4pk5

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) complexed with Amg-1

Structural highlights

4pk5 is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.79Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

I23O1_HUMAN Catalyzes the cleavage of the pyrrol ring of tryptophan and incorporates both atoms of a molecule of oxygen.^[1]

Publication Abstract from PubMed

Indoleamine 2,3-dioxygenase 1 (IDO1) is considered as a promising target for the treatment of several diseases, including neurological disorders and cancer. We report here the crystal structures of two IDO1/IDO1 inhibitor complexes, one of which shows that Amg-1 is directly bound to the heme iron of IDO1 with a clear induced fit. We also describe the identification and preliminary optimization of imidazothiazole derivatives as novel IDO1 inhibitors. Using our crystal structure information and structure-activity relationships (SAR) at the pocket-B of IDO1, we found a series of urea derivatives as potent IDO1 inhibitors and revealed that generation of an induced fit and the resulting interaction with Phe226 and Arg231 are essential for potent IDO1 inhibitory activity. The results of this study are very valuable for understanding the mechanism of IDO1 activation, which is very important for structure-based drug design (SBDD) to discover potent IDO1 inhibitors.

Crystal Structures and Structure-Activity Relationships of Imidazothiazole Derivatives as IDO1 Inhibitors.,Tojo S, Kohno T, Tanaka T, Kamioka S, Ota Y, Ishii T, Kamimoto K, Asano S, Isobe Y ACS Med Chem Lett. 2014 Aug 21;5(10):1119-23. doi: 10.1021/ml500247w. eCollection, 2014 Oct 9. PMID:25313323^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Metz R, Duhadaway JB, Kamasani U, Laury-Kleintop L, Muller AJ, Prendergast GC. Novel tryptophan catabolic enzyme IDO2 is the preferred biochemical target of the antitumor indoleamine 2,3-dioxygenase inhibitory compound D-1-methyl-tryptophan. Cancer Res. 2007 Aug 1;67(15):7082-7. PMID:17671174 doi:http://dx.doi.org/10.1158/0008-5472.CAN-07-1872
↑ Tojo S, Kohno T, Tanaka T, Kamioka S, Ota Y, Ishii T, Kamimoto K, Asano S, Isobe Y. Crystal Structures and Structure-Activity Relationships of Imidazothiazole Derivatives as IDO1 Inhibitors. ACS Med Chem Lett. 2014 Aug 21;5(10):1119-23. doi: 10.1021/ml500247w. eCollection, 2014 Oct 9. PMID:25313323 doi:http://dx.doi.org/10.1021/ml500247w

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4pk5"

Categories: Homo sapiens | Large Structures | Ishii T | Kohno T | Tojo S

@@ Line 1: / Line 1: @@
 ==Crystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) complexed with Amg-1==
-<StructureSection load='4pk5' size='340' side='right' caption='[[4pk5]], [[Resolution|resolution]] 2.79&Aring;' scene=''>
+<StructureSection load='4pk5' size='340' side='right'caption='[[4pk5]], [[Resolution|resolution]] 2.79&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4pk5]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PK5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PK5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4pk5]] is a 2 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=4PK5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PK5 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PKJ:N-(1,3-BENZODIOXOL-5-YL)-2-{[5-(4-METHYLPHENYL)[1,3]THIAZOLO[2,3-C][1,2,4]TRIAZOL-3-YL]SULFANYL}ACETAMIDE'>PKJ</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.79&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4pk6|4pk6]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PKJ:N-(1,3-BENZODIOXOL-5-YL)-2-{[5-(4-METHYLPHENYL)[1,3]THIAZOLO[2,3-C][1,2,4]TRIAZOL-3-YL]SULFANYL}ACETAMIDE'>PKJ</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Indoleamine_2,3-dioxygenase Indoleamine 2,3-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.52 1.13.11.52] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4pk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pk5 OCA], [https://pdbe.org/4pk5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pk5 RCSB], [https://www.ebi.ac.uk/pdbsum/4pk5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pk5 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4pk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pk5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4pk5 RCSB], [http://www.ebi.ac.uk/pdbsum/4pk5 PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/I23O1_HUMAN I23O1_HUMAN]] Catalyzes the cleavage of the pyrrol ring of tryptophan and incorporates both atoms of a molecule of oxygen.<ref>PMID:17671174</ref>
+[https://www.uniprot.org/uniprot/I23O1_HUMAN I23O1_HUMAN] Catalyzes the cleavage of the pyrrol ring of tryptophan and incorporates both atoms of a molecule of oxygen.<ref>PMID:17671174</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4pk5" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Indoleamine 2,3-dioxygenase]]
+[[Category: Homo sapiens]]
-[[Category: Ishii, T]]
+[[Category: Large Structures]]
-[[Category: Kohno, T]]
+[[Category: Ishii T]]
-[[Category: Tojo, S]]
+[[Category: Kohno T]]
-[[Category: 3-dioxygenagse 1]]
+[[Category: Tojo S]]
-[[Category: Imidazothiazole]]
-[[Category: Indoleamine 2]]
-[[Category: Induced fit]]
-[[Category: Oxidoreductase-oxidoreductase inhibitor complex]]
-[[Category: Structure based drug discovery]]

4pk5

From Proteopedia

Current revision

Crystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) complexed with Amg-1

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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