Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 11

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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Using sequence similarity networks for visualization of relationships across diverse protein superfamilies.

(2009) PLoS One 4

PubMed: 19190775 | PubMedCentral: PMC2631154 | DOI: 10.1371/journal.pone.0004345

The sequences that are associated with or that are extremely similar to high resolution structures are noted [PDB identifiers 1F88 [22] , 2VT4 [23] , 3EML �... 5b;26] , 2RH1 [24] , and 2R4R [25] ].

Publication Year: 2009


Tuning microbial hosts for membrane protein production.

(2009) Microb Cell Fact 8

PubMed: 20040113 | PubMedCentral: PMC2807855 | DOI: 10.1186/1475-2859-8-69

Protein Expression Host PDB coordinates Resolution (Å) Reference TRANSMEMBRANE PROTEINS: BETA-BARREL Beta-Barrel Membrane Proteins: Mitochondrial Outer Membrane Human VDAC-1 voltage dependent ... nion channel E. coli 2K4T 1 , 2JK4 2 4 [ 210 , 211 ] Murine VDAC-1 voltage dependent anion channel E. coli 3EMN 2.3 [ 212 ] TRANSMEMBRANE PROTEINS: ALPHA-HELICAL G Protein-Coupled Receptors Rhodopsin: Bovine Rod Outer Segment mutant N2C/D282C COS cells 2J4Y 3.4 [ 122 ] Engineered turkey β 1 adrenergic receptor Trichoplusia ni 2VT4 2.7 [ 1 ] Human β 2 adrenergic receptor, from β 2 AR365-Fab5 ( 2R4R ) and β 2 AR24/365- Fab5 complexes ( 2R4S ) Spodoptera frugiperda 2R4R , 2R4S 3.4/3.7 [ 2 ] Engineered human β 2 adrenergic receptor Spodoptera frugiperda 2RH1 , 3D4S 2.4/2.8 [ 3 , 4 ] Human A 2A adenosine receptor, In complex with a high-affinity subtype-selective antagonist ZM241385.

Publication Year: 2009


Forced unbinding of GPR17 ligands from wild type and R255I mutant receptor models through a computational approach.

(2010) BMC Struct Biol 10

PubMed: 20233425 | PubMedCentral: PMC2850907 | DOI: 10.1186/1472-6807-10-8

Table 1 Alignment among GPR17 model and X-ray templates of GPCRs RMSD (Å) after alignment of α -helical carbon 3EML 2R4R 2RH1 3D4S 2VT4 GPR17 2.867 2.458 2.688 2.738 2.413 b Rh 1.955 2... 210 2.362 2.277 2.862 Globally, the helical pack was highly conserved among all the structures, and also the alignment of the α -helical domains to the GPR17 bundle yielded a good fit, as shown in Figure 1 .

Recently, thanks to protein engineering, the modified structures of two human GPCRs have been solved, providing new templates suitable for homology modeling: the adenosine A 2 A receptor (A 2 A R) bound to the high-affinity antagonist ZM241385 (PDB code 3EML ) [ 22 ]; the β 2 -adrenergic receptor-Fab ( β 2 AR-Fab) (PDB code 2R4R ) [ 23 ] and the β 2 -adrenergic receptor-T4 ( β 2 AR-T4) (PDB code 2RH1 ) [ 24 , 25 ], both bound to their inverse agonist carazolol; the mutated β 2 -adrenergic receptor-(E122W)-T4 ( β 2 AR(E122W)-T4) (PDB code 3D4S ) bound to cholesterol and its partial inverse agonist timolol [ 26 ].

Ribbon representation of the β 2 AR-Fab ( 2R4R ), β 2 AR-T4 ( 2RH1 ), β 2 AR(E122W)-T4 ( 3D4S ), β 1 AR ( 2VT4 ) and A 2 A R structures after alignment of the α -helical domains to GPR17 model (in gray) are reported in cyan, orange, green, magenta and yellow respectively.

Publication Year: 2010


Action of molecular switches in GPCRs--theoretical and experimental studies.

(2012) Curr Med Chem 19

PubMed: 22300046 | PubMedCentral: PMC3343417 | DOI: null

Summary of All Available Crystal Structures of GPCRs (Based on [ 61 ]) GPCR Engineered Type of ligand Ligand name PDB ID (Resolution Å) [Reference] A 2A R (human) IC3 fusion Agonist UK-432097 ... QAK (2.71) [ 101 ] Inverse agonist ZM241385 3EML (2.6) [ 98 ] Point mutations Agonist Adenosine 2YDO (3.0) [ 105 ] Agonist NECA 2YDV (2.6) [ 105 ] Antagonist Caffeine 3RFM (3.60) [ 106 ] Antagonist XAC 3REY (3.31) [ 106 ] Inverse agonist ZM241385 3PWH (3.30) [ 106 ] β 1 AR (turkey) Point mutations Agonist Carmoterol 2Y02 (2.6) [ 104 ] Agonist Isoprenaline 2Y03 (2.85] [ 104 ] Antagonist Cyanopindolol 2VT4 (2.7) [ 74 ], 2YCX (3.25) [ 159 ], 2YCY (3.15) [ 159 ], 2YCZ (3.65) [ 159 ] Inverse agonist Carazolol 2YCW (3.0) [ 159 ] Partial agonist Dobutamine 2Y00 (2.5) [ 104 ], 2Y01 (2.6) [ 104 ] Partial agonist Salbutamol 2Y04 (3.05) [ 104 ] β 2 AR (human) IC3 fusion Agonist BI-167107, nanobody 3P0G (3.5) [ 96 ] Agonist FAUC50 3PDS (3.5) [ 96 ] Antagonist Alprenolol 3NYA (3.16) [ 97 ] Inverse agonist Carazolol 2RH1 (2.4) [ 18 ] Inverse agonist Compound #1 3NY9 (2.84) [ 97 ] Inverse agonist ICI118551 3NY8 (2.84 [ 97 ] Inverse agonist Timolol 3DS4 (2.8) [ 59 ] Inverse agonist FAB, not resolved 2R4R (3,4) [ 96 ], 2R4S (3.4) [ 96 ] Inverse agonist FAB, not resolved 3KJ6 (3.4) [ 135 ] N-terminal fusion Agonist BI-167107, Gαβγ, nanobody 3SN6 (3.2) [ 15 ] CXCR4 (human) IC3 fusion Antagonist CVX15 peptide 3OE0 (2.9) [ 33 ] Antagonist Molecule 1t 3ODU (2.5) [ 33 ], 3OE6 (3.2) [ 33 ], 3OE8 (3.1) [ 33 ], 3OE9 (3.1)[ 33 ] D 3 R (human) IC3 fusion Antagonist Eticlopride 3PBL (2.89) [ 99 ] H 1 R (human) IC3 fusion Inverse agonist Doxepin 3RZE (3.1) 36 [ 100 ] Opsin 3CAP (2.9) [ 89 ] Gα peptide 3DQB (3.2) [ 91 ] Rhodopsin (bovine) Agonist All- trans -retinal 2G87 (2.6) [ 139 ] Inverse agonist 11- cis -retinal 1F88 (2.8) [ 17 ], 1U19 (2.2) [ 83 ], 1GZM (2.65) [ 83 ], L9H (2.6) [ 83 ], 1HZX (2.8) [ 83 ], 2I37 (4.0) [ 83 ], 3OAX (2.6) [ 83 ], 3C9L (2.65) [ 83 ] Point mutations Agonist 11- trans -retinal, Ga peptide 2X72 (3.0) [ 122 ], 3PQR (2.85) [ 123 ], 3PXO (3.0) [ 123 ] 9- cis -retinal 2PED (2.95) 3385 [ 85 ] 2J4Y (3.4) 3 [ 83 ], 3C9M (3.4) [ 83 ] Rhodopsin (squid) Inverse agonist 11- cis -retinal 2ZIY (3.7) [ 86 ]

Publication Year: 2012


N-terminal T4 lysozyme fusion facilitates crystallization of a G protein coupled receptor.

(2012) PLoS One 7

PubMed: 23056231 | PubMedCentral: PMC3464249 | DOI: 10.1371/journal.pone.0046039

D. ICL2 in the β 2 AR-Fab5 structure (pdb 2R4R).

Publication Year: 2012


A minimal ligand binding pocket within a network of correlated mutations identified by multiple sequence and structural analysis of G protein coupled receptors.

(2012) BMC Biophys 5

PubMed: 22748306 | PubMedCentral: PMC3478154 | DOI: 10.1186/2046-1682-5-13

Table 1 GPCR summary table Receptor PDB IDs [number of structures] Ligands Bovine Rhodopsin ( BR ) 1 F88, 1GZM, 1HZX, 1JFP, 1L9H, 1LN6, 1U19, 2 G87, 2HPY, 2I35, 2I36, 2I37, 2J4Y, 2PED,... 3C9L, 3C9M, 3CAP, 3DQB [ 18 ] RT, Ligand free Squid Rhodopsin ( SR ) 2Z73, 2ZIY [ 2 ] RT Turkey β1 adrenergic receptor ( β1AR ) 2VT4, 2Y00, 2Y01, 2Y02, 2Y03, 2Y04 [ 6 ] Cyanopindilol, Dobutamine Carmoterol, Isoprenaline Salbutamol Human β2 adrenergic receptor ( β2AR ) 2R4R, 2R4S, 2RH1, 3D4S, 3KJ6, 3NY8, 3NY9, 3NYA, 3P0G, 3PDS [ 10 ] Carazalol, Timolol, ICI 118,551, (molecule from Kolb et al., 2009), Alprenolol, BI-167107, FAUC50 Human A2A adenosine receptor ( A2A ) 3EML [ 1 ] ZM241385 Human chemokine receptor ( CXCR4 ) 3ODU, 3OE0, 3OE6, 3OE8, 3OE9 [ 5 ] IT1t, CVX15 Human dopamine D3 receptor ( D3R ) 3PBL [ 1 ] Eticlopride Summary of structural information available on GPCRs as of January 2011.

Publication Year: 2012


DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications.

(2013) Nucleic Acids Res 41

PubMed: 23193290 | PubMedCentral: PMC3531199 | DOI: 10.1093/nar/gks1229

Furthermore, two modification sites Tyr141 (pTyr) and Cys341 ( S -palmitoyl cysteine) are further highlighted in red on the tertiary structure (PDB ID: 2R4R) using Jmol viewer, which indicates the sol... ent accessibility and distance between them.

Publication Year: 2013


PubMed ID is not available.

Published in 2010

PubMedCentral: PMC4052540

Seven additional years were required before the first crystal structures were reported by two different research groups of a GPCR activated by a noncovalently-bound ligand, the β2-aderenocepto... (PDB ID 2R4R, 2R4S, 2RH1) [ 12 , 14 , 33 , 94 ].

Homology modeling studies have used a variety of template structures including bacteriorhodopsin [ 158 , 159 ], the theoretical model developed by Pogozheva (PDB ID: 1BOJ [ 152 ]) [ 160 - 162 ], the bovine rhodopsin crystal structure published in 2000 (PDB ID 1F88 [ 93 ]) [ 61 , 163 - 169 ], the rhodopsin structure published in 2004 (PDB ID 1GZM [ 98 ]) [ 170 ], and the crystal structure of the β2 aderenoceptor (PDB ID: 2R4R [ 33 ]) [ 171 - 173 ].

Publication Year: 2010


The recombinant expression systems for structure determination of eukaryotic membrane proteins.

(2014) Protein Cell 5

PubMed: 25119489 | PubMedCentral: PMC4145085 | DOI: 10.1007/s13238-014-0086-4

Protein Species PDB code Reference Insect cell S. frugiperda 1 β 2 AR (Fab) Homo sapiens 2R4R 2R4S Rasmussen et al., 2007 2 β 2 AR (T4L) Homo sapiens 2RH1 Cherezov et al., 2007 3 �... b2; 2 AR-agonist complex Homo sapiens 3PDS Rosenbaum et al., 2011 4 β 2 AR-GS complex Homo sapiens 3SN6 Rasmussen et al., 2011a , b 5 A 2A adenosine receptor Homo sapiens 3EML Jaakola et al., 2008 6 CXCR4 Homo sapiens 3ODU 3OE8 Wu et al., 2010 7 Dopamine D3 receptor Homo sapiens 3PBL Chien et al., 2010 8 Sphingosine 1-phosphate receptor subtype 1 Homo sapiens 3V2 W 3V3Y Hanson et al., 2012 9 M2 muscarinic acetylcholine receptor Homo sapiens 3UON Haga et al., 2012 10 M3 muscarinic acetylcholine receptor Rattus norvegicus 4DAJ Kruse et al., 2012 11 κ-Opioid receptor Homo sapiens 4DJH Wu et al., 2012 12 μ-Opioid receptor Mus musculus 4DKL Manglik et al., 2012 13 δ-Opioid receptor Mus musculus 4EJ4 Granier et al., 2012 14 N/OFQ receptor Homo sapiens 4EA3 Thompson et al., 2012 15 CCR5 Homo sapiens 4MBS Tan et al., 2013 16 PAR1 Homo sapiens 3VW7 Zhang et al., 2012 17 5-HT 1B/2B serotonin receptor Homo sapiens 4IAR 4IB4 Wang et al., 2013a , b ; Wacker et al., 2013 18 Smoothened receptor Homo sapiens 4JKV Wang et al., 2013a , b 19 Glucagon receptor Homo sapiens 4L6R Siu et al., 2013 20 Metabotropic glutamate receptor1 Homo sapiens 4OR2 Wu et al., 2014 21 P2X 4 Danio rerio (Zebra fish) 3I5D 3H9 V 4DW1 Kawate et al., 2009 ; Hattori and Gouaux, 2012 22 ASIC1 Gallus gallus 2QTS 3HGC Jasti et al., 2007 ; Gonzales et al., 2009 23 GluA2 Rat 3KG2 3KGC Sobolevsky et al., 2009 24 GLuClα Caenorhabditis elegans 3RHW, 3RIF, 3RI5 3RIA Hibbs and Gouaux, 2011 25 CX26 Homo sapiens 2ZW3 Maeda et al., 2009 26 UT-B Bos taurus 4EZC 4EZD Levin et al., 2012 27 ZMPSTE24 Homo sapiens 4AW6 Quigley et al., 2013 28 ABCB10 Homo sapiens 4AYT Shintre et al., 2013 29 Caludin-15 Mus Musculus 4P79 Suzuki et al., 2014 30 NRT1.1 Arabidopsis thaliana 4OH3 Sun et al., 2014 Trichoplusia ni 31 β1 adrenergic receptor Meleagris gallopavo 2VT4 Warne et al., 2008 32 NTS1 Neurotensin Receptor Rattus norvegicus 4GRV White et al., 2012 33 CmClC Cyanidioschyzonmerolae 3ORG Feng et al., 2010 34 Corticotropin-releasing factor receptor Homo sapiens 4K5Y Hollenstein et al., 2013 35 GLUT1 Homo sapiens 4PYP Deng et al., 2014 * For some proteins like GPCR and potassium channel, only the representative ones are listed After the protein IL-2 was first expressed in large scale with the baculovirus-infected insect cells in 1985, this system has been quickly accepted and widely used (Smith et al., 1983 ; Maeda et al., 1985 ).

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4393300

Finally, 342 residues of target sequence was aligned with ten top-ranked BLAST search, 2Y00 (297 residues), 2VT4, 2R4R, 3KJ6, 2R4S, 3SN6, 4GBR, 3P0G, 2RH1 and 3PDS The average alignment score for manu... lly edited multiple sequence alignment is better (76.47) than the score obtained by raw multiple sequence alignment (74.89).

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4420846

Table 4 Compound counts for retrospective screening scenarios Group of compounds Total number of compounds Number of compounds after Ligprep actives 271 550 Inactives 324 601 DUDs 2000 2526 ZINC 2000 ... 557 Table 5 Crystal structures of beta-2 adrenergic receptor used in the study PDB ID Resolution [Å] 2RH1 2.40 3D4S 2.80 3NY8 2.84 3NY9 2.84 3NYA 3.16 3KJ6 3.40 2R4R 3.40 2R4S 3.40 3P0G 3.50 3PDS 3.50 After this initial models evaluation, all compounds from a particular group of molecules (actives, true inactives, DUDs, and ZINC) were docked into the constructed homology models and crystal structures.

Publication Year: 2015