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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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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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Abstract
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Factor Xa is a serine protease which activates thrombin (factor IIa) and plays a
key regulatory role in the blood-coagulation cascade. Factor Xa is, therefore,
an important target for the design of anti-thrombotics. Both factor Xa and
thrombin share sequence and structural homology with trypsin. As part of a
factor Xa inhibitor-design program, a number of factor Xa inhibitors were
crystallographically studied complexed to bovine trypsin. The structures of one
diaryl benzimidazole, one diaryl carbazole and three diaryloxypyridines are
described. All five compounds bind to trypsin in an extended conformation, with
an amidinoaryl group in the S1 pocket and a second basic/hydrophobic moiety
bound in the S4 pocket. These binding modes all bear a resemblance to the
reported binding mode of DX-9065a in bovine trypsin and human factor Xa.
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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
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(1999,
55,
1395-1404)
copyright 1999.
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Secondary reference #1
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Title
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Crystal structure analysis and refinement of two variants of trigonal trypsinogen: trigonal trypsin and peg (polyethylene glycol) trypsinogen and their comparison with orthorhombic trypsin and trigonal trypsinogen.
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Authors
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W.Bode,
R.Huber.
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Ref.
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FEBS Lett, 1978,
90,
265-269.
[DOI no: ]
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PubMed id
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Secondary reference #2
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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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Secondary reference #3
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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 #4
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Title
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Crystal structures of factor xa specific inhibitors in complex with trypsin: structural grounds for inhibition of factor xa and selectivity against thrombin.
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Authors
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M.T.Stubbs,
R.Huber,
W.Bode.
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Ref.
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FEBS Lett, 1995,
375,
103-107.
[DOI no: ]
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PubMed id
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Secondary reference #5
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Title
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Analytical and production seeding techniques
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Authors
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E.A.Stura,
I.A.Wilson.
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Ref.
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methods(san diego), 1990,
1,
38.
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Secondary reference #6
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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^
 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
reproduced from the cited reference
with permission from the ASBMB
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