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PDBsum entry 1f4b
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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.2.1.1.45
- thymidylate synthase.
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Pathway:
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Folate Coenzymes
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Reaction:
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dUMP + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate = 7,8-dihydrofolate + dTMP
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dUMP
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+
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(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate
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=
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7,8-dihydrofolate
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+
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dTMP
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Proc Natl Acad Sci U S A
97:9367-9372
(2000)
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PubMed id:
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Site-directed ligand discovery.
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D.A.Erlanson,
A.C.Braisted,
D.R.Raphael,
M.Randal,
R.M.Stroud,
E.M.Gordon,
J.A.Wells.
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ABSTRACT
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We report a strategy (called "tethering") to discover low molecular
weight ligands ( approximately 250 Da) that bind weakly to targeted sites on
proteins through an intermediary disulfide tether. A native or engineered
cysteine in a protein is allowed to react reversibly with a small library of
disulfide-containing molecules ( approximately 1,200 compounds) at
concentrations typically used in drug screening (10 to 200 microM). The
cysteine-captured ligands, which are readily identified by MS, are among the
most stable complexes, even though in the absence of the covalent tether the
ligands may bind very weakly. This method was applied to generate a potent
inhibitor for thymidylate synthase, an essential enzyme in pyrimidine metabolism
with therapeutic applications in cancer and infectious diseases. The affinity of
the untethered ligand (K(i) approximately 1 mM) was improved 3,000-fold by
synthesis of a small set of analogs with the aid of crystallographic structures
of the tethered complex. Such site-directed ligand discovery allows one to
nucleate drug design from a spatially targeted lead fragment.
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Selected figure(s)
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Figure 5.
Fig. 5. Grafting a glutamate residue onto
N-tosyl-D-proline improves the affinity 50-fold, and adding a
negatively charged appendage further increases the affinity by
an additional 70-fold.
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Figure 6.
Fig. 6. Overlay of three crystallographically determined
structures; only the inhibitor is shown for clarity. The
inhibition constant (K[i]) of each inhibitor is also shown.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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D.A.Bachovchin,
and
B.F.Cravatt
(2012).
The pharmacological landscape and therapeutic potential of serine hydrolases.
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Nat Rev Drug Discov,
11,
52-68.
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D.A.Erlanson,
J.W.Arndt,
M.T.Cancilla,
K.Cao,
R.A.Elling,
N.English,
J.Friedman,
S.K.Hansen,
C.Hession,
I.Joseph,
G.Kumaravel,
W.C.Lee,
K.E.Lind,
R.S.McDowell,
K.Miatkowski,
C.Nguyen,
T.B.Nguyen,
S.Park,
N.Pathan,
D.M.Penny,
M.J.Romanowski,
D.Scott,
L.Silvian,
R.L.Simmons,
B.T.Tangonan,
W.Yang,
and
L.Sun
(2011).
Discovery of a potent and highly selective PDK1 inhibitor via fragment-based drug discovery.
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Bioorg Med Chem Lett,
21,
3078-3083.
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PDB codes:
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H.Yanagida,
T.Matsuura,
Y.Kazuta,
and
T.Yomo
(2011).
In Vitro Selection of Proteins that Undergo Covalent Labeling with Small Molecules by Thiol-Disulfide Exchange by Using Ribosome Display.
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Chembiochem,
12,
962-969.
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J.D.Sadowsky,
M.A.Burlingame,
D.W.Wolan,
C.L.McClendon,
M.P.Jacobson,
and
J.A.Wells
(2011).
Turning a protein kinase on or off from a single allosteric site via disulfide trapping.
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Proc Natl Acad Sci U S A,
108,
6056-6061.
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PDB codes:
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J.Schulze Wischeler,
D.Sun,
N.U.Sandner,
U.Linne,
A.Heine,
U.Koert,
and
G.Klebe
(2011).
Stereo- and Regioselective Azide/Alkyne Cycloadditions in Carbonic Anhydrase II via Tethering, Monitored by Crystallography and Mass Spectrometry.
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Chemistry,
17,
5842-5851.
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PDB codes:
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M.T.Guarnieri,
B.S.Blagg,
and
R.Zhao
(2011).
A high-throughput TNP-ATP displacement assay for screening inhibitors of ATP-binding in bacterial histidine kinases.
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Assay Drug Dev Technol,
9,
174-183.
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R.W.Watkins,
U.Arnold,
and
R.T.Raines
(2011).
Ribonuclease S redux.
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Chem Commun (Camb),
47,
973-975.
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C.D.Andersson,
B.Y.Chen,
and
A.Linusson
(2010).
Mapping of ligand-binding cavities in proteins.
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Proteins,
78,
1408-1422.
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C.W.Diehnelt,
M.Shah,
N.Gupta,
P.E.Belcher,
M.P.Greving,
P.Stafford,
and
S.A.Johnston
(2010).
Discovery of high-affinity protein binding ligands--backwards.
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PLoS One,
5,
e10728.
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J.Scheuermann,
and
D.Neri
(2010).
DNA-encoded chemical libraries: a tool for drug discovery and for chemical biology.
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Chembiochem,
11,
931-937.
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L.Azéma,
K.Bathany,
and
B.Rayner
(2010).
2'-O-Appended polyamines that increase triple-helix-forming oligonucleotide affinity are selected by dynamic combinatorial chemistry.
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Chembiochem,
11,
2513-2516.
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P.T.Wilder,
T.H.Charpentier,
M.A.Liriano,
K.Gianni,
K.M.Varney,
E.Pozharski,
A.Coop,
E.A.Toth,
A.D.Mackerell,
and
D.J.Weber
(2010).
In vitro screening and structural characterization of inhibitors of the S100B-p53 interaction.
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Int J High Throughput Screen,
2010,
109-126.
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PDB codes:
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S.K.Mamidyala,
and
M.G.Finn
(2010).
In situ click chemistry: probing the binding landscapes of biological molecules.
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Chem Soc Rev,
39,
1252-1261.
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V.T.Bhat,
A.M.Caniard,
T.Luksch,
R.Brenk,
D.J.Campopiano,
and
M.F.Greaney
(2010).
Nucleophilic catalysis of acylhydrazone equilibration for protein-directed dynamic covalent chemistry.
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Nat Chem,
2,
490-497.
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A.Pushechnikov,
M.M.Lee,
J.L.Childs-Disney,
K.Sobczak,
J.M.French,
C.A.Thornton,
and
M.D.Disney
(2009).
Rational design of ligands targeting triplet repeating transcripts that cause RNA dominant disease: application to myotonic muscular dystrophy type 1 and spinocerebellar ataxia type 3.
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J Am Chem Soc,
131,
9767-9779.
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D.E.Scott,
G.J.Dawes,
M.Ando,
C.Abell,
and
A.Ciulli
(2009).
A fragment-based approach to probing adenosine recognition sites by using dynamic combinatorial chemistry.
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Chembiochem,
10,
2772-2779.
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PDB codes:
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F.C.Koyama,
D.Chakrabarti,
and
C.R.Garcia
(2009).
Molecular machinery of signal transduction and cell cycle regulation in Plasmodium.
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Mol Biochem Parasitol,
165,
1-7.
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G.Chessari,
and
A.J.Woodhead
(2009).
From fragment to clinical candidate--a historical perspective.
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Drug Discov Today,
14,
668-675.
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G.E.de Kloe,
D.Bailey,
R.Leurs,
and
I.J.de Esch
(2009).
Transforming fragments into candidates: small becomes big in medicinal chemistry.
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Drug Discov Today,
14,
630-646.
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L.Holm,
P.Moody,
and
M.Howarth
(2009).
Electrophilic affibodies forming covalent bonds to protein targets.
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J Biol Chem,
284,
32906-32913.
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M.F.Schmidt,
and
J.Rademann
(2009).
Dynamic template-assisted strategies in fragment-based drug discovery.
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Trends Biotechnol,
27,
512-521.
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M.M.Lee,
A.Pushechnikov,
and
M.D.Disney
(2009).
Rational and modular design of potent ligands targeting the RNA that causes myotonic dystrophy 2.
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ACS Chem Biol,
4,
345-355.
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W.Y.Lin,
Y.Wang,
S.Wang,
and
H.R.Tseng
(2009).
Integrated Microfluidic Reactors.
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Nano Today,
4,
470-481.
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Y.P.Pang,
S.K.Singh,
Y.Gao,
T.L.Lassiter,
R.K.Mishra,
K.Y.Zhu,
and
S.Brimijoin
(2009).
Selective and irreversible inhibitors of aphid acetylcholinesterases: steps toward human-safe insecticides.
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PLoS ONE,
4,
e4349.
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Y.Wang,
W.Y.Lin,
K.Liu,
R.J.Lin,
M.Selke,
H.C.Kolb,
N.Zhang,
X.Z.Zhao,
M.E.Phelps,
C.K.Shen,
K.F.Faull,
and
H.R.Tseng
(2009).
An integrated microfluidic device for large-scale in situ click chemistry screening.
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Lab Chip,
9,
2281-2285.
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B.D.Smith,
and
R.T.Raines
(2008).
Genetic selection for peptide inhibitors of angiogenin.
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Protein Eng Des Sel,
21,
289-294.
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D.Madan,
Z.Lin,
and
H.S.Rye
(2008).
Triggering protein folding within the GroEL-GroES complex.
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J Biol Chem,
283,
32003-32013.
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H.Ji,
B.Z.Stanton,
J.Igarashi,
H.Li,
P.Martásek,
L.J.Roman,
T.L.Poulos,
and
R.B.Silverman
(2008).
Minimal pharmacophoric elements and fragment hopping, an approach directed at molecular diversity and isozyme selectivity. Design of selective neuronal nitric oxide synthase inhibitors.
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J Am Chem Soc,
130,
3900-3914.
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PDB codes:
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Z.Miao,
M.R.McCoy,
D.D.Singh,
B.Barrios,
O.L.Hsu,
S.M.Cheal,
and
C.F.Meares
(2008).
Cysteinylated protein as reactive disulfide: an alternative route to affinity labeling.
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Bioconjug Chem,
19,
15-19.
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G.Gasparini,
M.Martin,
L.J.Prins,
and
P.Scrimin
(2007).
Limitations of the "tethering" strategy for the detection of a weak noncovalent interaction.
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Chem Commun (Camb),
(),
1340-1342.
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G.Tóth,
K.Mukhyala,
and
J.A.Wells
(2007).
Computational approach to site-directed ligand discovery.
|
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Proteins,
68,
551-560.
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H.Xie,
D.Ng,
S.N.Savinov,
B.Dey,
P.D.Kwong,
R.Wyatt,
A.B.Smith,
and
W.A.Hendrickson
(2007).
Structure-activity relationships in the binding of chemically derivatized CD4 to gp120 from human immunodeficiency virus.
|
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J Med Chem,
50,
4898-4908.
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I.S.Moreira,
P.A.Fernandes,
and
M.J.Ramos
(2007).
Hot spots--a review of the protein-protein interface determinant amino-acid residues.
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Proteins,
68,
803-812.
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J.K.Murray,
and
S.H.Gellman
(2007).
Targeting protein-protein interactions: lessons from p53/MDM2.
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Biopolymers,
88,
657-686.
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R.Srinivasan,
J.Li,
S.L.Ng,
K.A.Kalesh,
and
S.Q.Yao
(2007).
Methods of using click chemistry in the discovery of enzyme inhibitors.
|
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Nat Protoc,
2,
2655-2664.
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V.M.Krishnamurthy,
V.Semetey,
P.J.Bracher,
N.Shen,
and
G.M.Whitesides
(2007).
Dependence of effective molarity on linker length for an intramolecular protein-ligand system.
|
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J Am Chem Soc,
129,
1312-1320.
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A.Whitty,
and
G.Kumaravel
(2006).
Between a rock and a hard place?
|
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Nat Chem Biol,
2,
112-118.
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D.E.Hurt,
J.Widom,
and
J.Clardy
(2006).
Structure of Plasmodium falciparum dihydroorotate dehydrogenase with a bound inhibitor.
|
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Acta Crystallogr D Biol Crystallogr,
62,
312-323.
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PDB code:
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G.M.Keseru,
and
G.M.Makara
(2006).
Hit discovery and hit-to-lead approaches.
|
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Drug Discov Today,
11,
741-748.
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J.M.Scheer,
M.J.Romanowski,
and
J.A.Wells
(2006).
A common allosteric site and mechanism in caspases.
|
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Proc Natl Acad Sci U S A,
103,
7595-7600.
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PDB codes:
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J.Wang,
G.Sui,
V.P.Mocharla,
R.J.Lin,
M.E.Phelps,
H.C.Kolb,
and
H.R.Tseng
(2006).
Integrated microfluidics for parallel screening of an in situ click chemistry library.
|
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Angew Chem Int Ed Engl,
45,
5276-5281.
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Y.P.Pang
(2006).
Novel acetylcholinesterase target site for malaria mosquito control.
|
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PLoS ONE,
1,
e58.
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E.Buck,
and
J.A.Wells
(2005).
Disulfide trapping to localize small-molecule agonists and antagonists for a G protein-coupled receptor.
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Proc Natl Acad Sci U S A,
102,
2719-2724.
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H.Yin,
and
A.D.Hamilton
(2005).
Strategies for targeting protein-protein interactions with synthetic agents.
|
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Angew Chem Int Ed Engl,
44,
4130-4163.
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J.D.Cheeseman,
A.D.Corbett,
J.L.Gleason,
and
R.J.Kazlauskas
(2005).
Receptor-assisted combinatorial chemistry: thermodynamics and kinetics in drug discovery.
|
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Chemistry,
11,
1708-1716.
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K.F.Geoghegan,
and
M.A.Kelly
(2005).
Biochemical applications of mass spectrometry in pharmaceutical drug discovery.
|
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Mass Spectrom Rev,
24,
347-366.
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K.Levitsky,
M.D.Boersma,
C.J.Ciolli,
and
P.J.Belshaw
(2005).
Exo-mechanism proximity-accelerated alkylations: investigations of linkers, electrophiles and surface mutations in engineered cyclophilin-cyclosporin systems.
|
| |
Chembiochem,
6,
890-899.
|
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A.M.Aronov,
and
G.W.Bemis
(2004).
A minimalist approach to fragment-based ligand design using common rings and linkers: application to kinase inhibitors.
|
| |
Proteins,
57,
36-50.
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C.Lipinski,
and
A.Hopkins
(2004).
Navigating chemical space for biology and medicine.
|
| |
Nature,
432,
855-861.
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D.A.Erlanson,
J.A.Wells,
and
A.C.Braisted
(2004).
Tethering: fragment-based drug discovery.
|
| |
Annu Rev Biophys Biomol Struct,
33,
199-223.
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D.A.Erlanson,
and
S.K.Hansen
(2004).
Making drugs on proteins: site-directed ligand discovery for fragment-based lead assembly.
|
| |
Curr Opin Chem Biol,
8,
399-406.
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D.C.Rees,
M.Congreve,
C.W.Murray,
and
R.Carr
(2004).
Fragment-based lead discovery.
|
| |
Nat Rev Drug Discov,
3,
660-672.
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D.S.Sem,
B.Bertolaet,
B.Baker,
E.Chang,
A.D.Costache,
S.Coutts,
Q.Dong,
M.Hansen,
V.Hong,
X.Huang,
R.M.Jack,
R.Kho,
H.Lang,
C.T.Ma,
D.Meininger,
M.Pellecchia,
F.Pierre,
H.Villar,
and
L.Yu
(2004).
Systems-based design of bi-ligand inhibitors of oxidoreductases: filling the chemical proteomic toolbox.
|
| |
Chem Biol,
11,
185-194.
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J.A.Hardy,
J.Lam,
J.T.Nguyen,
T.O'Brien,
and
J.A.Wells
(2004).
Discovery of an allosteric site in the caspases.
|
| |
Proc Natl Acad Sci U S A,
101,
12461-12466.
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PDB codes:
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M.Castellanos,
D.B.Wilson,
and
M.L.Shuler
(2004).
A modular minimal cell model: purine and pyrimidine transport and metabolism.
|
| |
Proc Natl Acad Sci U S A,
101,
6681-6686.
|
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M.R.Ferguson,
X.Fan,
M.Mukherjee,
J.Luo,
R.Khan,
J.C.Ferreon,
V.J.Hilser,
R.E.Shope,
and
R.O.Fox
(2004).
Directed discovery of bivalent peptide ligands to an SH3 domain.
|
| |
Protein Sci,
13,
626-632.
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T.Berg
(2004).
Use of "tethering" for the identification of a small molecule that binds to a dynamic hot spot on the interleukin-2 surface.
|
| |
Chembiochem,
5,
1051-1053.
|
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V.P.Mocharla,
B.Colasson,
L.V.Lee,
S.Röper,
K.B.Sharpless,
C.H.Wong,
and
H.C.Kolb
(2004).
In situ click chemistry: enzyme-generated inhibitors of carbonic anhydrase II.
|
| |
Angew Chem Int Ed Engl,
44,
116-120.
|
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C.F.Wong,
and
J.A.McCammon
(2003).
Protein flexibility and computer-aided drug design.
|
| |
Annu Rev Pharmacol Toxicol,
43,
31-45.
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D.A.Erlanson,
J.W.Lam,
C.Wiesmann,
T.N.Luong,
R.L.Simmons,
W.L.DeLano,
I.C.Choong,
M.T.Burdett,
W.M.Flanagan,
D.Lee,
E.M.Gordon,
and
T.O'Brien
(2003).
In situ assembly of enzyme inhibitors using extended tethering.
|
| |
Nat Biotechnol,
21,
308-314.
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PDB codes:
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D.Hughes
(2003).
Exploiting genomics, genetics and chemistry to combat antibiotic resistance.
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Nat Rev Genet,
4,
432-441.
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J.H.Lin,
A.L.Perryman,
J.R.Schames,
and
J.A.McCammon
(2003).
The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme.
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Biopolymers,
68,
47-62.
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L.Cristian,
J.D.Lear,
and
W.F.DeGrado
(2003).
Use of thiol-disulfide equilibria to measure the energetics of assembly of transmembrane helices in phospholipid bilayers.
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Proc Natl Acad Sci U S A,
100,
14772-14777.
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M.Brown
(2003).
A tale of two necessities: breakaway technology versus diabetes.
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Drug Discov Today,
8,
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M.Congreve,
R.Carr,
C.Murray,
and
H.Jhoti
(2003).
A 'rule of three' for fragment-based lead discovery?
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Drug Discov Today,
8,
876-877.
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M.R.Arkin,
M.Randal,
W.L.DeLano,
J.Hyde,
T.N.Luong,
J.D.Oslob,
D.R.Raphael,
L.Taylor,
J.Wang,
R.S.McDowell,
J.A.Wells,
and
A.C.Braisted
(2003).
Binding of small molecules to an adaptive protein-protein interface.
|
| |
Proc Natl Acad Sci U S A,
100,
1603-1608.
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PDB codes:
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D.W.Byerly,
C.A.McElroy,
and
M.P.Foster
(2002).
Mapping the surface of Escherichia coli peptide deformylase by NMR with organic solvents.
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Protein Sci,
11,
1850-1853.
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G.M.Verkhivker,
D.Bouzida,
D.K.Gehlhaar,
P.A.Rejto,
S.T.Freer,
and
P.W.Rose
(2002).
Complexity and simplicity of ligand-macromolecule interactions: the energy landscape perspective.
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Curr Opin Struct Biol,
12,
197-203.
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M.van Dongen,
J.Weigelt,
J.Uppenberg,
J.Schultz,
and
M.Wikström
(2002).
Structure-based screening and design in drug discovery.
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Drug Discov Today,
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P.De Meyts,
and
J.Whittaker
(2002).
Structural biology of insulin and IGF1 receptors: implications for drug design.
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Nat Rev Drug Discov,
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W.L.DeLano
(2002).
Unraveling hot spots in binding interfaces: progress and challenges.
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Curr Opin Struct Biol,
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A.G.Cochran
(2001).
Protein-protein interfaces: mimics and inhibitors.
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Curr Opin Chem Biol,
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K.C.Nicolaou,
R.Hughes,
S.Y.Cho,
N.Winssinger,
H.Labischinski,
and
R.Endermann
(2001).
Synthesis and biological evaluation of vancomycin dimers with potent activity against vancomycin-resistant bacteria: target-accelerated combinatorial synthesis.
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Chemistry,
7,
3824-3843.
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P.H.Carter,
P.A.Scherle,
J.K.Muckelbauer,
M.E.Voss,
R.Q.Liu,
L.A.Thompson,
A.J.Tebben,
K.A.Solomon,
Y.C.Lo,
Z.Li,
P.Strzemienski,
G.Yang,
N.Falahatpisheh,
M.Xu,
Z.Wu,
N.A.Farrow,
K.Ramnarayan,
J.Wang,
D.Rideout,
V.Yalamoori,
P.Domaille,
D.J.Underwood,
J.M.Trzaskos,
S.M.Friedman,
R.C.Newton,
C.P.Decicco,
and
J.A.Muckelbauer
(2001).
Photochemically enhanced binding of small molecules to the tumor necrosis factor receptor-1 inhibits the binding of TNF-alpha.
|
| |
Proc Natl Acad Sci U S A,
98,
11879-11884.
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PDB code:
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P.J.Alaimo,
M.A.Shogren-Knaak,
and
K.M.Shokat
(2001).
Chemical genetic approaches for the elucidation of signaling pathways.
|
| |
Curr Opin Chem Biol,
5,
360-367.
|
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
