Citations in PubMed

Primary Citation PubMed: 16291688 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 3

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Core site-moiety maps reveal inhibitors and binding mechanisms of orthologous proteins by screening compound libraries.

(2012) PLoS One 7

PubMed: 22393385 | PubMedCentral: PMC3290551 | DOI: 10.1371/journal.pone.0032142

They were the apo-form structure (PDB code: 1ZUH [19] ) and the closed-form structure (PDB code: 1ZUI [19] ) of HpSK, and the apo-form structure (PDB code: 2IYT [21] ) and the closed-form structure (P... B code: 1ZYU [24] ) of MtSK.

Publication Year: 2012

Structures of Helicobacter pylori shikimate kinase reveal a selective inhibitor-induced-fit mechanism.

(2012) PLoS One 7

PubMed: 22438938 | PubMedCentral: PMC3306394 | DOI: 10.1371/journal.pone.0033481

Structural comparisons Comparison with the six HpSK structures (PDB codes, 1ZUH [33] , 1ZUI [33] , 3HR7, 3MUF, 3MRS, 3N2E) and other SKs were carried out using the program LSQMAN in O [46] to superimp... se Cα atoms, based on the optimized alignment.

A distinctive induced-fit conformational change of the inhibitor complex Superposition of various structures (HpSK•SO 4 open form; HpSK•shikimate•PO 4 , PDB code 1ZUI [33] ; HpSK•S3P•ADP and E114A•162535) reveals a significant conformational change in the LID-containing segment after the β4 region of the CORE domain (residues 101–138; α5, LID and α6 regions; Fig. 2 ).

Based on the HpSK·shikimate·PO 4 structure (1ZUI) [33] , shikimate binds to residues from three subsites: (i) C X , where a carboxyl moiety of shikimate makes contact with R57, R116, and R132; (ii) O CORE , where two hydroxyl groups of shikimate make contact with M10, D33, G79–G81, and E114; and (iii) O LID , where a trans hydroxyl group of shikimate interacts with V44, F48, E114, and R116.

(A–D) The binding pockets of HpSK: (A) open HpSK (3HR7), (B) HpSK·shikimate·PO 4 (1ZUI), (C) HpSK·S3P·ADP (3MUF), and (D) E114A·162535 (3N2E).

Comparison by ITC of the association between wild-type or mutant HpSKs with shikimate or the inhibitor, NSC162535 Using GEMDOCK docking algorithms, we modeled a pocket that consists of the crucial SB residues (D33, F48, R57, R116, R132) involved in catalysis, based on the HpSK·shikimate·PO 4 structure (1ZUI) [33] to search for putative inhibitors [37] , [38] in the Maybridge and NCI databases.

Publication Year: 2012

Pathway-based screening strategy for multitarget inhibitors of diverse proteins in metabolic pathways.

(2013) PLoS Comput Biol 9

PubMed: 23861662 | PubMedCentral: PMC3701698 | DOI: 10.1371/journal.pcbi.1003127

For defining binding sites, the apo-form structures of SDH (3PHG) and SK (1ZUH [19] ) were aligned to their respective closed-form structures SDH (3PHI) and SK (1ZUI [19] ), using a structural alignme... t tool [38] .

Publication Year: 2013