Primary Citation PubMed: 16291688
Citations in PubMed
This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.
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.
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  ) and the closed-form structure (PDB code: 1ZUI  ) of HpSK, and the apo-form structure (PDB code: 2IYT  ) and the closed-form structure (P... B code: 1ZYU  ) of MtSK.
Publication Year: 2012
Structures of Helicobacter pylori shikimate kinase reveal a selective inhibitor-induced-fit mechanism.
PubMed: 22438938 | PubMedCentral: PMC3306394 | DOI: 10.1371/journal.pone.0033481
Structural comparisons Comparison with the six HpSK structures (PDB codes, 1ZUH  , 1ZUI  , 3HR7, 3MUF, 3MRS, 3N2E) and other SKs were carried out using the program LSQMAN in O  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  ; 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)  , 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)  to search for putative inhibitors  ,  in the Maybridge and NCI databases.
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  ) were aligned to their respective closed-form structures SDH (3PHI) and SK (1ZUI  ), using a structural alignme... t tool  .
Publication Year: 2013
RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics: Rutgers and UCSD/SDSC
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.