Citations in PubMed

Primary Citation PubMed: 12446723 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 6

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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Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

(2008) BMC Genomics 9

PubMed: 18564434 | PubMedCentral: PMC2453528 | DOI: 10.1186/1471-2164-9-293

Following iterative backbone annealing based on the structure of Hif1an (PDB entry 1h2k ), 2OG and Fe(II) were added to the 3D model of Jmjd6.

This first step showed a significant probability (= 95%) of structural similarity of Jmjd6 to the three structurally resolved 2OG- and Fe(II)-dependent dioxygenases Hif1an (PDB entry 1h2k ), putative asparaginyl hydroxylase – 2636534 from Bacillus subtilis (PDB entry 1vrb ) and Jmjd2a (PDB entry 2gp5 ), respectively.

Jmjd6 sequence alignments (Fig. 5) and HHpred were used to model Jmjd6 utilising the PDB structures of Hif1an ( 1h2k ), Putative asparaginyl hydroxylase – 2636534 ( 1vrb ) and Jmjd2a ( 2gp5 ), respectively.

Publication Year: 2008

Asparagine and aspartate hydroxylation of the cytoskeletal ankyrin family is catalyzed by factor-inhibiting hypoxia-inducible factor.

(2011) J Biol Chem 286

PubMed: 21177872 | PubMedCentral: PMC3045019 | DOI: 10.1074/jbc.M110.193540

Except for the N-terminal 15 residues, the overall FIH Q239H structure is very similar to that reported for wt FIH (root mean square deviation for Cα 0.22 Å, PDB ID 1H2K ).

Peptide 2 adopts a slightly different conformation compared with the HIF fragment (root mean square deviation for Cα 0.62 Å, PDB ID 1H2K ).

The structure was solved by molecular replacement using PHASER (search model PDB ID 1H2K ) and was initially refined with CNS ( 25 ).

Publication Year: 2011

Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification.

(2011) Nucleic Acids Res 39

PubMed: 20972222 | PubMedCentral: PMC3045595 | DOI: 10.1093/nar/gkq919

The crystal structures of the cofactor-bound forms of hTYW5 and FIH complexed with substrate peptide (PDB ID: 1h2k) are shown in ribbon representations.

Publication Year: 2011

Factor-inhibiting hypoxia-inducible factor (FIH) catalyses the post-translational hydroxylation of histidinyl residues within ankyrin repeat domains.

(2011) FEBS J 278

PubMed: 21251231 | PubMedCentral: PMC3569879 | DOI: 10.1111/j.1742-4658.2011.08022.x

A comparison of all FIH complexes suggests that the pro- S hydrogen of His 553 in TNKS2 538–558 is likely analogously positioned as that observed for hydroxylated asparagines in FIH&#x... 00b7;mNotch1 1930–1949 (PDB ID: 3P3N) and FIH·HIF-1αCAD 788–826 (PDB ID: 1H2K) complexes.

Structure was solved by molecular replacement using phaser (search model PDB ID 1H2K) and was refined with CNS [ 33 ].

(C) Stereoview stick representation of the superimposed FIH·mNotch1 1930–1949 (PDB ID: 3P3N, FIH in green and N1 1930–1949 in white) and FIH·HIF-1αCAD 788–826 (PDB ID: 1H2K; FIH in purple and HIF-1αCAD 788-826 in salmon) complexes.

Publication Year: 2011

A network pharmacology approach to understanding the mechanisms of action of traditional medicine: Bushenhuoxue formula for treatment of chronic kidney disease.

(2014) PLoS One 9

PubMed: 24598793 | PubMedCentral: PMC3943740 | DOI: 10.1371/journal.pone.0089123

Protein Targets Name Gene Symbol PDB-ID Positive Drugs Cutoff Value No a Known target proteins Carbonic anhydrase II CA2 1BN3 Topiramate −8.4 10 Raf kinase RAF1 1C1Y Sorafenib −9.6 12 ... acrophage migration inhibitory factor MIF 1GCZ ethyl 7-hydroxy-2-oxochromene-3-carboxylate −8.9 10 Hepatocyte growth factor HGF 1GMO N,O6-Disulfo-Glucosamine −7 79 Hypoxia-inducible factor 1α HIF1A 1H2K Everolimus −6.3 66 Soluble epoxide hydrolase EPHX2 1ZD3 4-{[(cyclohexylamino)carbonyl]amino} butanoic acid −7.4 15 Carbonic anhydrase XII CA12 1JD0 Hydrochlorothiazide −6.9 26 Peroxisome proliferator-activated receptor PPARG 1K74 Fenofibrate −9.4 39 Angiotensin converting enzyme ACE 1O86 Candoxatril −9 74 Monoamine oxidase B MAOB 1OJ9 Pargyline −9.2 39 Mitogen-activated protein kinase 1 MAPK1 1PME 4-[4-(4-fluorophenyl)-2-[4-[(S)-methylsulfinyl]phenyl]-1H-imidazol-5-yl] pyridine −9.4 27 Mast stem cell growth factor receptor KIT 1T46 Sorafenib −10.1 34 Thymidine phosphorylase TYMP 1UOU Chloro-6-[(2-Iminopyrrolidin-1-Yl)Methyl]Pyrimidine-2,4(1 h,3 h)-Dione −7.7 76 Macrophage metalloelastase MMP12 1UTT (6R)-4-benzyl-6-(1-methyl-2,2-dioxido-1,3-dihydro-2,1-benzisothiazol-5-yl)morpholin-3-one −10.6 6 β2 adrenergic receptor ADRB2 3D4S Carvedilol −9.3 45 Adenosine A2α receptor ADORA2A 3EML Mefloquine −9.8 71 C-C chemokine receptor type 1 CCR1 1Y5D Maraviroc −8.2 35 Mitogen-activated protein kinase 14 MAPK14 1ZZ2 N-[(3z)-5-Tert-Butyl-2-Phenyl-1,2-Dihydro-3h-Pyrazol-3-Ylidene]-N ′ -(4-Chlorophenyl)Urea −8.4 14 Lymphocyte function-associated antigen ITGAL 1CQP Lovastatin −7.2 0 Vasopressin V1α receptor AVPR1A 1YTV Conivaptan −10.5 20 Placeta growth factor PGF 1FZV Suplatast tosylate −5 25 Transforming growth factor beta 1 TGFB1 1KLD NO ligand Tumor necrosis factor ligand superfamily member 5 TNFSF5 1I9R NO ligand Nuclear factor NF-κB NFKB1 1NFI NO ligand Carbonic anhydrase IV CA4 1ZNC NO ligand C-C motif chemokine-2 CCL2/MCP1 2BDN NO ligand DNA-directed RNA polymerase II 19 kDa polypeptide POLR2D 2C35 NO ligand Carbonic anhydrase IX CA9 2HKF NO ligand Known target proteins Plasminogen activator inhibitor-1 SERPINE1 1OC0 NO ligand RAC-α serine/threonine kinase No symbol 1AO2 NO ligand Protein-glutamine γ-glutamyltransferase TGM2 2Q3Z NO ligand Putative targets Tyrosine-protein kinase BTK BTK 3OCS Staurosporine −9.6 53 Small inducible cytokine A5 CCL5 1U4M Heparin_Disaccharide_I-S −6 15 Epidermal growth factor receptor EGFR 2GS7 Flavopiridol −9 19 Estrogen receptor ESR1 3Q97 Estradiol −10 1 Heat shock cognate 71 kDa protein HSPA8 3FZK (2R,3R,4S,5R)-2-[6-amino-8-[(3,4-dichlorophenyl)methylamino]purin-9-yl]-5-(hydroxymethyl)oxolane-3,4-diol −8.2 34 Insulin receptor INSR 2HR7 Hydrochloride) −9.5 21 Proto-oncogene tyrosine-protein kinase LCK LCK 3AC1 N-(2-chloro-6-methylphenyl)-8-[(3S)-3-methylpiperazin-1-yl]imidazo[1,5-a]quinoxalin-4-amine −8.2 60 Hepatocyte nuclear factor 4-alpha HNF4A 1PZL 1_methyl_2-nitro_benzo[e]benzofuran −7.4 79 Glucocorticoid receptor NR3C1 3K22 Flunisolide −10 26 Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha isoform PIK3CA 3HHM Wortmannin −9.1 20 Plasminogen activator, tissue PLAT 1A5H Iloprost −8.5 87 Acyl-CoA dehydrogenase family member 8, mitochondrial ACTN1 1RX0 Methacrylyl-Coenzyme_A −9 16 Protein tyrosine phosphatase PTPN1 1BZH (Oxalyl-Amino)-Naphthalene-2-Carboxylic_Acid −8 19 Protein kinase C, beta PRKCB 2I0E Vitamin_E −9.7 13 E3 ubiquitin protein ligase VHL 3ZRC 4-((naphthalen-2-ylamino)methyl)benzene-1,2-diol −7.7 21 FYN oncogene related to SRC, FGR, YES FYN 1AOT 2,5,8,11-Tetraoxadodecane −6.6 29 9-mer from C-C chemokine receptor type 5 CCR5 2RLL NO ligand Fc fragment of IgG, low affinity IIb, receptor (CD32) FCGR2B 2FCB NO ligand Fibronectin 1 FN1 3MQL NO ligand Myeloma immunoglobulin D lambda IGHG1 1ZVO NO ligand Solute carrier family 4 SLC4A1 1BTT NO ligand Signal transducer and activator of transcription STAT1 1BF5 NO ligand Jun proto-oncogene JUN 1FOS NO ligand KIAA0101 KIAA0101 No PDB data Catechol-O-methyltransferase COMT No PDB data Protein Targets Name Gene Symbol PDB-ID Positive Drugs Cutoff Value No Putative targets Decorin DCN No PDB data Clusterin CLU No PDB data Transforming growth factor, beta receptor 1 TGFBR1 No PDB data Interleukin 8 IL8 No PDB data Apolipoprotein A–I APOA1 No PDB data Signal transducer and activator of transcription 5B STAT5B No PDB data No a : The number of effective molecular docking.

Publication Year: 2014

Ribosomal oxygenases are structurally conserved from prokaryotes to humans.

(2014) Nature 510

PubMed: 24814345 | PubMedCentral: PMC4066111 | DOI: 10.1038/nature13263

Protein topologies of ( a ) Mina53·Mn·2OG·rpL27a (32-50) , ( b ) NO66·Mn·NOG·rpL8 (205-224) , ( c ) ycfD RM ·Mn·NOG·L16 (72-91) ... ( d ) FIH·Fe·NOG·HIF-1α (786-826) (PDB: 1H2K), ( e ) PHF8·Fe·NOG·histone H3K4me3K9me2 (2-25) (PDB: 3KV4), and ( f ) KDM4A·Ni·NOG·histone H3K9me2 (7-14) (PDB: 2OX0) (substrates are not shown).

Figure 2 Comparison of the substrate structures for ROX/JmjC enzymes Ribbons representations from ROX and related 2OG-oxygenase-substrate complexes: a , Mina53·Mn·2OG·rpL27a (32-50) ( P 2 1 2 1 2 1 , 2.05 Å), b , NO66·Mn·NOG·rpL8 (205-224) (C2, 2.35 Å), c , ycfD RM ·Mn·NOG·L16 (72-91) ( P 2 1 2 1 2 1 , 3.0 Å), d , FIH·Fe·NOG·HIF-1α (786-826) (PDB: 1H2K), e , PHF8·Fe·NOG·histone H3K4me3K9me2 (2-25) (PDB: 3KV4), f , KDM4A·Ni·NOG·histone H3K9me2 (7-14) (PDB: 2OX0).

Publication Year: 2014