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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Preparation, Characterization, And the crystal structure of the inhibitor zk-807834 (ci-1031) complexed with factor xa.
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Authors
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M.Adler,
D.D.Davey,
G.B.Phillips,
S.H.Kim,
J.Jancarik,
G.Rumennik,
D.R.Light,
M.Whitlow.
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Ref.
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Biochemistry, 2000,
39,
12534-12542.
[DOI no: ]
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PubMed id
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Abstract
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Factor Xa plays a critical role in the formation of blood clots. This serine
protease catalyzes the conversion of prothrombin to thrombin, the first joint
step that links the intrinsic and extrinsic coagulation pathways. There is
considerable interest in the development of factor Xa inhibitors for the
intervention in thrombic diseases. This paper presents the structure of the
inhibitor ZK-807834, also known as CI-1031, bound to factor Xa and provides the
details of the protein purification and crystallization. Results from mass
spectrometry indicate that the factor Xa underwent autolysis during
crystallization and the first EGF-like domain was cleaved from the protein. The
crystal structure of the complex shows that the amidine of ZK-807834 forms a
salt bridge with Asp189 in the S1 pocket and the basic imidazoline fits snugly
into the S4 site. The central pyridine ring provides a fairly rigid linker
between these groups. This rigidity helps minimize entropic losses during
binding. In addition, the structure reveals new interactions that were not found
in the previous factor Xa/inhibitor complexes. ZK-807834 forms a strong hydrogen
bond between an ionized 2-hydroxy group and Ser195 of factor Xa. There is also
an aromatic ring-stacking interaction between the inhibitor and Trp215 in the S4
pocket. These interactions contribute to both the potency of this compound (K(I)
= 0.11 nM) and the >2500-fold selectivity against homologous serine proteases
such as trypsin.
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Secondary reference #1
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Title
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Structural basis for chemical inhibition of human blood coagulation factor xa.
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Authors
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K.Kamata,
H.Kawamoto,
T.Honma,
T.Iwama,
S.H.Kim.
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Ref.
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Proc Natl Acad Sci U S A, 1998,
95,
6630-6635.
[DOI no: ]
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PubMed id
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Figure 1.
Fig. 1. Chemical formulae of the FX-2212a inhibitor
(2S)-(3'-amidino-3-biphenylyl)-5-(4-pyridylamino)pentanoic acid
and the DX9065a
(2S)-{4-[1-acetimidoyl-(3S)-pyrrolidinyl]oxyphenyl}-3-(7-amidino-2-naphthyl)propionic
acid. Schematic drawing of the interactions between two
inhibitors, DX9065a and FX-2212a, and factor Xa. Hydrogen bonds
are shown as thin dashed lines, and hydrophobic interactions are
shown as thick dashed lines. In the case of Q192, the aliphatic
chain portion of Q192 makes the hydrophobic interaction. The
symbol "  " indicates
that the two interacting aromatic groups are not stacked but are
perpendicular to each other.
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Figure 5.
Fig. 5. (a) Stereo view of the electron density for
FX-2212a in difference electron density maps (contoured at 1.6
 )
calculated after modeling the first EGF domain and the simulated
annealing refinement. The final structure is superimposed. (b)
Binding interactions of FX-2212a (magenta ball and stick) with
Des[1-44] factor Xa in the form 1 crystal. The C  backbone is
shown in blue, and residues involved in interaction are shown as
a yellow ball-and-stick model. Conserved hydrogen bonds in the
three crystallographically independent molecules are shown in
green and a unique hydrogen bond in this interaction is shown in
orange.
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Secondary reference #2
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Title
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X-Ray structure of active site-Inhibited clotting factor xa. Implications for drug design and substrate recognition.
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Authors
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H.Brandstetter,
A.Kühne,
W.Bode,
R.Huber,
W.Von der saal,
K.Wirthensohn,
R.A.Engh.
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Ref.
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J Biol Chem, 1996,
271,
29988-29992.
[DOI no: ]
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PubMed id
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Figure 1.
Fig. 1. Chemical formula of the DX-9065a inhibitor:
(2S)-{4-[1-acetimidoyl-(3S)-pyrrolidinyl]-oxyphenyl}-3-(7-amidino-2-naphthyl)propionic^
acid hydrochloride pentahydrate.
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Figure 3.
Fig. 3. Binding interactions of DX-9065a with fXa. The C^
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and side chains involved in inhibitor binding of DX-9065a-bound^
fXa (yellow) are superimposed with the corresponding atoms of^
arginine-bound fXa (turquoise). The ligand-induced structural
changes at the S1-binding site may be seen at the side chain of^
Asp-189 and along the main chain at Gln-192. The hydrophobic
sleeve^ at the aryl-binding site (S4) is also apparent, with the
cation hole formed by Glu-97 and the carbonyl oxygens of Glu-97
and Lys-96^ at the back.
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The above figures are
reproduced from the cited reference
with permission from the ASBMB
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Secondary reference #3
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Title
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Crystallographic analysis of potent and selective factor xa inhibitors complexed to bovine trypsin.
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Authors
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M.Whitlow,
D.O.Arnaiz,
B.O.Buckman,
D.D.Davey,
B.Griedel,
W.J.Guilford,
S.K.Koovakkat,
A.Liang,
R.Mohan,
G.B.Phillips,
M.Seto,
K.J.Shaw,
W.Xu,
Z.Zhao,
D.R.Light,
M.M.Morrissey.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 1999,
55,
1395-1404.
[DOI no: ]
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PubMed id
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Figure 5.
Figure 5 Superposition of bovine trypsin (I) and Daiichi's
DX-9065a (PDB entry 1mtw) complexes. The C atoms of the
inhibitor (I) and DX-9065a are colored green and blue,
respectively. The majority of the C atoms in the trypsin bound
to (I) are gray and those bound to DX-9065a are black. C atoms
of specific residues have been colored. Asp189 (177) at the
bottom of the S1 pocket is colored light blue. The catalytic
triad Ser195 (183), His57 (46) and Asp102 (90), are colored
orange. Residues which form the S4 pocket, Thr98 (86), Leu99
(87), Gln175 (161) and Trp215 (199), are colored purple.
Hydrogen bonds are depicted as dashed lines. Hydrogen bonds to
the naphthylamidine in DX-9065a have been omitted for clarity,
as they are identical in both complexes.
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Figure 6.
Figure 6 Superposition of the bovine trypsin (V) and human
factor Xa DX-9065a (PDB entry 1fax) complexes. The C atoms of
the inhibitor (V) and DX-9065a are colored green and blue,
respectively. The majority of the C atoms in trypsin are colored
gray and in factor Xa are colored black. C atoms of the five
amino-acid changes between bovine trypsin and human factor Xa
(Asn/Asp97, Tyr/Leu99, Gln175/Phe174, Ser/Ala190 and Ser/Glu217)
have been colored green in trypsin and purple in human factor
Xa. The catalytic triad residues (Ser195, His57 and Asp102) in
both structures are colored orange.
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The above figures are
reproduced from the cited reference
with permission from the IUCr
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Secondary reference #4
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Title
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Discovery of n-[2-[5-[Amino(imino)methyl]-2-Hydroxyphenoxy]-3, 5-Difluoro-6-[3-(4, 5-Dihydro-1-Methyl-1h-Imidazol-2-Yl)phenoxy]pyridin-4-Yl]-N-Methylgl y cine (zk-807834): a potent, Selective, And orally active inhibitor of the blood coagulation enzyme factor xa.
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Authors
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G.B.Phillips,
B.O.Buckman,
D.D.Davey,
K.A.Eagen,
W.J.Guilford,
J.Hinchman,
E.Ho,
S.Koovakkat,
A.Liang,
D.R.Light,
R.Mohan,
H.P.Ng,
J.M.Post,
K.J.Shaw,
D.Smith,
B.Subramanyam,
M.E.Sullivan,
L.Trinh,
R.Vergona,
J.Walters,
K.White,
M.Whitlow,
S.Wu,
W.Xu,
M.M.Morrissey.
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Ref.
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J Med Chem, 1998,
41,
3557-3562.
[DOI no: ]
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PubMed id
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Secondary reference #5
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Title
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Design, Synthesis, And activity of 2,6-Diphenoxypyridine-Derived factor xa inhibitors.
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Authors
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G.Phillips,
D.D.Davey,
K.A.Eagen,
S.K.Koovakkat,
A.Liang,
H.P.Ng,
M.Pinkerton,
L.Trinh,
M.Whitlow,
A.M.Beatty,
M.M.Morrissey.
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Ref.
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J Med Chem, 1999,
42,
1749-1756.
[DOI no: ]
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PubMed id
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