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* Residue conservation analysis
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Enzyme class:
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Chains L, C:
E.C.3.4.21.6
- coagulation factor Xa.
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Reaction:
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Preferential cleavage: Arg-|-Thr and then Arg-|-Ile bonds in prothrombin to form thrombin.
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DOI no:
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Proc Natl Acad Sci U S A
95:6630-6635
(1998)
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PubMed id:
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Structural basis for chemical inhibition of human blood coagulation factor Xa.
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K.Kamata,
H.Kawamoto,
T.Honma,
T.Iwama,
S.H.Kim.
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ABSTRACT
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Factor Xa, the converting enzyme of prothrombin to thrombin, has emerged as an
alternative (to thrombin) target for drug discovery for thromboembolic diseases.
An inhibitor has been synthesized and the crystal structure of the complex
factor Xa and the inhibitor has been determined by
crystallographic methods in two different crystal forms to 2.3- and 2.4-A
resolution. The racemic mixture of inhibitor FX-2212,
(2RS)-(3'-amidino-3-biphenylyl)-5-(4-pyridylamino)pentanoic acid, inhibits
factor Xa activity by 50% at 272 nM in vitro. The S-isomer of FX-2212 (FX-2212a)
was found to bind to the active site of factor Xa in both crystal forms. The
biphenylamidine of FX-2212a occupies the S1-pocket, and the pyridine ring makes
hydrophobic interactions with the factor Xa aryl-binding site. Several water
molecules meditate inhibitor binding to residues in the active site. In contrast
factor Xa in complex with a naphthyl inhibitor DX-9065a,
two epidermal growth factor-like domains of factor Xa are well ordered in both
our crystal forms as well as the region between the two domains, which recently
was found to be the binding site of the effector cell protease receptor-1. This
structure provides a basis for designing next generation inhibitors of factor Xa.
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Selected figure(s)
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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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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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Y.K.Lee,
and
M.R.Player
(2011).
Developments in factor Xa inhibitors for the treatment of thromboembolic disorders.
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Med Res Rev,
31,
202-283.
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Y.Ono,
K.Ojima,
F.Torii,
E.Takaya,
N.Doi,
K.Nakagawa,
S.Hata,
K.Abe,
and
H.Sorimachi
(2010).
Skeletal muscle-specific calpain is an intracellular Na+-dependent protease.
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J Biol Chem,
285,
22986-22998.
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R.Chattopadhyay,
R.Iacob,
S.Sen,
R.Majumder,
K.B.Tomer,
and
B.R.Lentz
(2009).
Functional and structural characterization of factor Xa dimer in solution.
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Biophys J,
96,
974-986.
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A.Venceslá,
M.A.Corral-Rodríguez,
M.Baena,
M.Cornet,
M.Domènech,
M.Baiget,
P.Fuentes-Prior,
and
E.F.Tizzano
(2008).
Identification of 31 novel mutations in the F8 gene in Spanish hemophilia A patients: structural analysis of 20 missense mutations suggests new intermolecular binding sites.
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Blood,
111,
3468-3478.
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N.Singh,
and
J.M.Briggs
(2008).
Molecular dynamics simulations of Factor Xa: insight into conformational transition of its binding subsites.
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Biopolymers,
89,
1104-1113.
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R.Abel,
T.Young,
R.Farid,
B.J.Berne,
and
R.A.Friesner
(2008).
Role of the active-site solvent in the thermodynamics of factor Xa ligand binding.
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J Am Chem Soc,
130,
2817-2831.
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R.E.Saunders,
and
S.J.Perkins
(2008).
CoagMDB: a database analysis of missense mutations within four conserved domains in five vitamin K-dependent coagulation serine proteases using a text-mining tool.
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Hum Mutat,
29,
333-344.
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V.Chandrasekaran,
C.J.Lee,
R.E.Duke,
L.Perera,
and
L.G.Pedersen
(2008).
Computational study of the putative active form of protein Z (PZa): sequence design and structural modeling.
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Protein Sci,
17,
1354-1361.
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C.J.Lee,
V.Chandrasekaran,
R.E.Duke,
L.Perera,
and
L.G.Pedersen
(2007).
A proposed structural model of human protein Z.
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J Thromb Haemost,
5,
1558-1561.
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K.M.Bromfield,
N.S.Quinsey,
P.J.Duggan,
and
R.N.Pike
(2006).
Approaches to selective peptidic inhibitors of factor Xa.
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Chem Biol Drug Des,
68,
11-19.
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L.Autin,
M.Steen,
B.Dahlbäck,
and
B.O.Villoutreix
(2006).
Proposed structural models of the prothrombinase (FXa-FVa) complex.
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Proteins,
63,
440-450.
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K.Schärer,
M.Morgenthaler,
R.Paulini,
U.Obst-Sander,
D.W.Banner,
D.Schlatter,
J.Benz,
M.Stihle,
and
F.Diederich
(2005).
Quantification of cation-pi interactions in protein-ligand complexes: crystal-structure analysis of Factor Xa bound to a quaternary ammonium ion ligand.
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Angew Chem Int Ed Engl,
44,
4400-4404.
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PDB code:
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H.C.Whinna,
E.B.Lesesky,
D.M.Monroe,
K.A.High,
P.J.Larson,
and
F.C.Church
(2004).
Role of the gamma-carboxyglutamic acid domain of activated factor X in the presence of calcium during inhibition by antithrombin-heparin.
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J Thromb Haemost,
2,
1127-1134.
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T.Morita
(2004).
Use of snake venom inhibitors in studies of the function and tertiary structure of coagulation factors.
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Int J Hematol,
79,
123-129.
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B.R.Lentz
(2003).
Exposure of platelet membrane phosphatidylserine regulates blood coagulation.
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Prog Lipid Res,
42,
423-438.
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B.V.Norledge,
R.J.Petrovan,
W.Ruf,
and
A.J.Olson
(2003).
The tissue factor/factor VIIa/factor Xa complex: a model built by docking and site-directed mutagenesis.
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Proteins,
53,
640-648.
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PDB code:
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J.P.Ludeman,
R.N.Pike,
K.M.Bromfield,
P.J.Duggan,
J.Cianci,
B.Le Bonniec,
J.C.Whisstock,
and
S.P.Bottomley
(2003).
Determination of the P1', P2' and P3' subsite-specificity of factor Xa.
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Int J Biochem Cell Biol,
35,
221-225.
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S.Deam,
J.Uprichard,
J.T.Eaton,
S.J.Perkins,
and
G.Dolan
(2003).
Factor X Leicester: Ile411Phe associated with a low antigen level and a disproportionately low functional activity of factor X.
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J Thromb Haemost,
1,
603-605.
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D.Venkateswarlu,
L.Perera,
T.Darden,
and
L.G.Pedersen
(2002).
Structure and dynamics of zymogen human blood coagulation factor X.
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Biophys J,
82,
1190-1206.
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H.Mizuno,
Z.Fujimoto,
H.Atoda,
and
T.Morita
(2001).
Crystal structure of an anticoagulant protein in complex with the Gla domain of factor X.
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Proc Natl Acad Sci U S A,
98,
7230-7234.
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PDB code:
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E.J.Enyedy,
and
I.M.Kovach
(2000).
Reversible modulation of human factor Xa activity with phosphonate esters: media effects.
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Bioorg Med Chem,
8,
549-556.
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M.Adler,
D.D.Davey,
G.B.Phillips,
S.H.Kim,
J.Jancarik,
G.Rumennik,
D.R.Light,
and
M.Whitlow
(2000).
Preparation, characterization, and the crystal structure of the inhibitor ZK-807834 (CI-1031) complexed with factor Xa.
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Biochemistry,
39,
12534-12542.
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PDB code:
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R.M.Camire,
P.J.Larson,
D.W.Stafford,
and
K.A.High
(2000).
Enhanced gamma-carboxylation of recombinant factor X using a chimeric construct containing the prothrombin propeptide.
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Biochemistry,
39,
14322-14329.
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R.Tranter,
J.A.Read,
R.Jones,
and
R.L.Brady
(2000).
Effector sites in the three-dimensional structure of mammalian sperm beta-acrosin.
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Structure,
8,
1179-1188.
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PDB codes:
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V.L.Nienaber,
D.Davidson,
R.Edalji,
V.L.Giranda,
V.Klinghofer,
J.Henkin,
P.Magdalinos,
R.Mantei,
S.Merrick,
J.M.Severin,
R.A.Smith,
K.Stewart,
K.Walter,
J.Wang,
M.Wendt,
M.Weitzberg,
X.Zhao,
and
T.Rockway
(2000).
Structure-directed discovery of potent non-peptidic inhibitors of human urokinase that access a novel binding subsite.
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Structure,
8,
553-563.
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A.C.Pike,
A.M.Brzozowski,
S.M.Roberts,
O.H.Olsen,
and
E.Persson
(1999).
Structure of human factor VIIa and its implications for the triggering of blood coagulation.
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Proc Natl Acad Sci U S A,
96,
8925-8930.
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PDB code:
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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,
and
M.M.Morrissey
(1999).
Crystallographic analysis of potent and selective factor Xa inhibitors complexed to bovine trypsin.
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Acta Crystallogr D Biol Crystallogr,
55,
1395-1404.
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PDB codes:
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P.E.Sanderson
(1999).
Small, noncovalent serine protease inhibitors.
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Med Res Rev,
19,
179-197.
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U.Sinha
(1999).
Synthetic inhibitors of coagulation factor Xa.
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Expert Opin Investig Drugs,
8,
567-573.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
