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References listed in PDB file
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Key reference
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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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Abstract
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Crystal structures of DX9065a and a related bisamidino-aryl inhibitor specific
for the blood-clotting factor Xa have been solved in complex with bovine
beta-trypsin to a resolution of 1.9 A. Each inhibitor exhibits an extended
conformation along the active site, in contrast to the compact folded structures
observed for thrombin specific inhibitors. Few direct contacts (predominantly in
the S1 pocket) are made between trypsin and the inhibitors. Transfer of the
inhibitors to the active site of factor Xa suggests a three-site interaction:
salt bridge formation at the base of the primary specificity pocket, extensive
hydrophobic surface burial and a weak electrostatic interaction between the
distal basic component of the inhibitor and an electronegative cavity of factor
Xa formed by three backbone carbonyl oxygens. Additivity of these three
interactions is the basis for the observed strong inhibition of factor Xa and
provides a framework for the design of novel factor Xa inhibitors. A propionic
acid group of the inhibitor would clash with the thrombin specific '60-insertion
loop', thus conferring selectivity against thrombin.
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Secondary reference #1
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Title
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The second kunitz domain of human tissue factor pathway inhibitor: cloning, Structure determination and interaction with factor xa.
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Authors
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M.J.Burgering,
L.P.Orbons,
A.Van der doelen,
J.Mulders,
H.J.Theunissen,
P.D.Grootenhuis,
W.Bode,
R.Huber,
M.T.Stubbs.
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Ref.
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J Mol Biol, 1997,
269,
395-407.
[DOI no: ]
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PubMed id
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Figure 4.
Figure 4. Overall view of the presumed complex between TFPI-kII and factor Xa, looking down on the active site of
the proteinase. To the west of the active site, the interaction is mediated largely by hydrophobic surface burial (see
Figure 5). Basic residues of TFPI reach towards the acidic 39-loop to the east. The acidic southern face of TFPI juxta-
poses the basic 148-loop, which by analogy to similar proteinases may be flexible enough to form direct salt bridges.
Figure prepared using SETOR (Evans, 1992).
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Figure 5.
Figure 5. Details of the factor
Xa:TFPI-kII interaction to the west
of the active site. Residues of TFPI-
kII as observed in the trypsin com-
plex are shown in orange, while
those of unliganded factor Xa are
shown in green; the side-chain of
TyrF99 would clash with the disul-
phide bridge Cys14.Cys38. Swing-
ing out the side-chain with
subsequent energy minimization of
the complex results in the structure
shown in light blue. Mutual burial
of the hydrophobic side-chains of
factor Xa (TyrF99, PheF174 and
TrpF215) by the cystine Cys14.
Cys38, Ile13 and Leu39 of TFPI-kII
presumably contributes to complex
stabilisation.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #2
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Title
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The ornithodorin-Thrombin crystal structure, A key to the tap enigma?
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Authors
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A.Van de locht,
M.T.Stubbs,
W.Bode,
T.Friedrich,
C.Bollschweiler,
W.Höffken,
R.Huber.
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Ref.
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Embo J, 1996,
15,
6011-6017.
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PubMed id
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Secondary reference #3
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Title
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Structural aspects of factor xa inhibition
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Author
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M.T.Stubbs.
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Ref.
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curr pharm des, 1996,
2,
543.
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Secondary reference #4
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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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Secondary reference #5
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Title
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Structure of human des(1-45) factor xa at 2.2 a resolution.
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Authors
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K.Padmanabhan,
K.P.Padmanabhan,
A.Tulinsky,
C.H.Park,
W.Bode,
R.Huber,
D.T.Blankenship,
A.D.Cardin,
W.Kisiel.
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Ref.
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J Mol Biol, 1993,
232,
947-966.
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PubMed id
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Secondary reference #6
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Title
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Geometry of binding of the n alpha-Tosylated piperidides of m-Amidino-, P-Amidino- And p-Guanidino phenylalanine to thrombin and trypsin. X-Ray crystal structures of their trypsin complexes and modeling of their thrombin complexes.
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Authors
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D.Turk,
J.Stürzebecher,
W.Bode.
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Ref.
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FEBS Lett, 1991,
287,
133-138.
[DOI no: ]
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PubMed id
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Secondary reference #7
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Title
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Geometry of binding of the benzamidine- And arginine-Based inhibitors n alpha-(2-Naphthyl-Sulphonyl-Glycyl)-Dl-P-Amidinophenylalanyl-Pipe ridine (napap) and (2r,4r)-4-Methyl-1-[N alpha-(3-Methyl-1,2,3,4-Tetrahydro-8- Quinolinesulphonyl)-L-Arginyl]-2-Piperidine carboxylic acid (mqpa) to human alpha-Thrombin. X-Ray crystallographic determination of the napap-Trypsin complex and modeling of napap-Thrombin and mqpa-Thrombin.
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Authors
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W.Bode,
D.Turk,
J.Stürzebecher.
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Ref.
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Eur J Biochem, 1990,
193,
175-182.
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PubMed id
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Secondary reference #8
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Title
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Crystal structure of bovine beta-Trypsin at 1.5 a resolution in a crystal form with low molecular packing density. Active site geometry, Ion pairs and solvent structure.
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Authors
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H.D.Bartunik,
L.J.Summers,
H.H.Bartsch.
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Ref.
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J Mol Biol, 1989,
210,
813-828.
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PubMed id
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Secondary reference #9
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Title
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The refined crystal structure of bovine beta-Trypsin at 1.8 a resolution. Ii. Crystallographic refinement, Calcium binding site, Benzamidine binding site and active site at ph 7.0.
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Authors
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W.Bode,
P.Schwager.
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Ref.
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J Mol Biol, 1975,
98,
693-717.
[DOI no: ]
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PubMed id
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Figure 4.
FiG. 4. Stereo pair of the calcium-bindng loop including the calcium ion and internal water
molecules.
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Figure 7.
Fro. 7. Stereo pair of the region aroun the salt bridge between the benzamidine and Asp189
in benzamidine-inhibited trpsin (a) and side chain of LyslS(I) an Asp189 in he trysin-
inhibitor complex (b), both in complex orientation.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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