Citations in PubMed

Primary Citation PubMed: 10559988 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 21

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

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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Inferring protein domain interactions from databases of interacting proteins.

(2005) Genome Biol 6

PubMed: 16207360 | PubMedCentral: PMC1257472 | DOI: 10.1186/gb-2005-6-10-r89

As another example, Cyclin N-terminal domains [Pfam:PF00134, Cyclin_N] are known from structural studies [PDB: 1QMZ ] [ 35 ] to interact with protein kinase domains [Pfam:PF00069, Pkinase].

Publication Year: 2005

Computational analyses of the surface properties of protein-protein interfaces.

(2007) Acta Crystallogr D Biol Crystallogr 63

PubMed: 17164526 | PubMedCentral: PMC2483497 | DOI: 10.1107/S0907444906046762

( a ) A molecular surface is generated from the CDK2 chain in a structure of the CDK2–cyclin A complex (PDB code 1qmz ; Brown et al. , 1999 ▶ ).

Publication Year: 2007

Binding to DNA of the RNA-polymerase II C-terminal domain allows discrimination between Cdk7 and Cdk9 phosphorylation.

(2009) Nucleic Acids Res 37

PubMed: 19136461 | PubMedCentral: PMC2651791 | DOI: 10.1093/nar/gkn1061

Cdk7/CycH complex was modeled on pCdk2/CycA structure (PDB 1QMZ) using Cdk7 and CycH structures (PDB 1UA2 and 1KXU).

CTD/DNA complex was docked into Cdk7/CycH by superimposing 5 SP 6 to the corresponding amino acids of the substrate peptide co-crystallized with pCdk2/CycA (PDB 1QMZ).

Publication Year: 2009

Insights into the conformational variability and regulation of human Nek2 kinase.

(2009) J Mol Biol 386

PubMed: 19124027 | PubMedCentral: PMC2741569 | DOI: 10.1016/j.jmb.2008.12.033

(a) Superposition of nucleotide-binding clefts of two inactive kinase conformations [Nek2-T175A ATPγS (yellow) and ATP-bound Cdk2 (cyan, Protein Data Bank code 1B39 )] and two active kinase co... formations [ADP-bound Aurora-A (magenta, Protein Data Bank code 1OL5 ) and ATP-bound Cdk2 (blue, Protein Data Bank code 1QMZ )].

Publication Year: 2009

The interwinding nature of protein-protein interfaces and its implication for protein complex formation.

(2009) Bioinformatics 25

PubMed: 19789269 | PubMedCentral: PMC2778332 | DOI: 10.1093/bioinformatics/btp563

The maximum SF values of the two fragments, namely Ile35-Val44 and Leu148-Glu162 (PDB ID: 1QMZ chain A), are 1.14 and 0.97, respectively, which are high, although below the cutoff of 1.25 used here.

Publication Year: 2009

A model of a MAPK?substrate complex in an active conformation: a computational and experimental approach.

(2011) PLoS One 6

PubMed: 21494553 | PubMedCentral: PMC3073974 | DOI: 10.1371/journal.pone.0018594

In addition, the proline in the Thr-Pro motif was restrained to adopt a similar binding mode to that in Ser-Pro motif of HHASPRK bound to the cyclin-dependent kinase (CDK2) (PDB ID: 1QMZ).

Publication Year: 2011

Cofactor-mediated conformational control in the bifunctional kinase/RNase Ire1.

(2011) BMC Biol 9

PubMed: 21729334 | PubMedCentral: PMC3158555 | DOI: 10.1186/1741-7007-9-48

Coordinates are from PDB ID: 1hcl (apo-CDK2), 1b39 (ATP-bound CDK2), 1qmz (ATP-bound CDK2 with cyclin) and 1gy3 (ADP-bound CDK2 with cyclin).

Publication Year: 2011

Fluorescent peptide biosensor for probing the relative abundance of cyclin-dependent kinases in living cells.

(2011) PLoS One 6

PubMed: 22028905 | PubMedCentral: PMC3196589 | DOI: 10.1371/journal.pone.0026555

A. Sequence and schematic representation of CDKSENS together with the crystal structures of CDK2/cyclin A/HHASPRK peptide substrate (PDB 1QMZ) and CDK2/cyclin A/p107 RRLFGE peptide (PDB 1H28).

Publication Year: 2011

Structural and evolutionary divergence of eukaryotic protein kinases in Apicomplexa.

(2011) BMC Evol Biol 11

PubMed: 22047078 | PubMedCentral: PMC3239843 | DOI: 10.1186/1471-2148-11-321

In a solved structure of human Cdk2 [PDB: 1QMZ ], the residue V164, equivalent to C258 in Pfcrk-5, is located spatially between the bound substrate and the APE motif.

Publication Year: 2011

Design principles underpinning the regulatory diversity of protein kinases.

(2012) Philos Trans R Soc Lond B Biol Sci 367

PubMed: 22889905 | PubMedCentral: PMC3415841 | DOI: 10.1098/rstb.2012.0015

The structures used for generating the alignment are: CDK (1QMZ) [ 35 ], PKA (1ATP) [ 36 ], EGFR (2GS2) [ 37 ], choK or choline kinase (2IG7), APH or aminoglycoside kinase (3R78), fruK or fructosamine... kinase (3F7W), HSK or homoserine kinase (1FWK) [ 38 ], Rio kinase (1ZP9) [ 39 ], CHAK or TRP channel kinase (1IA9) [ 40 ], PI3K or phosphoinositide kinase (3T8M) and actinK or actin–fragmin kinase (1CJA) [ 26 ].

The structure figures were generated in PyMOL based on the crystal structure of cyclin-dependent kinase (pdb: 1QMZ).

Publication Year: 2012

Price to be paid for two-metal catalysis: magnesium ions that accelerate chemistry unavoidably limit product release from a protein kinase.

(2012) J Am Chem Soc 134

PubMed: 22891849 | PubMedCentral: PMC3446636 | DOI: 10.1021/ja304419t

The backbone rmsd from ADP·2Mg structure to 1JST (a complex with ATPγS·Mn 2+ ) = 1.24 Å, 1QMZ (AMPPNP·Mg 2+ /peptide) = 0.65 Å, 3QHR (ADP·2Mg/Mg... 3 – /peptide TS) = 0.57 Å.

(C) Two Mg 2+ ions are identified in the ADP·2Mg structure (maroon) but not ATPγS-bound pCDK2 (gray, 1JST) 3 or AMPPNP-bound pCDK2 (black, 1QMZ).

Publication Year: 2012

The CDK9 tail determines the reaction pathway of positive transcription elongation factor b.

(2012) Structure 20

PubMed: 22959624 | PubMedCentral: PMC3469819 | DOI: 10.1016/j.str.2012.08.011

Modeling of a CDK9/Cyclin T/Substrate Complex The polypeptide backbone of the CDK9 FL /cyclin T 259 /DRB and CDK2/cyclin A/peptide (1QMZ) complexes were superimposed on the C-terminal kinase domain (r... sidues 111–315 and 88–286, respectively) and the substrate peptide was copied into the CDK9/cyclin T 259 structure.

Publication Year: 2012

Comparative structural and functional studies of 4-(thiazol-5-yl)-2-(phenylamino)pyrimidine-5-carbonitrile CDK9 inhibitors suggest the basis for isotype selectivity.

(2013) J Med Chem 56

PubMed: 23252711 | PubMedCentral: PMC3579457 | DOI: 10.1021/jm301495v

(D) Detail of the conformational change induced by the binding of 3 and 12t (cylinder representation) on CDK2/cyclin A (blue ribbon representation), relative to CDK2/cyclin A in the absence of inhibit... r (PDB code 1QMZ , yellow ribbon representation).

(B) The protein conformations in representative novel CDK2/cyclin A/inhibitor structures (blue ribbon representations) are compared with that of CDK2/cyclin A in the absence of inhibitor (PDB code 1QMZ , yellow ribbon representation).

Publication Year: 2013

A structure-guided approach for protein pocket modeling and affinity prediction.

(2013) J Comput Aided Mol Des 27

PubMed: 24214361 | PubMedCentral: PMC3851759 | DOI: 10.1007/s10822-013-9688-9

Figure  2 shows the cognate ligands of these structures (molecules 4–9 , respectively corresponding to 1QMZ, 1KE6, 1KE8, 1JVP, and 1H07).

PDB codes of the pool of protein structures considered for model guidance in the CDK2 study: 1AQ1, 1FVT, 1FVV, 1GIH, 1B38, 1B39, 1FIN, 1FQ1, 1GY3, 1HCK, 1JST, 1QMZ, 1H08, 1DI8, 1H01, 1H00, 1E9H, 1JVP, 1KE5, 1KE6, 1KE7, 1KE8, 1KE9, 1H07, 1E1X, 1JSV 26.

Publication Year: 2013

Structural basis of GSK-3 inhibition by N-terminal phosphorylation and by the Wnt receptor LRP6.

(2014) Elife 3

PubMed: 24642411 | PubMedCentral: PMC3953950 | DOI: 10.7554/eLife.01998

Superposition of the GSK-3/LRP6 c-motif structure with the ( A ) PKA:PKI peptide (PDB 1L3R); ( B ) CDK2:p107 peptide (PDB 1QMZ); ( C ) AKT:GSK-3 peptide (PDB 3CQU); and ( D ) DYRK:consensus peptide (P... B 2WO6) substrate complexes.

Publication Year: 2014

An inhibitor's-eye view of the ATP-binding site of CDKs in different regulatory states.

(2014) ACS Chem Biol 9

PubMed: 24669831 | PubMedCentral: PMC4068217 | DOI: 10.1021/cb500135f

The CDK2 ATP-binding site residues from a pCDK2/A structure (PDB code: 1QMZ) are colored according to the degree of sequence conservation between the 4 CDK sequences, calculated as described in the Su... plementary Methods , from blue (highly conserved) to red (highly variable).

Publication Year: 2014

Quantitative network mapping of the human kinome interactome reveals new clues for rational kinase inhibitor discovery and individualized cancer therapy.

(2014) Oncotarget 5

PubMed: 25003367 | PubMedCentral: PMC4116514 | DOI: 10.18632/oncotarget.1984

(B) A substrate peptide binding pocket of CDK2 (PDB ID: 1QMZ).

Publication Year: 2014

Exploiting holistic approaches to model specificity in protein phosphorylation.

(2014) Front Genet 5

PubMed: 25324856 | PubMedCentral: PMC4179730 | DOI: 10.3389/fgene.2014.00315

The structures from left to right show IR in complex with a peptide (pdb 1IR3), CDK2 in complex with a substrate peptide and cyclin A (pdb 1QMZ), which contributes to peptide specificity with a negati... e charged surface shown in the upper right of the figure, and PKA in complex with a peptide inhibitor (pdb 3FJQ).

Publication Year: 2014

Cross-talk of phosphorylation and prolyl isomerization of the C-terminal domain of RNA Polymerase II.

(2014) Molecules 19

PubMed: 24473209 | PubMedCentral: PMC4350670 | DOI: 10.3390/molecules19021481

( A ) Phosphorylated CDK2 (green) at its activation loop on T160 shown with its substrate HHASPRK (yellow) where P+1 position is occupied by proline (PDB ID: 1QMZ) [ 87 ].

Publication Year: 2014

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4370755

A) Structural alignment of MAPK β4-β5 loop with representative canonical CMGC kinase, where orange denotes Casen Kinase II (CK2) (PDBID: 1JWH), green denotes cyclin dependent kinase (C... K) (PDBID: 1QMZ), and blue denotes MAPK with insert colored in cyan with rectangle representation (PDBID: 4LOO).

Publication Year: 2015

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4381256

( A ) Structural representation of CDK2; ( B ) Structural representation of CDK2/Cyclin A complex (PDB: 1QMZ); ( C ) Structural representation of phospho Thr160-CDK2/Cyclin A; ( D ) Structural represe... tation of phospho Thr160-CDK2/Cyclin A bound to a peptide substrate.

( A ) Structure and inhibitors of CDK2/Cyclin A PDB: 1QMZ; ( B ) Structure and inhibitors of CDK4/Cyclin D PDB 3G33 [CycD3]; ( C ) Structure and inhibitors of CDK5/p25.

Publication Year: 2015