Chlorine in PDB 1wu1: Factor Xa in Complex with the Inhibitor 4-[(5-Chloroindol-2-Yl) Sulfonyl]-2-(2-Methylpropyl)-1-[[5-(Pyridin-4-Yl) Pyrimidin-2- Yl]Carbonyl]Piperazine

Enzymatic activity of Factor Xa in Complex with the Inhibitor 4-[(5-Chloroindol-2-Yl) Sulfonyl]-2-(2-Methylpropyl)-1-[[5-(Pyridin-4-Yl) Pyrimidin-2- Yl]Carbonyl]Piperazine

All present enzymatic activity of Factor Xa in Complex with the Inhibitor 4-[(5-Chloroindol-2-Yl) Sulfonyl]-2-(2-Methylpropyl)-1-[[5-(Pyridin-4-Yl) Pyrimidin-2- Yl]Carbonyl]Piperazine:
3.4.21.6;

Protein crystallography data

The structure of Factor Xa in Complex with the Inhibitor 4-[(5-Chloroindol-2-Yl) Sulfonyl]-2-(2-Methylpropyl)-1-[[5-(Pyridin-4-Yl) Pyrimidin-2- Yl]Carbonyl]Piperazine, PDB code: 1wu1 was solved by M.Suzuki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	25.00 / 2.30
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	56.569, 72.487, 79.020, 90.00, 90.00, 90.00
*R / R_free (%)*	18.9 / 23.5

Other elements in 1wu1:

The structure of Factor Xa in Complex with the Inhibitor 4-[(5-Chloroindol-2-Yl) Sulfonyl]-2-(2-Methylpropyl)-1-[[5-(Pyridin-4-Yl) Pyrimidin-2- Yl]Carbonyl]Piperazine also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Factor Xa in Complex with the Inhibitor 4-[(5-Chloroindol-2-Yl) Sulfonyl]-2-(2-Methylpropyl)-1-[[5-(Pyridin-4-Yl) Pyrimidin-2- Yl]Carbonyl]Piperazine (pdb code 1wu1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total only one binding site of Chlorine was determined in the Factor Xa in Complex with the Inhibitor 4-[(5-Chloroindol-2-Yl) Sulfonyl]-2-(2-Methylpropyl)-1-[[5-(Pyridin-4-Yl) Pyrimidin-2- Yl]Carbonyl]Piperazine, PDB code: 1wu1:

Chlorine binding site 1 out of 1 in 1wu1

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Chlorine Binding Sites List in 1wu1

Chlorine binding site 1 out of 1 in the Factor Xa in Complex with the Inhibitor 4-[(5-Chloroindol-2-Yl) Sulfonyl]-2-(2-Methylpropyl)-1-[[5-(Pyridin-4-Yl) Pyrimidin-2- Yl]Carbonyl]Piperazine

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Factor Xa in Complex with the Inhibitor 4-[(5-Chloroindol-2-Yl) Sulfonyl]-2-(2-Methylpropyl)-1-[[5-(Pyridin-4-Yl) Pyrimidin-2- Yl]Carbonyl]Piperazine within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl700 b:46.4 occ:1.00	CL	A:D91700	0.0	46.4	1.0
	C6	A:D91700	1.7	46.9	1.0
	C5	A:D91700	2.6	47.0	1.0
	C1	A:D91700	2.7	44.7	1.0
	CZ	A:TYR228	3.4	32.4	1.0
	OH	A:TYR228	3.5	30.9	1.0
	CG1	A:VAL213	3.5	34.5	1.0
	O	A:TRP215	3.5	46.6	1.0
	O	A:ILE227	3.6	37.4	1.0
	CA	A:GLY226	3.6	41.3	1.0
	CE2	A:TYR228	3.7	35.4	1.0
	CB	A:ALA190	3.7	39.7	1.0
	N	A:ILE227	3.8	37.0	1.0
	CE1	A:TYR228	3.8	34.1	1.0
	C4	A:D91700	3.9	46.0	1.0
	C	A:GLY226	4.0	39.5	1.0
	C2	A:D91700	4.0	43.6	1.0
	C	A:ILE227	4.2	36.5	1.0
	C	A:TRP215	4.3	45.1	1.0
	CD2	A:TYR228	4.3	33.2	1.0
	O	A:HOH300	4.3	40.1	1.0
	N	A:SER214	4.4	35.2	1.0
	C3	A:D91700	4.4	45.8	1.0
	CD1	A:TYR228	4.4	32.8	1.0
	CA	A:VAL213	4.4	33.4	1.0
	N	A:TRP215	4.5	40.5	1.0
	CB	A:VAL213	4.5	34.2	1.0
	CA	A:ILE227	4.6	36.3	1.0
	CG	A:TYR228	4.6	33.5	1.0
	OD1	A:ASP189	4.7	50.8	1.0
	C	A:VAL213	4.8	34.2	1.0
	CA	A:TRP215	4.8	43.4	1.0
	O	A:GLY226	4.9	38.2	1.0
	CG2	A:VAL213	5.0	36.3	1.0

Reference:

S.Komoriya, N.Haginoya, S.Kobayashi, T.Nagata, A.Mochizuki, M.Suzuki, T.Yoshino, H.Horino, T.Nagahara, M.Suzuki, Y.Isobe, T.Furugoori. Design, Synthesis, and Biological Activity of Non-Basic Compounds As Factor Xa Inhibitors: Sar Study of S1 and Aryl Binding Sites Bioorg.Med.Chem. V. 13 3927 2005.
ISSN: ISSN 0968-0896
PubMed: 15911309
DOI: 10.1016/J.BMC.2005.04.006

Page generated: Thu Jul 10 20:19:46 2025

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