Calcium in PDB 3kl6: Discovery of Tetrahydropyrimidin-2(1H)-One Derivative Tak-442: A Potent, Selective and Orally Active Factor Xa Inhibitor

Enzymatic activity of Discovery of Tetrahydropyrimidin-2(1H)-One Derivative Tak-442: A Potent, Selective and Orally Active Factor Xa Inhibitor

All present enzymatic activity of Discovery of Tetrahydropyrimidin-2(1H)-One Derivative Tak-442: A Potent, Selective and Orally Active Factor Xa Inhibitor:
3.4.21.6;

Protein crystallography data

The structure of Discovery of Tetrahydropyrimidin-2(1H)-One Derivative Tak-442: A Potent, Selective and Orally Active Factor Xa Inhibitor, PDB code: 3kl6 was solved by K.Aertgeerts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	35.17 / 1.45
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	49.002, 70.345, 78.546, 90.00, 90.00, 90.00
*R / R_free (%)*	19.4 / 21.2

Other elements in 3kl6:

The structure of Discovery of Tetrahydropyrimidin-2(1H)-One Derivative Tak-442: A Potent, Selective and Orally Active Factor Xa Inhibitor also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Discovery of Tetrahydropyrimidin-2(1H)-One Derivative Tak-442: A Potent, Selective and Orally Active Factor Xa Inhibitor (pdb code 3kl6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Discovery of Tetrahydropyrimidin-2(1H)-One Derivative Tak-442: A Potent, Selective and Orally Active Factor Xa Inhibitor, PDB code: 3kl6:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3kl6

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Calcium Binding Sites List in 3kl6

Calcium binding site 1 out of 3 in the Discovery of Tetrahydropyrimidin-2(1H)-One Derivative Tak-442: A Potent, Selective and Orally Active Factor Xa Inhibitor

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Discovery of Tetrahydropyrimidin-2(1H)-One Derivative Tak-442: A Potent, Selective and Orally Active Factor Xa Inhibitor within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca252 b:3.7 occ:1.00	OD1	A:ASP126	1.9	9.1	1.0
	OE1	A:GLU124	2.0	11.2	1.0
	NE2	B:HIS13	2.0	10.7	1.0
	CD	A:GLU124	2.7	11.3	1.0
	CG	A:ASP126	2.7	7.1	1.0
	OE2	A:GLU124	2.8	11.4	1.0
	OD2	A:ASP126	2.9	6.7	1.0
	CE1	B:HIS13	2.9	10.4	1.0
	CD2	B:HIS13	3.0	10.4	1.0
	O	A:HOH365	4.0	40.7	1.0
	ND1	B:HIS13	4.1	11.0	1.0
	CG	A:GLU124	4.1	11.6	1.0
	CG	B:HIS13	4.1	10.1	1.0
	CB	A:ASP126	4.2	7.8	1.0
	N	A:ASP126	4.4	8.6	1.0
	N	A:TRP127	4.4	8.4	1.0
	CA	A:ASP126	4.7	8.4	1.0
	O	B:HOH295	4.7	24.0	1.0
	C	A:ASP126	5.0	8.6	1.0

Calcium binding site 2 out of 3 in 3kl6

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Calcium Binding Sites List in 3kl6

Calcium binding site 2 out of 3 in the Discovery of Tetrahydropyrimidin-2(1H)-One Derivative Tak-442: A Potent, Selective and Orally Active Factor Xa Inhibitor

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Discovery of Tetrahydropyrimidin-2(1H)-One Derivative Tak-442: A Potent, Selective and Orally Active Factor Xa Inhibitor within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca2 b:21.9 occ:1.00	O	A:LYS224	2.3	10.2	1.0
	O	A:TYR185	2.3	12.9	1.0
	O	A:HOH387	2.3	17.5	1.0
	O	A:ARG222	2.3	12.0	1.0
	O	A:ASP185A	2.7	15.0	1.0
	C	A:ASP185A	3.4	14.9	1.0
	C	A:ARG222	3.4	12.0	1.0
	C	A:LYS224	3.4	9.7	1.0
	C	A:TYR185	3.5	13.1	1.0
	N	A:LYS224	3.8	10.6	1.0
	CA	A:ASP185A	4.0	14.8	1.0
	N	A:GLY223A	4.1	14.6	1.0
	C	A:ALA221	4.1	11.6	1.0
	N	A:ARG222	4.1	11.5	1.0
	CA	A:LYS224	4.2	10.2	1.0
	N	A:ASP185A	4.2	13.9	1.0
	O	A:HOH265	4.3	20.1	1.0
	N	A:THR185B	4.3	15.1	1.0
	O	A:ALA221	4.3	12.0	1.0
	N	A:LYS223	4.3	12.8	1.0
	CA	A:LYS223	4.4	12.3	1.0
	CA	A:ARG222	4.4	11.9	1.0
	C	A:LYS223	4.5	13.3	1.0
	CA	A:ALA221	4.5	11.1	1.0
	CB	A:LYS224	4.5	10.1	1.0
	N	A:TYR225	4.5	9.5	1.0
	CA	A:TYR185	4.6	12.7	1.0
	O	A:LYS186	4.6	14.2	1.0
	CA	A:THR185B	4.7	15.0	1.0
	N	A:TYR185	4.7	12.2	1.0
	C	A:GLY223A	4.8	15.3	1.0
	CA	A:TYR225	4.8	9.8	1.0
	CA	A:GLY223A	4.9	15.2	1.0
	CD1	A:TYR225	5.0	10.6	1.0

Calcium binding site 3 out of 3 in 3kl6

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Calcium Binding Sites List in 3kl6

Calcium binding site 3 out of 3 in the Discovery of Tetrahydropyrimidin-2(1H)-One Derivative Tak-442: A Potent, Selective and Orally Active Factor Xa Inhibitor

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Discovery of Tetrahydropyrimidin-2(1H)-One Derivative Tak-442: A Potent, Selective and Orally Active Factor Xa Inhibitor within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca3 b:24.6 occ:1.00	O	A:ASN72	2.3	21.9	1.0
	OD2	A:ASP70	2.3	23.1	1.0
	OE2	A:GLU80	2.4	25.5	1.0
	O	A:GLN75	2.5	28.6	1.0
	OE2	A:GLU77	2.7	30.5	1.0
	OE1	A:GLU80	3.0	26.7	1.0
	CD	A:GLU80	3.0	24.7	1.0
	C	A:ASN72	3.4	22.0	1.0
	CG	A:ASP70	3.4	21.2	1.0
	CD	A:GLU77	3.6	31.0	1.0
	C	A:GLN75	3.7	28.8	1.0
	OD1	A:ASP70	4.0	24.4	1.0
	CG	A:GLU77	4.1	30.3	1.0
	N	A:ASN72	4.1	20.8	1.0
	N	A:THR73	4.2	22.8	1.0
	CA	A:THR73	4.2	23.7	1.0
	CA	A:ASN72	4.3	21.5	1.0
	CB	A:ASP70	4.4	18.9	1.0
	N	A:GLN75	4.4	27.6	1.0
	CG	A:GLU80	4.5	21.9	1.0
	C	A:THR73	4.5	24.6	1.0
	OE1	A:GLU77	4.5	31.4	1.0
	CA	A:ASP70	4.5	18.5	1.0
	N	A:GLU76	4.6	29.4	1.0
	CA	A:GLN75	4.6	28.3	1.0
	N	A:ARG71	4.6	19.5	1.0
	CA	A:GLU76	4.7	29.9	1.0
	O	A:THR73	4.7	24.8	1.0
	CB	A:ASN72	4.7	21.3	1.0
	N	A:GLU77	4.7	29.9	1.0
	CB	A:GLU77	4.8	29.9	1.0
	CB	A:GLU80	4.9	19.8	1.0
	C	A:GLU76	4.9	30.0	1.0

Reference:

T.Fujimoto, Y.Imaeda, N.Konishi, K.Hiroe, M.Kawamura, G.P.Textor, K.Aertgeerts, K.Kubo. Discovery of A Tetrahydropyrimidin-2(1H)-One Derivative (Tak-442) As A Potent, Selective, and Orally Active Factor Xa Inhibitor. J.Med.Chem. V. 53 3517 2010.
ISSN: ISSN 0022-2623
PubMed: 20355714
DOI: 10.1021/JM901699J

Page generated: Tue Jul 8 13:51:19 2025

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