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* Residue conservation analysis
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Enzyme class:
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Chains A, L:
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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J Biol Chem
271:29988-29992
(1996)
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PubMed id:
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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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H.Brandstetter,
A.Kühne,
W.Bode,
R.Huber,
W.von der Saal,
K.Wirthensohn,
R.A.Engh.
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ABSTRACT
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The 3.0-A resolution x-ray structure of human des-Gla-coagulation factor Xa
(fXa) has been determined in complex with the synthetic inhibitor DX-9065a. The
binding geometry is characterized primarily by two interaction sites: the
naphthamidine group is fixed in the S1 pocket by a typical salt bridge to
Asp-189, while the pyrrolidine ring binds in the unique aryl-binding site (S4)
of fXa. Unlike the large majority of inhibitor complexes with serine
proteinases, Gly-216 (S3) does not contribute to hydrogen bond formation. In
contrast to typical thrombin binding modes, the S2 site of fXa cannot be used by
DX-9065a since it is blocked by Tyr-99, and the aryl-binding site (S4) of fXa is
lined by carbonyl oxygen atoms that can accommodate positive charges. This has
implications for natural substrate recognition as well as for drug design.
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Selected figure(s)
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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^
plot
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
reprinted
by permission from the ASBMB:
J Biol Chem
(1996,
271,
29988-29992)
copyright 1996.
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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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V.Castro-López,
L.F.Harris,
J.S.O'Donnell,
and
A.J.Killard
(2011).
Comparative study of Factor Xa fluorogenic substrates and their influence on the quantification of LMWHs.
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Anal Bioanal Chem,
399,
691-700.
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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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S.K.Buddai,
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An anticoagulant RNA aptamer that inhibits proteinase-cofactor interactions within prothrombinase.
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J Biol Chem,
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H.Fan,
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Molecular docking screens using comparative models of proteins.
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J Thromb Haemost,
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Activation mechanisms of coagulation factor IX.
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Biol Chem,
390,
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T.Zögg,
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Structural basis of the cofactor- and substrate-assisted activation of human coagulation factor IXa.
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Structure,
17,
1669-1678.
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PDB codes:
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Y.Chen,
S.Qin,
W.Tan,
Y.Lu,
J.Zhang,
H.Li,
H.Bu,
and
J.Cheng
(2009).
Cloning and comparison of factor X from rhesus monkey (Macaca mulatta).
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Comp Med,
59,
476-481.
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C.T.Chen,
E.W.Yang,
H.J.Hsu,
Y.K.Sun,
W.L.Hsu,
and
A.S.Yang
(2008).
Protease substrate site predictors derived from machine learning on multilevel substrate phage display data.
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Bioinformatics,
24,
2691-2697.
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D.Reid,
B.S.Sadjad,
Z.Zsoldos,
and
A.Simon
(2008).
LASSO-ligand activity by surface similarity order: a new tool for ligand based virtual screening.
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J Comput Aided Mol Des,
22,
479-487.
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H.J.Hsu,
K.C.Tsai,
Y.K.Sun,
H.J.Chang,
Y.J.Huang,
H.M.Yu,
C.H.Lin,
S.S.Mao,
and
A.S.Yang
(2008).
Factor Xa active site substrate specificity with substrate phage display and computational molecular modeling.
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J Biol Chem,
283,
12343-12353.
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|
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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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A.Di Fenza,
A.Heine,
U.Koert,
and
G.Klebe
(2007).
Understanding Binding Selectivity toward Trypsin and Factor Xa: the Role of Aromatic Interactions.
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ChemMedChem,
2,
297-308.
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PDB codes:
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T.Noguchi,
N.Tanaka,
T.Nishimata,
R.Goto,
M.Hayakawa,
A.Sugidachi,
T.Ogawa,
F.Asai,
and
K.Fujimoto
(2007).
Cinnamylindoline derivatives: synthesis and factor Xa (FXa) inhibitory activities.
|
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Chem Pharm Bull (Tokyo),
55,
1494-1504.
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C.Williams
(2006).
Reverse fingerprinting, similarity searching by group fusion and fingerprint bit importance.
|
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Mol Divers,
10,
311-332.
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D.N.Gosalia,
W.S.Denney,
C.M.Salisbury,
J.A.Ellman,
and
S.L.Diamond
(2006).
Functional phenotyping of human plasma using a 361-fluorogenic substrate biosensing microarray.
|
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Biotechnol Bioeng,
94,
1099-1110.
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D.Zhang,
and
I.M.Kovach
(2006).
Deuterium solvent isotope effect and proton-inventory studies of factor Xa-catalyzed reactions.
|
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Biochemistry,
45,
14175-14182.
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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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N.Murayama,
M.Nakaoka,
and
K.Sudo
(2006).
Contribution of lysosomes to concentrative uptake of DX-9065a into rat liver.
|
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J Pharm Sci,
95,
1763-1770.
|
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T.Noguchi,
N.Tanaka,
T.Nishimata,
R.Goto,
M.Hayakawa,
A.Sugidachi,
T.Ogawa,
F.Asai,
Y.Matsui,
and
K.Fujimoto
(2006).
Indoline derivatives I: synthesis and factor Xa (FXa) inhibitory activities.
|
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Chem Pharm Bull (Tokyo),
54,
163-174.
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D.N.Gosalia,
C.M.Salisbury,
D.J.Maly,
J.A.Ellman,
and
S.L.Diamond
(2005).
Profiling serine protease substrate specificity with solution phase fluorogenic peptide microarrays.
|
| |
Proteomics,
5,
1292-1298.
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J.H.Alexander,
and
K.P.Singh
(2005).
Inhibition of Factor Xa : a potential target for the development of new anticoagulants.
|
| |
Am J Cardiovasc Drugs,
5,
279-290.
|
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|
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|
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S.Komoriya,
N.Haginoya,
S.Kobayashi,
T.Nagata,
A.Mochizuki,
M.Suzuki,
T.Yoshino,
H.Horino,
T.Nagahara,
M.Suzuki,
Y.Isobe,
and
T.Furugoori
(2005).
Design, synthesis, and biological activity of non-basic compounds as factor Xa inhibitors: SAR study of S1 and aryl binding sites.
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Bioorg Med Chem,
13,
3927-3954.
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PDB codes:
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S.Krishnaswamy
(2005).
Exosite-driven substrate specificity and function in coagulation.
|
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J Thromb Haemost,
3,
54-67.
|
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|
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|
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W.Bode
(2005).
The structure of thrombin, a chameleon-like proteinase.
|
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J Thromb Haemost,
3,
2379-2388.
|
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|
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C.A.Kontogiorgis,
and
D.Hadjipavlou-Litina
(2004).
Current trends in quantitative structure activity relationships on FXa inhibitors: evaluation and comparative analysis.
|
| |
Med Res Rev,
24,
687-747.
|
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|
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|
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B.R.Lentz
(2003).
Exposure of platelet membrane phosphatidylserine regulates blood coagulation.
|
| |
Prog Lipid Res,
42,
423-438.
|
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|
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|
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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.
|
| |
Int J Biochem Cell Biol,
35,
221-225.
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K.Carlsson,
P.O.Freskgård,
E.Persson,
U.Carlsson,
and
M.Svensson
(2003).
Probing the interface between factor Xa and tissue factor in the quaternary complex tissue factor-factor VIIa-factor Xa-tissue factor pathway inhibitor.
|
| |
Eur J Biochem,
270,
2576-2582.
|
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|
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L.A.O'Brien,
A.R.Stafford,
J.C.Fredenburgh,
and
J.I.Weitz
(2003).
Glycosaminoglycans bind factor Xa in a Ca2+-dependent fashion and modulate its catalytic activity.
|
| |
Biochemistry,
42,
13091-13098.
|
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|
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S.S.Ahmad,
F.S.London,
and
P.N.Walsh
(2003).
The assembly of the factor X-activating complex on activated human platelets.
|
| |
J Thromb Haemost,
1,
48-59.
|
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|
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|
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S.X.Wang,
E.Hur,
C.A.Sousa,
L.Brinen,
E.J.Slivka,
and
R.J.Fletterick
(2003).
The extended interactions and Gla domain of blood coagulation factor Xa.
|
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Biochemistry,
42,
7959-7966.
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PDB code:
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D.Rauh,
S.Reyda,
G.Klebe,
and
M.T.Stubbs
(2002).
Trypsin mutants for structure-based drug design: expression, refolding and crystallisation.
|
| |
Biol Chem,
383,
1309-1314.
|
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|
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|
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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.
|
| |
Biophys J,
82,
1190-1206.
|
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|
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H.Nishida,
Y.Miyazaki,
T.Mukaihira,
F.Saitoh,
M.Fukui,
K.Harada,
M.Itoh,
A.Muraoka,
T.Matsusue,
A.Okamoto,
Y.Hosaka,
M.Matsumoto,
S.Ohnishi,
and
H.Mochizuki
(2002).
Synthesis and evaluation of 1-arylsulfonyl-3-piperazinone derivatives as a factor Xa inhibitor II. Substituent effect on biological activities.
|
| |
Chem Pharm Bull (Tokyo),
50,
1187-1194.
|
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|
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M.M.Mueller,
S.Sperl,
J.Stürzebecher,
W.Bode,
and
L.Moroder
(2002).
(R)-3-Amidinophenylalanine-derived inhibitors of factor Xa with a novel active-site binding mode.
|
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Biol Chem,
383,
1185-1191.
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PDB codes:
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D.Kirchhofer,
C.Eigenbrot,
M.T.Lipari,
P.Moran,
M.Peek,
and
R.F.Kelley
(2001).
The tissue factor region that interacts with factor Xa in the activation of factor VII.
|
| |
Biochemistry,
40,
675-682.
|
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|
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F.C.Peterson,
N.C.Gordon,
and
P.G.Gettins
(2001).
High-level bacterial expression and 15N-alanine-labeling of bovine trypsin. Application to the study of trypsin-inhibitor complexes and trypsinogen activation by NMR spectroscopy.
|
| |
Biochemistry,
40,
6275-6283.
|
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|
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J.E.Grundy,
N.Lavigne,
T.Hirama,
C.R.MacKenzie,
and
E.L.Pryzdial
(2001).
Binding of plasminogen and tissue plasminogen activator to plasmin-modulated factor X and factor Xa.
|
| |
Biochemistry,
40,
6293-6302.
|
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|
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|
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R.Walser,
and
W.F.van Gunsteren
(2001).
Viscosity dependence of protein dynamics.
|
| |
Proteins,
42,
414-421.
|
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|
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J.L.Harris,
B.J.Backes,
F.Leonetti,
S.Mahrus,
J.A.Ellman,
and
C.S.Craik
(2000).
Rapid and general profiling of protease specificity by using combinatorial fluorogenic substrate libraries.
|
| |
Proc Natl Acad Sci U S A,
97,
7754-7759.
|
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|
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|
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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.
|
| |
Biochemistry,
39,
12534-12542.
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PDB code:
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|
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R.Krishnan,
I.Mochalkin,
R.Arni,
and
A.Tulinsky
(2000).
Structure of thrombin complexed with selective non-electrophilic inhibitors having cyclohexyl moieties at P1.
|
| |
Acta Crystallogr D Biol Crystallogr,
56,
294-303.
|
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PDB codes:
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|
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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.
|
| |
Biochemistry,
39,
14322-14329.
|
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|
|
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|
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R.St Charles,
K.Padmanabhan,
R.V.Arni,
K.P.Padmanabhan,
and
A.Tulinsky
(2000).
Structure of tick anticoagulant peptide at 1.6 A resolution complexed with bovine pancreatic trypsin inhibitor.
|
| |
Protein Sci,
9,
265-272.
|
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|
PDB code:
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|
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S.Sperl,
A.Bergner,
J.Stürzebecher,
V.Magdolen,
W.Bode,
and
L.Moroder
(2000).
Urethanyl-3-amidinophenylalanine derivatives as inhibitors of factor Xa. X-ray crystal structure of a trypsin/inhibitor complex and modeling studies.
|
| |
Biol Chem,
381,
321-329.
|
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|
|
|
|
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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.
|
| |
Structure,
8,
553-563.
|
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|
|
|
|
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A.Betz,
P.W.Wong,
and
U.Sinha
(1999).
Inhibition of factor Xa by a peptidyl-alpha-ketothiazole involves two steps. Evidence for a stabilizing conformational change.
|
| |
Biochemistry,
38,
14582-14591.
|
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|
|
|
|
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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.
|
| |
Proc Natl Acad Sci U S A,
96,
8925-8930.
|
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|
PDB code:
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|
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|
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H.Czapinska,
and
J.Otlewski
(1999).
Structural and energetic determinants of the S1-site specificity in serine proteases.
|
| |
Eur J Biochem,
260,
571-595.
|
 |
|
|
|
|
 |
I.Mochalkin,
and
A.Tulinsky
(1999).
Structures of thrombin retro-inhibited with SEL2711 and SEL2770 as they relate to factor Xa binding.
|
| |
Acta Crystallogr D Biol Crystallogr,
55,
785-793.
|
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|
PDB codes:
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|
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K.P.Hopfner,
A.Lang,
A.Karcher,
K.Sichler,
E.Kopetzki,
H.Brandstetter,
R.Huber,
W.Bode,
and
R.A.Engh
(1999).
Coagulation factor IXa: the relaxed conformation of Tyr99 blocks substrate binding.
|
| |
Structure,
7,
989-996.
|
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PDB code:
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|
 |
M.S.Rao,
and
A.J.Olson
(1999).
Modelling of factor Xa-inhibitor complexes: a computational flexible docking approach.
|
| |
Proteins,
34,
173-183.
|
 |
|
|
|
|
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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.
|
| |
Acta Crystallogr D Biol Crystallogr,
55,
1395-1404.
|
 |
|
PDB codes:
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|
|
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|
 |
P.E.Sanderson
(1999).
Small, noncovalent serine protease inhibitors.
|
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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
codes are
shown on the right.
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}
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