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PDBsum entry 1us0
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Oxidoreductase
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PDB id
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1us0
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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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Ultrahigh resolution drug design i: details of interactions in human aldose reductase-Inhibitor complex at 0.66 a.
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Authors
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E.I.Howard,
R.Sanishvili,
R.E.Cachau,
A.Mitschler,
B.Chevrier,
P.Barth,
V.Lamour,
M.Van zandt,
E.Sibley,
C.Bon,
D.Moras,
T.R.Schneider,
A.Joachimiak,
A.Podjarny.
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Ref.
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Proteins, 2004,
55,
792-804.
[DOI no: ]
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PubMed id
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Abstract
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The first subatomic resolution structure of a 36 kDa protein [aldose reductase
is presented. AR was cocrystallized at pH 5.0 with its cofactor NADP+ and
inhibitor IDD 594, a therapeutic candidate for the treatment of diabetic
complications. X-ray diffraction data were collected up to 0.62 A resolution and
treated up to 0.66 A resolution. Anisotropic refinement followed by a blocked
matrix inversion produced low standard deviations (<0.005 A). The model was
very well ordered overall (CA atoms' mean B factor is 5.5 A2). The model and the
electron-density maps revealed fine features, such as H-atoms, bond densities,
and significant deviations from standard stereochemistry. Other features, such
as networks of hydrogen bonds (H bonds), a large number of multiple
conformations, and solvent structure were also better defined. Most of the atoms
in the active site region were extremely well ordered (mean B approximately 3
A2), leading to the identification of the protonation states of the residues
involved in catalysis. The electrostatic interactions of the inhibitor's charged
carboxylate head with the catalytic residues and the charged coenzyme NADP+
explained the inhibitor's noncompetitive character. Furthermore, a short contact
involving the IDD 594 bromine atom explained the selectivity profile of the
inhibitor, important feature to avoid toxic effects. The presented structure and
the details revealed are instrumental for better understanding of the inhibition
mechanism of AR by IDD 594, and hence, for the rational drug design of future
inhibitors. This work demonstrates the capabilities of subatomic resolution
experiments and stimulates further developments of methods allowing the use of
the full potential of these experiments.
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Figure 1.
Figure 1. Contacts of IDD 594 with AR and NADP^+. (a) 3D view
of inhibitor contacts. View of the inhibitor-binding site down
the barrel axis with the semitransparent representation of AR
surface. The active site cleft (marked A), is occupied by the
inhibitor (stick only; color code: C = gray, N = blue, O = red,
F = pink, S = orange, Br = green) and surrounded by the
catalytic residues His 110, Tyr 48, and the coenzyme NADP^+. The
residues within 3.9 Å and NADP^+ are shown (balls and
sticks). The specificity pocket between Leu 300, Phe 122, and
Trp 111 (marked S) is occupied by the brominated aromatic ring
of the inhibitor. (b) Scheme of IDD 594 and its contacts. Red
dashed lines show contacts between 3.5 and 3.0 Å, and blue
dashed lines show contacts <3.0 Å. The exact values are
given in Table IV.
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Figure 5.
Figure 5. Model of residues Cys 44 and Ala 45 superimposed with
 A-weighted
Fo-Fc map with omitted hydrogen atoms (a), contoured magenta at
at 0.25 e/Å^3 (2.5 )
showing the position of the hydrogen atoms and the bond
densities. Model of residues Ser 76 and Lys 77(b), viewed down
the C  N
peptide bond showing the  angle
of -167.3° stabilized by an H-bond.
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2004,
55,
792-804)
copyright 2004.
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