Citations in PubMed

Primary Citation PubMed: 12861225 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 12

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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Rapid birth-death evolution specific to xenobiotic cytochrome P450 genes in vertebrates.

(2007) PLoS Genet 3

PubMed: 17500592 | PubMedCentral: PMC1866355 | DOI: 10.1371/journal.pgen.0030067

Accession Numbers The Protein Data Base ( ) number for the structure discussed in this paper is 1OG5.

Publication Year: 2007

The role of hydrophobic interactions in positioning of peripheral proteins in membranes.

(2007) BMC Struct Biol 7

PubMed: 17603894 | PubMedCentral: PMC1934363 | DOI: 10.1186/1472-6807-7-44

Protein Category Conformation 1 a Conformation 2 a PDB id Δ G calc D τ PDB id Δ G calc D τ Signal peptidase A.1 1kn9 -4.5 4.5 83 1t7d -5.9 3.7 66 Cytochrome P450 2b4 A.... 1po5 -6.9 9.7 39 2bdm -18.2 10.5 45 Cytochrome P450 2c5 A.1 1nr6 -11.6 12.5 54 1dt6 -8.4 7.5 17 Cytochrome P450 2c9 A.1 1og5 -13.6 7.5 74 1r9o -10.7 7.5 57 Cytochrome P450 3a4 A.1 1tqn -20.7 10.2 61 1w0f -15.2 6.2 68 Bile-salt activated lipase C.1 1aql -9.7 6.0 80 1akn -6.6 5.7 67 Triacylglycerol lipase C.1 1tib -3.3 1.9 42 1dt5 -4.8 2.9 84 Lipase/colipase complex C.1 1lpa -22.1 8.7 89 1lpb -26.2 10.3 87 Ganglioside GM2 activator C.2 1tjj -9.3 4.6 55 1pub -7.8 5.2 44 Phosducin/βγ complex C.3 1a0r -3.7 2.7 45 2trc -2.9 4.4 64 Tubby protein C.4 1c8z -4.2 6.2 87 1i7e -3.6 2.6 78 a All structures were solved by X-ray crystallography.

Publication Year: 2007

Construction of 3D models of the CYP11B family as a tool to predict ligand binding characteristics.

(2007) J Comput Aided Mol Des 21

PubMed: 17646925 | PubMedCentral: PMC2039848 | DOI: 10.1007/s10822-007-9128-9

Glu310 coincides with an aspartic acid in the CYP2 family which from visual inspection of the crystal structures of CYP2C5 (pdb-code 1NR6) and CYP2C9 (pdb-code 1OG5) seems to play a specific stabilisi... g role in the active site structure; it is expected that Glu310 has the same stabilising role.

Publication Year: 2007

SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions.

(2010) Nucleic Acids Res 38

PubMed: 19934256 | PubMedCentral: PMC2808967 | DOI: 10.1093/nar/gkp970

Overview of the coverage of the CYP-classes with experimentally determined structures CYP PDB-ID 1A2 2hi4 2A6 1z10, 1z11, 1fdu, 2fdv, 2fdw, 2fdy, 2pg5, 2pg6, 2pg7 2A13 2p85 2C8 1pq2, 2nni, 2vn0 2C9 1o... 2, 1og5, 1r9o 2D6 2f9q 2R1 3c6g 3A4 1w0e, 1w0f, 1w0g, 1tqn, 2j0d, 2v0m 8A1 2iag With 1170 drugs and ∼3800 interactions, SuperCYP provides the largest number of CYP relations and corresponding information available online.

Publication Year: 2010

Bioactivities of berberine metabolites after transformation through CYP450 isoenzymes.

(2011) J Transl Med 9

PubMed: 21569619 | PubMedCentral: PMC3103436 | DOI: 10.1186/1479-5876-9-62

Structure-based BBR-CYP450 docking analysis The crystal structures of the six CYP450 isoforms were retrieved from the Protein Data Bank (PDB ID code 2HI4 for CYP1A2, solved at 1.95-Å resolutio... [ 12 ]; 1Z11 for CYP2A6, 2.05-Å [ 13 ]; 1OG5 for CYP2C9, 2.55-Å [ 14 ]; 2F9Q for CYP2D6, 3.00-Å [ 15 ]; 3E4E for CYP2E1, 2.60-Å [ 16 ]; 1TQN for CYP3A4, 2.05-Å [ 17 , 18 ]).

Publication Year: 2011

A comparative reverse docking strategy to identify potential antineoplastic targets of tea functional components and binding mode.

(2011) Int J Mol Sci 12

PubMed: 21954353 | PubMedCentral: PMC3179160 | DOI: 10.3390/ijms12085200

PDB_ID Target Name Predicted by Procedures Implicated by Experiment Energy Score (kcal/mol) Reference or Related Disease 3BCH 67 kD laminin receptor Autodock YES −3.75 [ 2 ] 7HVP HIV protease ... utodock/Tarfisdock YES −5.01/−44.87 [ 18 ] 1GRE glutathione reductase Autodock YES −6.80 [ 19 , 20 ] 1IJH cholesterol oxidase Autodock YES −6.77 [ 21 ] 8CAT catalase Autodock YES −6.23 [ 22 ] 1JNY eEF1-α Autodock YES −5.70 [ 3 ] 1BOO DNA methyltransferase Autodock YES −4.66 [ 23 ] 2OZO ZAP-70 Autodock YES −3.81 [ 24 ] 2DQ7 Fyn kinase Autodock YES −4.91 [ 25 ] 1HS6 Leukotriene A4 Autodock/Tarfisdock NO −5.22/−48.2 Esophagus cancer 1FT2 Farnesyl protein transferase Autodock/Tarfisdock NO −4.1/−44.94 Cancer/Tumour 1UTR Mammalian PCB-binding protein Autodock NO −7.19 Lung Cancer 1JVM Voltage-Gated Potassium Channel Autodock NO −6.58 Cardiomyopathie 1OG5 CYP450 Autodock NO −6.49 Tumour 1VKG Histone deacetylase Autodock NO −5.63 Tumour 1OOQ Dihyrofolate reductase Tarfisdock NO −46.42 Tumour 1IYH Hematopoietic Prostagladin Synthase Tarfisdock NO −44.50 Cancer 1PY5 TGF-beta receptor type I Tarfisdock NO −44.33 Renal carcinoma Table 2.

Publication Year: 2011

Does compound I vary significantly between isoforms of cytochrome P450?

(2011) J Am Chem Soc 133

PubMed: 21863858 | PubMedCentral: PMC3180200 | DOI: 10.1021/ja203157u

Table 1 Residues in P450 cam , CYP2C9, CYP2D6, and CYP3A4 (Res n +1 , Res n +2 , and Res n +3 ) Involved in the Hydrogen-Bond Network Surrounding the Fe-Bound Cysteinate (Res n ) a isoform PDB code Re... n Res n +1 Res n +2 Res n +3 P450 cam 1DZ9 Cys357 Leu358 Gly359 Gln360 CYP2C9 1OG5 Cys435 Val436 Gly437 Glu438 CYP2D6 2F9Q Cys443 Leu444 Gly445 Glu446 CYP3A4 1TQN Cys442 Ile443 Gly444 Met445 a The numbering of the residues corresponds to the crystal structures 1DZ9 ,( 25 ) 1OG5 ,( 26 ) 2F9Q ,( 27 ) and 1TQN .

Three separate simulations were carried out that originated from the 1OG5 crystal structure.

The second simulation, referred to as 2C9_2warf , used the 1OG5 structure with a second molecule of S -warfarin docked into the active site, directly above Cpd I, in a position favoring oxidation at the C7 position.

Figure 2 Residues surrounding the cysteinate sulfur in the crystal structures of P450 cam ( 1DZ9 , green), CYP2C9 ( 1OG5 , black), CYP2D6 ( 2F9Q , blue), and CYP3A4 ( 1TQN , red).

Two crystal structures, both obtained by Williams et al.,( 43 ) were used for the calculations on CYP2C9; the 1OG2 structure was used for simulating CYP2C9 in the absence of substrate, while the 1OG5 structure was used for all simulations containing the substrate S -warfarin.

Publication Year: 2011

Membrane position of ibuprofen agrees with suggested access path entrance to cytochrome P450 2C9 active site.

(2011) J Phys Chem A 115

PubMed: 21744854 | PubMedCentral: PMC3257864 | DOI: 10.1021/jp204488j

Right panel shows RMSF per residue for simulations of wt CYP2C9 in membrane (black line), wt CYP2C9 in water (green line), CYP2C9 based on crystal structure 1OG2 (without N-terminal anchor) in water (... ed line), as well as RMSF calculated from the B-factors of crystals structures 1OG2 and 1OG5 (cyan and blue lines, respectively).

PPM 2.0 protein membrane positioning approach for 1OG5 from OPM database ( 23 ) (blue), and the same PPM 2.0 approach applied to on our wt CYP2C9 model with the N-terminal anchor present (white).

Publication Year: 2011

Quantum mechanics/molecular mechanics modeling of regioselectivity of drug metabolism in cytochrome P450 2C9.

(2013) J Am Chem Soc 135

PubMed: 23641937 | PubMedCentral: PMC3670427 | DOI: 10.1021/ja402016p

31 There are significant differences between the 1R9O and 1OG5 crystal structures, most notably the conformation of the Arg108 side chain, which points in toward the active site in 1R9O, and hydrogen-... onds to the carboxylic acid group of flurbiprofen.

The 1OG2 and 1OG5 structures correspond to the apo form and a complex containing S -warfarin, respectively.

The coordinates of S -warfarin were taken from the 1OG5 crystal structure and hydrogen atoms were added.

Publication Year: 2013

Distal effect of amino acid substitutions in CYP2C9 polymorphic variants causes differences in interatomic interactions against (S)-warfarin.

(2013) PLoS One 8

PubMed: 24023924 | PubMedCentral: PMC3759441 | DOI: 10.1371/journal.pone.0074053

Construction of WT, R144C, I359L, and L90P structures Ligand-bound crystal structure of CYP2C9 (PDB: 1OG5 [23] ) was used as a starting structure for construction of substrate-free forms of wild-type ... WT) and mutants (R144C, I359L, and L90P).

Re-docking of (S)-warfarin in WT In ( S )-warfarin-bound complex (PDB: 1OG5), ( S )-warfarin is located approximately 10 Å away from the heme center and is not in a catalytically productive orientation for monooxygenation reaction [25] .

Results Re-docking of (S)-warfarin ( S )-warfarin was re-docked into binding pocket of WT as the orientation of ( S )-warfarin in the X-ray crystal structure of CYP2C9 (PDB ID: 1OG5) might not result in catalytic activity of CYP2C9.

Overall structural conformations retained structurally conserved features of CYPs, and low deviation from 1OG5 was observed as RMSD of stable trajectories was less than 2 Å.

Therefore, three-dimensional structure of ( S )-warfarin obtained from 1OG5 was applied in re-docking for a putative catalytic conformation of ( S )-warfarin in active-site cavity of WT that could yield a major metabolite 7-hydroxywarfarin [26] , using AutoDock 4.0 [27] .

Publication Year: 2013

In Silico Investigation of Cytochrome P450 2C9 in relation to Aging Using Traditional Chinese Medicine.

(2014) Evid Based Complement Alternat Med 2014

PubMed: 24899908 | PubMedCentral: PMC4034651 | DOI: 10.1155/2014/404505

The sequence of CYP2C9 was generated from Uniprot ( , CYP2C9_HUMAN, P11712) and the 3D crystal structure (PDB: 1OG5) was downloaded from the Protein Data Bank ( http://www.rcsb... org/pdb/home/ ).

Publication Year: 2014

Ensemble generation and the influence of protein flexibility on geometric tunnel prediction in cytochrome P450 enzymes.

(2014) PLoS One 9

PubMed: 24956479 | PubMedCentral: PMC4067289 | DOI: 10.1371/journal.pone.0099408

Methods MD Simulations High resolution CYP crystal structures where both the apo and holo forms were available were selected for this study; CYP119 (apo: 1IO9, resolution 2.05 Å and holo: 1F4T... resolution 1.93 Å), CYP2C9 (apo: 1OG2, resolution 2.60 Å and holo: 1OG5, resolution 2.55 Å), and CYP3A4 (apo: 4I3Q, resolution 2.60 Å and holo: 3UA1, resolution 2.15 Å).

For example in the case of the pseudo-apo ensemble the original ensemble is the true-holo ensemble because both were derived from the 1OG5 crystal structure.

Publication Year: 2014