3KL6

Discovery of Tetrahydropyrimidin-2(1H)-one derivative TAK-442: A potent, selective and orally active factor Xa inhibitor

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	25.% .PEG 3350, 0.1M .tris pH 8.5 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.002	α = 90
b = 70.345	β = 90
c = 78.546	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD			2009-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	1.0	ALS	5.0.3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.45	50	99.3				48381		19.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.48	99.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1EZQ	1.45	35.17	45527	2419	98.81	0.19503	0.19414	0.21169	RANDOM	14.669

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.05			0.34		-0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.711
r_dihedral_angle_4_deg	15.141
r_dihedral_angle_3_deg	12.928
r_dihedral_angle_1_deg	5.938
r_scangle_it	2.443
r_scbond_it	1.634
r_angle_refined_deg	1.147
r_mcangle_it	1.071
r_mcbond_it	0.652
r_symmetry_metal_ion_refined	0.368
r_nbtor_refined	0.303
r_metal_ion_refined	0.261
r_nbd_refined	0.2
r_symmetry_vdw_refined	0.175
r_xyhbond_nbd_refined	0.09
r_chiral_restr	0.08
r_symmetry_hbond_refined	0.068
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2203
Nucleic Acid Atoms
Solvent Atoms	204
Heterogen Atoms	51

Software

Software
Software Name	Purpose
REFMAC	refinement