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Yorodumi- PDB-6st3: HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with 4-hydroxy-... -
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-Basic information
Entry | Database: PDB / ID: 6st3 | ||||||
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Title | HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with 4-hydroxy-N-(4-phenoxybenzyl)-2-(1H-pyrazol-1-yl)pyrimidine-5-carboxamide | ||||||
Components | Egl nine homolog 1 | ||||||
Keywords | OXIDOREDUCTASE / NON-HEME DIOXYGENASE / IRON / 2-OXOGLUTARATE / HYPOXIA-INDUCIBLE FACTOR / HIF / HIF PROLYL HYDROXYLASE DOMAIN 2 / PHD2 / EGLN1 / OXYGENASE / HYPOXIA / DNA-BINDING / METAL-BINDING / TRANSCRIPTION / HELIX-LOOP-HELIX-BETA / DSBH / FACIAL TRIAD / CYTOPLASM / TRANSCRIPTION/EPIGENETIC REGULATION / SIGNALING / DEVELOPMENT / CELL STRUCTURE / BETA-HYDROXYLATION / TRANSCRIPTION ACTIVATOR/INHIBITOR / UBL CONJUGATION / POLYMORPHISM / VITAMIN C / ZINC-FINGER / FAMILIAL ERYTHROCYTOSIS / BREAST CANCER / TRANSCRIPTION COMPLEX | ||||||
Function / homology | Function and homology information hypoxia-inducible factor-proline dioxygenase activity / peptidyl-proline 4-dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline dioxygenase activity / negative regulation of cyclic-nucleotide phosphodiesterase activity / regulation protein catabolic process at postsynapse / intracellular oxygen homeostasis / labyrinthine layer development / cardiac muscle tissue morphogenesis / heart trabecula formation ...hypoxia-inducible factor-proline dioxygenase activity / peptidyl-proline 4-dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline dioxygenase activity / negative regulation of cyclic-nucleotide phosphodiesterase activity / regulation protein catabolic process at postsynapse / intracellular oxygen homeostasis / labyrinthine layer development / cardiac muscle tissue morphogenesis / heart trabecula formation / 2-oxoglutarate-dependent dioxygenase activity / regulation of modification of postsynaptic structure / L-ascorbic acid binding / response to nitric oxide / ventricular septum morphogenesis / regulation of angiogenesis / ferrous iron binding / negative regulation of DNA-binding transcription factor activity / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / cellular response to hypoxia / intracellular iron ion homeostasis / postsynaptic density / response to hypoxia / intracellular membrane-bounded organelle / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.426 Å | ||||||
Authors | Chowdhury, R. / Holt-Martyn, J.P. / Schofield, C.J. | ||||||
Citation | Journal: Chemmedchem / Year: 2020 Title: Structure-Activity Relationship and Crystallographic Studies on 4-Hydroxypyrimidine HIF Prolyl Hydroxylase Domain Inhibitors. Authors: Holt-Martyn, J.P. / Chowdhury, R. / Tumber, A. / Yeh, T.L. / Abboud, M.I. / Lippl, K. / Lohans, C.T. / Langley, G.W. / Figg Jr., W. / McDonough, M.A. / Pugh, C.W. / Ratcliffe, P.J. / Schofield, C.J. #1: Journal: ACS Chem. Biol. / Year: 2013 Title: Selective small molecule probes for the hypoxia inducible factor (HIF) prolyl hydroxylases. Authors: Chowdhury, R. / Candela-Lena, J.I. / Chan, M.C. / Greenald, D.J. / Yeoh, K.K. / Tian, Y.M. / McDonough, M.A. / Tumber, A. / Rose, N.R. / Conejo-Garcia, A. / Demetriades, M. / Mathavan, S. / ...Authors: Chowdhury, R. / Candela-Lena, J.I. / Chan, M.C. / Greenald, D.J. / Yeoh, K.K. / Tian, Y.M. / McDonough, M.A. / Tumber, A. / Rose, N.R. / Conejo-Garcia, A. / Demetriades, M. / Mathavan, S. / Kawamura, A. / Lee, M.K. / van Eeden, F. / Pugh, C.W. / Ratcliffe, P.J. / Schofield, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6st3.cif.gz | 250.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6st3.ent.gz | 204.4 KB | Display | PDB format |
PDBx/mmJSON format | 6st3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6st3_validation.pdf.gz | 844.6 KB | Display | wwPDB validaton report |
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Full document | 6st3_full_validation.pdf.gz | 847.2 KB | Display | |
Data in XML | 6st3_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 6st3_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/st/6st3 ftp://data.pdbj.org/pub/pdb/validation_reports/st/6st3 | HTTPS FTP |
-Related structure data
Related structure data | 4bqxS S: Starting model for refinement |
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Similar structure data |
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-Assembly
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Noncrystallographic symmetry (NCS) | NCS domain:
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