:17.6 occ:1.00	F43	A:QEY301	0.0	17.6	1.0
	C34	A:QEY301	1.3	15.9	1.0
	C33	A:QEY301	2.4	15.2	1.0
	C35	A:QEY301	2.4	17.0	1.0
	N37	A:QEY301	2.7	15.8	1.0
	CL1	A:QEY301	2.9	16.0	1.0
	H71	A:QEY301	3.0	17.5	1.0
	N	A:TRP215	3.1	13.4	1.0
	C38	A:QEY301	3.1	18.9	1.0
	CG2	A:THR213	3.2	11.3	1.0
	N42	A:QEY301	3.3	17.5	1.0
	C	A:SER214	3.3	15.1	1.0
	N	A:SER214	3.4	13.9	1.0
	CA	A:TRP215	3.4	13.9	1.0
	N41	A:QEY301	3.5	15.2	1.0
	C	A:TRP215	3.6	18.3	1.0
	C32	A:QEY301	3.6	17.4	1.0
	C36	A:QEY301	3.6	17.4	1.0
	O	A:SER214	3.7	12.3	1.0
	O	A:TRP215	3.8	14.2	1.0
	C	A:THR213	3.9	17.0	1.0
	CA	A:SER214	3.9	13.4	1.0
	H72	A:QEY301	4.0	17.5	1.0
	C39	A:QEY301	4.1	18.2	1.0
	C31	A:QEY301	4.1	17.5	1.0
	C40	A:QEY301	4.2	17.5	1.0
	N	A:GLY216	4.3	16.2	1.0
	O	A:VAL227	4.3	15.2	1.0
	CA	A:THR213	4.3	13.5	1.0
	CB	A:THR213	4.3	20.0	1.0
	H68	A:QEY301	4.5	17.5	1.0
	H69	A:QEY301	4.5	17.5	1.0
	O	A:THR213	4.5	15.2	1.0
	CB	A:ALA190	4.6	15.2	1.0
	CB	A:SER195	4.8	11.7	1.0
	CB	A:TRP215	4.9	12.2	1.0

Reference:

J.R.Corte, D.J.P.Pinto, T.Fang, H.Osuna, W.Yang, Y.Wang, A.Lai, C.Clark, J.H.Sun, R.A.Rampulla, A.Mathur, M.Kaspady, P.R.Neithnadka, Y.X.Li, K.A.Rossi, J.E.Myers, S.Sheriff, Z.Lou, T.W.Harper, C.S.Huang, J.J.Zheng, J.M.Bozarth, Y.Wu, P.C.Wong, E.Crain, D.A.Seiffert, J.M.Luettgen, P.Lam, R.R.Wexler, W.R.Ewing. Potent, Orally Bioavailable and Efficacious Macrocyclic Inhibitors of Factor Xia. Discovery of Pyridine-Based Macrocycles Possessing Phenylazole Carboxamide P1 Groups. J.Med.Chem. 2019.
ISSN: ISSN 0022-2623
PubMed: 31833761
DOI: 10.1021/ACS.JMEDCHEM.9B01768

Page generated: Tue Jul 15 06:35:07 2025

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