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PDBsum entry 1ly4
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Oxidoreductase
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PDB id
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1ly4
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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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Analysis of quinazoline and pyrido[2,3-D]pyrimidine n9-C10 reversed-Bridge antifolates in complex with NADP+ and pneumocystis carinii dihydrofolate reductase.
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Authors
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V.Cody,
N.Galitsky,
J.R.Luft,
W.Pangborn,
S.F.Queener,
A.Gangjee.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2002,
58,
1393-1399.
[DOI no: ]
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PubMed id
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Abstract
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Structural studies of two ternary complexes of Pneumocystis carinii
dihydrofolate reductase (pcDHFR) with the cofactor NADP(+) and potent
antifolates, the N9-C10 reversed-bridge inhibitor
2,4-diamino-6-[N-(2',5'-dimethoxybenzyl)-N-methylamino]quinazoline (1) and its
3',5'-dimethoxypyrido[2,3-d]pyrimidine analog (2), were carried out. Data for
the monoclinic crystals were refined to 1.90 A resolution for the complex with
(1) (R = 0.178) and to 2.1 A resolution for the complex with (2) (R = 0.193).
The effect of the N9-C10 reversed-bridge geometry is to distort the bridge from
coplanarity with the pyrido[2,3-d]pyrimidine or quinazoline ring system and to
twist the C10 methylene conformation toward a gauche conformation. This change
also influences the conformation of the methoxybenzyl ring, moving it away from
a trans position. This change places the 5'-methoxy group deeper within the
hydrophobic pocket made by Ile65, Pro66 and Phe69 of the pcDHFR active site.
These results also revealed the first observation of an unusual conformation for
the reversed-bridge geometry (C5-C6-N9-C10 torsion angle) in antifolate (2). The
electron density is consistent with the presence of two models (conformers 2-1
and 2-2) that result from inversion of the geometry at N9. The four examples of
N9-C10 reversed-bridge antifolates cluster in two conformations, with the
structure of quinazoline (1) similar to that previously reported for its
2',5'-dimethoxypyrido[2,3-d]pyrimidine analog (3). The two conformers of (2)
differ from these and each other by a twisted-bridge geometry that results in
the dimethoxybenzyl ring occupying the same conformational space. Conformer 2-2
also has the N9-C10 reversed bridge perpendicular to the pyrido[2,3-d]pyrimidine
plane, in contrast to the gauche-trans conformation normally observed. As a
result of these changes, the N9 methyl probes conformational space in the active
site not normally occupied by antifolate structures. The N9 methyl of conformer
2-2 makes close contacts to the conserved Leu25 as well as the hydroxyl O atoms
of the nicotinamide ribose and Ser64, whereas the other three reversed-bridge
conformers make weak hydrophobic contacts with Ile123, Thr61 and Ile65. These
antifolates are ten times more selective for pcDHFR than the C9-N10 bridge
parent trimetrexate. However, pyrido[2,3-d]pyrimidines (2) and (3) are three
times more selective for pcDHFR than quinazoline (1) is for rat liver DHFR.
These data suggest that the loss of hydrogen-bonding interactions with N8 is
more important to potency than the interactions of the methoxybenzyl
substituents.
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Figure 3.
Figure 3 Model of the tertiary structure of the pcDHFR-NADP+-(2)
ternary complex. Helices are in yellow, sheets are in red and
loops are in green. Active-site hydrophobic residues Leu25,
Ile33, Pro66, Phe69 and Ile72 are shown. Models were produced
with SETOR (Evans, 1993[Evans, S. V. (1993). J. Mol. Graph. 11,
134-138.]).
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Figure 4.
Figure 4 Stereoview of the electron density (2F[o] - F[c], 1
 )
(blue) and (F[o] - F[c], -3 )
(red) that results from phases of conformer 1 only, showing the
fit of the inhibitor (2) in conformation 1 (red) and
conformation 2 (yellow) in pcDHFR-NADP+ ternary complex. Diagram
produced with CHAIN (Sack, 1988[Sack, J. S. (1988). J. Mol.
Graph. 6, 244-245.]).
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2002,
58,
1393-1399)
copyright 2002.
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Secondary reference #1
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Title
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The structure of pneumocystis carinii dihydrofolate reductase to 1.9 a resolution.
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Authors
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J.N.Champness,
A.Achari,
S.P.Ballantine,
P.K.Bryant,
C.J.Delves,
D.K.Stammers.
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Ref.
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Structure, 1994,
2,
915-924.
[DOI no: ]
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PubMed id
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Figure 5.
Figure 5. Chemical structures of the inhibitors (a)
trimethoprim and (b) piritrexim.
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Figure 6.
Figure 6. Binding of inhibitor molecules within the active
site of P. carinii DHFR. (a) Electron density difference map
from difference Fourier analysis of the enzyme-trimethoprim
complex contoured at the 2.5s density level with the
trimethoprim skeletal model superimposed. (b) The corresponding
difference map for the enzyme-piritrexim complex difference
Fourier, contoured at a similar density level. (c)Comparison of
the binding of the inhibitors trimethoprim (yellow) and
piritrexim (blue) to P. carinii DHFR by superimposing the two
complexes. Regions where the overlap between the two structures
is closest are shown as white.
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The above figures are
reproduced from the cited reference
with permission from Cell Press
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Secondary reference #2
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Title
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Ligand-Induced conformational changes in the crystal structures of pneumocystis carinii dihydrofolate reductase complexes with folate and NADP+.
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Authors
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V.Cody,
N.Galitsky,
D.Rak,
J.R.Luft,
W.Pangborn,
S.F.Queener.
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Ref.
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Biochemistry, 1999,
38,
4303-4312.
[DOI no: ]
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PubMed id
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