Primary Citation PubMed: 11335721
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Prediction of calcium-binding sites by combining loop-modeling with machine learning.
(2009) BMC Struct Biol 9
PubMed: 20003365 | PubMedCentral: PMC2808310 | DOI: 10.1186/1472-6807-9-72
The RMSDs of the rebuilt loop of 1GIH to the 15 experimentally solved loop structures of others CDK2 range from 1 to 6 Å, suggesting that we have modeled reasonable loop conformations.
1GIH and 1U5R both possess a typical protein kinase two-domain architecture.
A close-up view of Figure 4 shows that the rebuilt loop of 1GIH forms microenvironments suitable for calcium binding.
Figure 4 The predicted calcium-binding site in the structure of human cell division protein kinase 2 (PDB ID: 1GIH ) and the experimentally observed site in the structural homolog of 1GIH .
The counterparts of unstructured loop 149-164 ( 1GIH ) in 1U5R are residues 174-183, which constitute the activation loop of 1U5R .
1GIH binds to 1PU (sphere colored by element, gray blue for carbon, dark blue for nitrogen, and red for oxygen) .
The human cyclin-dependent protein kinase 2 (CDK2) (PDB ID: 1GIH ) binds to 1PU (1-(5-OXO-2,3,5,9B-TETRAHYDRO-1H-PYRROLO [2,1-A]ISOINDOL-9-YL)-3-PYRIDIN-2-YL-UREA) [ 24 ].
A structural homolog of 1GIH is the structure of rat TAO2 (a mitogen-activated protein kinase kinase kinase) in complex with MgATP (PDB ID: 1U5R ).
We modeled and scanned the other 15 loops and identified three calcium-binding sites ( 1GIH , 1GIJ and 1G5S ).
The PRA between 1GIH and 1U5R is 81%.
In our predictions, we have predicted that calcium binding regulates the binding of 1PU or other consequent activity changes to the cell division protein kinase 2 ( 1GIH ) (see the Results).
Publication Year: 2009
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
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
Insight into the interactions between novel isoquinolin-1,3-dione derivatives and cyclin-dependent kinase 4 combining QSAR and molecular docking.
(2014) PLoS One 9
PubMed: 24722522 | PubMedCentral: PMC3983096 | DOI: 10.1371/journal.pone.0093704
g007 Figure 7 The binding mode between selected compound 12 and the ATP pocket of CDK4 (PDB code: 1GIH).
The crystal structure of CDK4 with ligand 1GIH was retrieved from the RCSB Protein Data Bank  .
Publication Year: 2014
PubMed ID is not available.
Published in 2015
PDB ID Resolution (Å) 1GZ8 1.30 1JVP 1.53 1H00 1.60 1OIT 1.60 1URW 1.60 1H01 1.79 1H08 1.80 1E1X 1.85 1H07 1.85 1H0V 1.90 1OIR 1.91 1E1V 1.95 1PXI 1.95 1JSV 1.96 1PXO 1.96 1AQ1 2.00 1GII 2.00 ... KE6 2.00 1KE7 2.00 1KE8 2.00 1KE9 2.00 1PYE 2.00 1R78 2.00 1CKP 2.05 1DM2 2.10 1H0W 2.10 1DI8 2.20 1FVT 2.20 1GIJ 2.20 1KE5 2.20 1W0X 2.20 1VYZ 2.21 1PXJ 2.30 1PXP 2.30 1OIQ 2.31 1V1K 2.31 1P2A 2.50 1PXL 2.50 1PXN 2.50 1PF8 2.51 1PXM 2.53 1G5S 2.61 1GIH 2.80 1PXK 2.80 The final score used to rank compounds was purposely designed to be the average score across these 44 structures of CDK2 so as to account for structural variability.
Publication Year: 2015
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