4ddr

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{{STRUCTURE_4ddr| PDB=4ddr | SCENE= }}
 
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===Human dihydrofolate reductase complexed with NADPH and P218===
 
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{{ABSTRACT_PUBMED_23035243}}
 
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==Disease==
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==Human dihydrofolate reductase complexed with NADPH and P218==
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[[http://www.uniprot.org/uniprot/DYR_HUMAN DYR_HUMAN]] Defects in DHFR are the cause of megaloblastic anemia due to dihydrofolate reductase deficiency (DHFRD) [MIM:[http://omim.org/entry/613839 613839]]. DHFRD is an inborn error of metabolism, characterized by megaloblastic anemia and/or pancytopenia, severe cerebral folate deficiency, and cerebral tetrahydrobiopterin deficiency. Clinical features include variable neurologic symptoms, ranging from severe developmental delay and generalized seizures in infancy, to childhood absence epilepsy with learning difficulties, to lack of symptoms.<ref>PMID:21310276</ref><ref>PMID:21310277</ref>
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<StructureSection load='4ddr' size='340' side='right'caption='[[4ddr]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[4ddr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DDR FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MMV:3-(2-{3-[(2,4-DIAMINO-6-ETHYLPYRIMIDIN-5-YL)OXY]PROPOXY}PHENYL)PROPANOIC+ACID'>MMV</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4ddr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ddr OCA], [https://pdbe.org/4ddr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ddr RCSB], [https://www.ebi.ac.uk/pdbsum/4ddr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ddr ProSAT]</span></td></tr>
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</table>
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== Disease ==
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[https://www.uniprot.org/uniprot/DYR_HUMAN DYR_HUMAN] Defects in DHFR are the cause of megaloblastic anemia due to dihydrofolate reductase deficiency (DHFRD) [MIM:[https://omim.org/entry/613839 613839]. DHFRD is an inborn error of metabolism, characterized by megaloblastic anemia and/or pancytopenia, severe cerebral folate deficiency, and cerebral tetrahydrobiopterin deficiency. Clinical features include variable neurologic symptoms, ranging from severe developmental delay and generalized seizures in infancy, to childhood absence epilepsy with learning difficulties, to lack of symptoms.<ref>PMID:21310276</ref> <ref>PMID:21310277</ref>
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== Function ==
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[https://www.uniprot.org/uniprot/DYR_HUMAN DYR_HUMAN] Key enzyme in folate metabolism. Contributes to the de novo mitochondrial thymidylate biosynthesis pathway. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis. Binds its own mRNA and that of DHFRL1.<ref>PMID:21876188</ref> <ref>PMID:12096917</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Malarial dihydrofolate reductase (DHFR) is the target of antifolate antimalarial drugs such as pyrimethamine and cycloguanil, the clinical efficacy of which have been compromised by resistance arising through mutations at various sites on the enzyme. Here, we describe the use of cocrystal structures with inhibitors and substrates, along with efficacy and pharmacokinetic profiling for the design, characterization, and preclinical development of a selective, highly efficacious, and orally available antimalarial drug candidate that potently inhibits both wild-type and clinically relevant mutated forms of Plasmodium falciparum (Pf) DHFR. Important structural characteristics of P218 include pyrimidine side-chain flexibility and a carboxylate group that makes charge-mediated hydrogen bonds with conserved Arg122 (PfDHFR-TS amino acid numbering). An analogous interaction of P218 with human DHFR is disfavored because of three species-dependent amino acid substitutions in the vicinity of the conserved Arg. Thus, P218 binds to the active site of PfDHFR in a substantially different fashion from the human enzyme, which is the basis for its high selectivity. Unlike pyrimethamine, P218 binds both wild-type and mutant PfDHFR in a slow-on/slow-off tight-binding mode, which prolongs the target residence time. P218, when bound to PfDHFR-TS, resides almost entirely within the envelope mapped out by the dihydrofolate substrate, which may make it less susceptible to resistance mutations. The high in vivo efficacy in a SCID mouse model of P. falciparum malaria, good oral bioavailability, favorable enzyme selectivity, and good safety characteristics of P218 make it a potential candidate for further development.
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==Function==
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Malarial dihydrofolate reductase as a paradigm for drug development against a resistance-compromised target.,Yuthavong Y, Tarnchompoo B, Vilaivan T, Chitnumsub P, Kamchonwongpaisan S, Charman SA, McLennan DN, White KL, Vivas L, Bongard E, Thongphanchang C, Taweechai S, Vanichtanankul J, Rattanajak R, Arwon U, Fantauzzi P, Yuvaniyama J, Charman WN, Matthews D Proc Natl Acad Sci U S A. 2012 Oct 16;109(42):16823-8. doi:, 10.1073/pnas.1204556109. Epub 2012 Oct 3. PMID:23035243<ref>PMID:23035243</ref>
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[[http://www.uniprot.org/uniprot/DYR_HUMAN DYR_HUMAN]] Key enzyme in folate metabolism. Contributes to the de novo mitochondrial thymidylate biosynthesis pathway. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis. Binds its own mRNA and that of DHFRL1.<ref>PMID:21876188</ref><ref>PMID:12096917</ref>
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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[[4ddr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DDR OCA].
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</div>
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<div class="pdbe-citations 4ddr" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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<references group="xtra"/><references/>
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*[[Dihydrofolate reductase 3D structures|Dihydrofolate reductase 3D structures]]
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[[Category: Dihydrofolate reductase]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Arwon, U.]]
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[[Category: Large Structures]]
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[[Category: Bongard, E.]]
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[[Category: Arwon U]]
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[[Category: Charman, S A.]]
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[[Category: Bongard E]]
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[[Category: Charman, W N.]]
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[[Category: Charman SA]]
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[[Category: Chitnumsub, P.]]
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[[Category: Charman WN]]
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[[Category: Fantauzzi, P.]]
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[[Category: Chitnumsub P]]
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[[Category: Kamchonwongpaisan, S.]]
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[[Category: Fantauzzi P]]
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[[Category: Matthews, D.]]
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[[Category: Kamchonwongpaisan S]]
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[[Category: McLennan, D N.]]
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[[Category: Matthews D]]
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[[Category: Rattanajak, R.]]
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[[Category: McLennan DN]]
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[[Category: Tarnchompoo, B.]]
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[[Category: Rattanajak R]]
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[[Category: Taweechai, S.]]
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[[Category: Tarnchompoo B]]
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[[Category: Thongphanchang, C.]]
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[[Category: Taweechai S]]
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[[Category: Vanichtanankul, J.]]
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[[Category: Thongphanchang C]]
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[[Category: Vilaivan, T.]]
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[[Category: Vanichtanankul J]]
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[[Category: Vivas, L.]]
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[[Category: Vilaivan T]]
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[[Category: White, K L.]]
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[[Category: Vivas L]]
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[[Category: Yuthavong, Y.]]
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[[Category: White KL]]
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[[Category: Yuvaniyama, J.]]
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[[Category: Yuthavong Y]]
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[[Category: Antifolate]]
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[[Category: Yuvaniyama J]]
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[[Category: Nadph]]
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[[Category: Oxidoreductase-oxidoreductase inhibitor complex]]
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Current revision

Human dihydrofolate reductase complexed with NADPH and P218

PDB ID 4ddr

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