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* Residue conservation analysis
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Enzyme class:
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Chains L, H:
E.C.3.4.21.5
- thrombin.
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Reaction:
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Preferential cleavage: Arg-|-Gly; activates fibrinogen to fibrin and releases fibrinopeptide A and B.
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DOI no:
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Biochemistry
36:1034-1040
(1997)
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PubMed id:
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Molecular design and characterization of an alpha-thrombin inhibitor containing a novel P1 moiety.
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J.A.Malikayil,
J.P.Burkhart,
H.A.Schreuder,
R.J.Broersma,
C.Tardif,
L.W.Kutcher,
S.Mehdi,
G.L.Schatzman,
B.Neises,
N.P.Peet.
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ABSTRACT
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An inhibitor of alpha-thrombin was designed on the basis of the X-ray crystal
structures of thrombin and trypsin. The design strategy employed the geometric
and electrostatic differences between the specificity pockets of the two
enzymes. These differences arise due to the replacement of Ser 190 in trypsin by
Ala 190 in thrombin. The new inhibitor contained a tryptophan side chain instead
of the arginine side chain that is present in the prototypical thrombin
inhibitors. This inhibitor had a Ki value of 0.25 microM, displayed more than
400-fold specificity for thrombin over trypsin, and doubled the rat plasma APTT
at a concentration of 44.9 microM. The X-ray crystal structure of the
inhibitor/alpha-thrombin complex was determined. This represents the first
reported three-dimensional structure of a thrombin/ inhibitor complex where the
specificity pocket of the enzyme is occupied by a chemical moiety other than a
guanidino or an amidino group. As was predicted by the molecular model, the
tryptophan side chain docks into the specificity pocket of the enzyme. This
finding is in contrast with the indole binding region of thrombin reported
earlier [Berliner, L. J., & Shen, Y. Y. L. (1977) Biochemistry 16,
4622-4626]. The lower binding affinity of the new inhibitor for trypsin,
compared to that for thrombin, appears to be due to (i) the extra energy
required to deform the smaller specificity pocket of trypsin to accommodate the
bulky indole group and (ii) the favorable electrostatic interactions of the
indole group with the more hydrophobic specificity pocket of thrombin. The
neutral indole group may be of pharmacological significance because the severe
hypotension and respiratory distress observed following the administration of
some thrombin inhibitors have been linked to the positively charged guanidino or
amidino functionalities.
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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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A.R.Kinjo,
and
H.Nakamura
(2009).
Comprehensive structural classification of ligand-binding motifs in proteins.
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Structure,
17,
234-246.
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L.A.Bush,
R.W.Nelson,
and
E.Di Cera
(2006).
Murine thrombin lacks Na+ activation but retains high catalytic activity.
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J Biol Chem,
281,
7183-7188.
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A.von Matt,
C.Ehrhardt,
P.Burkhard,
R.Metternich,
M.Walkinshaw,
and
C.Tapparelli
(2000).
Selective boron-containing thrombin inhibitors--X-ray analysis reveals surprising binding mode.
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Bioorg Med Chem,
8,
2291-2303.
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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.
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Acta Crystallogr D Biol Crystallogr,
56,
294-303.
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PDB codes:
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V.Nienaber,
J.Wang,
D.Davidson,
and
J.Henkin
(2000).
Re-engineering of human urokinase provides a system for structure-based drug design at high resolution and reveals a novel structural subsite.
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J Biol Chem,
275,
7239-7248.
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Y.Zhou,
and
M.E.Johnson
(1999).
Comparative molecular modeling analysis of-5-amidinoindole and benzamidine binding to thrombin and trypsin: specific H-bond formation contributes to high 5-amidinoindole potency and selectivity for thrombin and factor Xa.
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J Mol Recognit,
12,
235-241.
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K.Kamata,
H.Kawamoto,
T.Honma,
T.Iwama,
and
S.H.Kim
(1998).
Structural basis for chemical inhibition of human blood coagulation factor Xa.
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Proc Natl Acad Sci U S A,
95,
6630-6635.
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PDB codes:
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M.P.Weir,
S.S.Bethell,
A.Cleasby,
C.J.Campbell,
R.J.Dennis,
C.J.Dix,
H.Finch,
H.Jhoti,
C.J.Mooney,
S.Patel,
C.M.Tang,
M.Ward,
A.J.Wonacott,
and
C.W.Wharton
(1998).
Novel natural product 5,5-trans-lactone inhibitors of human alpha-thrombin: mechanism of action and structural studies.
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Biochemistry,
37,
6645-6657.
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PDB codes:
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R.Krishnan,
E.Zhang,
K.Hakansson,
R.K.Arni,
A.Tulinsky,
M.S.Lim-Wilby,
O.E.Levy,
J.E.Semple,
and
T.K.Brunck
(1998).
Highly selective mechanism-based thrombin inhibitors: structures of thrombin and trypsin inhibited with rigid peptidyl aldehydes.
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Biochemistry,
37,
12094-12103.
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PDB codes:
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S.L.Lee,
R.S.Alexander,
A.Smallwood,
R.Trievel,
L.Mersinger,
P.C.Weber,
and
C.Kettner
(1997).
New inhibitors of thrombin and other trypsin-like proteases: hydrogen bonding of an aromatic cyano group with a backbone amide of the P1 binding site replaces binding of a basic side chain.
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Biochemistry,
36,
13180-13186.
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PDB code:
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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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Links
