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References listed in PDB file
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Key reference
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Title
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Kinetic and crystallographic studies of glucopyranose spirohydantoin and glucopyranosylamine analogs inhibitors of glycogen phosphorylase.
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Authors
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K.A.Watson,
E.D.Chrysina,
K.E.Tsitsanou,
S.E.Zographos,
G.Archontis,
G.W.Fleet,
N.G.Oikonomakos.
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Ref.
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Proteins, 2005,
61,
966-983.
[DOI no: ]
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PubMed id
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Abstract
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Glycogen phosphorylase (GP) is currently exploited as a target for inhibition of
hepatic glycogenolysis under high glucose conditions. Spirohydantoin of
glucopyranose and N-acetyl-beta-D-glucopyranosylamine have been identified as
the most potent inhibitors of GP that bind at the catalytic site. Four
spirohydantoin and three beta-D-glucopyranosylamine analogs have been designed,
synthesized and tested for inhibition of GP in kinetic experiments. Depending on
the functional group introduced, the K(i) values varied from 16.5 microM to 1200
microM. In order to rationalize the kinetic results, we determined the crystal
structures of the analogs in complex with GP. All the inhibitors bound at the
catalytic site of the enzyme, by making direct and water-mediated hydrogen bonds
with the protein and by inducing minor movements of the side chains of Asp283
and Asn284, of the 280s loop that blocks access of the substrate glycogen to the
catalytic site, and changes in the water structure in the vicinity of the site.
The differences observed in the Ki values of the analogs can be interpreted in
terms of variations in hydrogen bonding and van der Waals interactions,
desolvation effects, ligand conformational entropy, and displacement of water
molecules on ligand binding to the catalytic site.
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Figure 1.
Figure 1. A schematic diagram of the GPb dimeric molecule
viewed down the molecular dyad. One subunit is colored in dark
green and the other in light green. The position is shown for
the catalytic site. The catalytic site, marked by glucose (GLC)
and the essential cofactor pyridoxal 5  -phosphate
(PLP), shown in ball-and-stick representations, is buried at the
center of the subunit and is accessible to the bulk solvent
through a 15-Å long channel. Close-up: Details of the
interactions of glucose with residues of the catalytic site.
 -D-Glucose,
a competitive inhibitor (K[i] = 1.7 mM), on binding at the
catalytic site, promotes the less active T state through
stabilization of the closed position of the 280s loop (shown in
cream) which blocks access for the substrate (glycogen) to the
catalytic site. In particular, the -1-OH
is hydrogen-bonded to Asp283 (OD1), through a water molecule,
and the 2-OH is hydrogen-bonded directly to Asn284 (ND2).
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Figure 2.
Figure 2. Interactions of compound 1 (A), compound 2 (B),
compound 3 (C), compound 4 (D), compound 5 (E), compound 6 (F),
compound 7 (G), compound 8 (H), compound 8, 100 K (I), compound
9 (J), compound 10 (K) with GPb in the vicinity of the catalytic
site, shown in stereo. The interactions of the glucopyranose
ring are retained throughout the structures analyzed and were
not incorporated in the figures for clarity reasons.
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2005,
61,
966-983)
copyright 2005.
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Secondary reference #1
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Title
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Crystal structure of an actinidin-E-64 complex.
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Authors
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K.I.Varughese,
Y.Su,
D.Cromwell,
S.Hasnain,
N.H.Xuong.
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Ref.
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Biochemistry, 1992,
31,
5172-5176.
[DOI no: ]
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PubMed id
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Secondary reference #2
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Title
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Refined X-Ray structure of papain.E-64-C complex at 2.1-A resolution.
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Authors
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D.Yamamoto,
K.Matsumoto,
H.Ohishi,
T.Ishida,
M.Inoue,
K.Kitamura,
H.Mizuno.
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Ref.
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J Biol Chem, 1991,
266,
14771-14777.
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PubMed id
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Secondary reference #3
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Title
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Structure of actinidin, After refinement at 1.7 angstroms resolution
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Author
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E.N.Baker.
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Ref.
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j mol biol, 1980,
141,
441.
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Secondary reference #4
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Title
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Crystal structure of a caricain d158e mutant in complex with e-64.
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Authors
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N.A.Katerelos,
M.A.Taylor,
M.Scott,
P.W.Goodenough,
R.W.Pickersgill.
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Ref.
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FEBS Lett, 1996,
392,
35-39.
[DOI no: ]
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PubMed id
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Secondary reference #5
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Title
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Mode of binding of e-64-C, A potent thiol protease inhibitor, To papain as determined by X-Ray crystal analysis of the complex.
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Authors
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K.Matsumoto,
D.Yamamoto,
H.Ohishi,
K.Tomoo,
T.Ishida,
M.Inoue,
T.Sadatome,
K.Kitamura,
H.Mizuno.
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Ref.
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FEBS Lett, 1989,
245,
177-180.
[DOI no: ]
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PubMed id
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Secondary reference #6
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Title
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The importance of val-157 hydrophobic interaction for papain inhibitory activity of an epoxysuccinyl amino acid derivative. A structure-Activity relationship based on the crystal structure of the papain-E-64-C complex.
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Authors
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D.Yamamoto,
K.Matsumoto,
H.Ohishi,
T.Ishida,
M.Inoue,
K.Kitamura,
K.Hanada.
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Ref.
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FEBS Lett, 1990,
263,
134-136.
[DOI no: ]
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PubMed id
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Secondary reference #7
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Title
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Crystal structure of papain-E64-C complex. Binding diversity of e64-C to papain s2 and s3 subsites.
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Authors
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M.J.Kim,
D.Yamamoto,
K.Matsumoto,
M.Inoue,
T.Ishida,
H.Mizuno,
S.Sumiya,
K.Kitamura.
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Ref.
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Biochem J, 1992,
287,
797-803.
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PubMed id
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