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PDBsum entry 1c5w
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Blood clotting
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PDB id
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1c5w
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Contents |
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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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Structural basis for selectivity of a small molecule, S1-Binding, Submicromolar inhibitor of urokinase-Type plasminogen activator.
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Authors
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B.A.Katz,
R.Mackman,
C.Luong,
K.Radika,
A.Martelli,
P.A.Sprengeler,
J.Wang,
H.Chan,
L.Wong.
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Ref.
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Chem Biol, 2000,
7,
299-312.
[DOI no: ]
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PubMed id
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Abstract
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BACKGROUND: Urokinase-type plasminogen activator (uPA) is a protease associated
with tumor metastasis and invasion. Inhibitors of uPA may have potential as
drugs for prostate, breast and other cancers. Therapeutically useful inhibitors
must be selective for uPA and not appreciably inhibit the related, and
structurally and functionally similar enzyme, tissue-type plasminogen activator
(tPA), involved in the vital blood-clotting cascade. RESULTS: We produced
mutagenically deglycosylated low molecular weight uPA and determined the crystal
structure of its complex with 4-iodobenzo[b]thiophene 2-carboxamidine (K(i) =
0.21 +/- 0.02 microM). To probe the structural determinants of the affinity and
selectivity of this inhibitor for uPA we also determined the structures of its
trypsin and thrombin complexes, of apo-trypsin, apo-thrombin and apo-factor Xa,
and of uPA, trypsin and thrombin bound by compounds that are less effective uPA
inhibitors, benzo[b]thiophene-2-carboxamidine,
thieno[2,3-b]-pyridine-2-carboxamidine and benzamidine. The K(i) values of each
inhibitor toward uPA, tPA, trypsin, tryptase, thrombin and factor Xa were
determined and compared. One selectivity determinant of the
benzo[b]thiophene-2-carboxamidines for uPA involves a hydrogen bond at the S1
site to Ogamma(Ser190) that is absent in the Ala190 proteases, tPA, thrombin and
factor Xa. Other subtle differences in the architecture of the S1 site also
influence inhibitor affinity and enzyme-bound structure. CONCLUSIONS: Subtle
structural differences in the S1 site of uPA compared with that of related
proteases, which result in part from the presence of a serine residue at
position 190, account for the selectivity of small thiophene-2-carboxamidines
for uPA, and afford a framework for structure-based design of small, potent,
selective uPA inhibitors.
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Figure 3.
Figure 3. (a) Structure of
uPA–thieno[2,3-b]pyridine-2-carboxamidine, pH 6.5, at 1.65
Å resolution, on the (2|F[o]|–|F[c]|), α[c] map. The
occupancies of conformation 1 (with green carbons) and 2 (light
green carbons) are 66% and 34%, respectively. In the trypsin
complex the corresponding occupancies are 54% and 46% at pH 5.5,
and 31% and 69% at pH 8.2. (b) Superposition of uPA– and
trypsin–thieno[2,3-b]pyridine-2-carboxamidine, pH 5.5. For
clarity only the first conformation of the bound inhibitors is
shown. In each complex the aromatic rings of the two bound
conformations of the inhibitors lie in the same plane as one
another (see Figure 4a). The two locations of the Hγ proton of
Ser195 for the trypsin complex are shown.
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Figure 4.
Figure 4. Structures and associated (2|F[o]|–|F[c]|),
α[c] maps for (a) apo-trypsin, pH 7.7; and (b) apo-thrombin, pH
7.5, 1.47 Å resolution. In (b), the long
water1–O[Trp215] distance (3.4 Å) is indicated in cyan.
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The above figures are
reprinted
by permission from Cell Press:
Chem Biol
(2000,
7,
299-312)
copyright 2000.
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