Entry | Database: PDB / ID: 6plg |
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Title | Crystal structure of human PHGDH complexed with Compound 15 |
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Components | D-3-phosphoglycerate dehydrogenase |
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Keywords | OXIDOREDUCTASE/INHIBITOR / DEHYDROGENASE / SERINE METABOLISM / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex |
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Function / homology | Function and homology information
2-oxoglutarate reductase / threonine metabolic process / glial cell development / phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / taurine metabolic process / gamma-aminobutyric acid metabolic process / Serine metabolism / glycine metabolic process / malate dehydrogenase ...2-oxoglutarate reductase / threonine metabolic process / glial cell development / phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / taurine metabolic process / gamma-aminobutyric acid metabolic process / Serine metabolism / glycine metabolic process / malate dehydrogenase / L-serine biosynthetic process / L-malate dehydrogenase (NAD+) activity / glutamine metabolic process / G1 to G0 transition / neural tube development / spinal cord development / brain development / NAD binding / neuron projection development / regulation of gene expression / electron transfer activity / extracellular exosome / cytosolSimilarity search - Function D-3-phosphoglycerate dehydrogenase / D-3-phosphoglycerate dehydrogenase, ASB domain / D-3-phosphoglycerate dehydrogenase intervening domain / Allosteric substrate binding domain superfamily / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain ...D-3-phosphoglycerate dehydrogenase / D-3-phosphoglycerate dehydrogenase, ASB domain / D-3-phosphoglycerate dehydrogenase intervening domain / Allosteric substrate binding domain superfamily / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha BetaSimilarity search - Domain/homology |
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Biological species | Homo sapiens (human) |
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Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å |
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Authors | Olland, A. / Lakshminarasimhan, D. / White, A. / Suto, R.K. |
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Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2019 Title: Inhibition of 3-phosphoglycerate dehydrogenase (PHGDH) by indole amides abrogates de novo serine synthesis in cancer cells. Authors: Mullarky, E. / Xu, J. / Robin, A.D. / Huggins, D.J. / Jennings, A. / Noguchi, N. / Olland, A. / Lakshminarasimhan, D. / Miller, M. / Tomita, D. / Michino, M. / Su, T. / Zhang, G. / Stamford, ...Authors: Mullarky, E. / Xu, J. / Robin, A.D. / Huggins, D.J. / Jennings, A. / Noguchi, N. / Olland, A. / Lakshminarasimhan, D. / Miller, M. / Tomita, D. / Michino, M. / Su, T. / Zhang, G. / Stamford, A.W. / Meinke, P.T. / Kargman, S. / Cantley, L.C. |
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History | Deposition | Jun 30, 2019 | Deposition site: RCSB / Processing site: RCSB |
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Revision 1.0 | Jul 24, 2019 | Provider: repository / Type: Initial release |
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Revision 1.1 | Aug 7, 2019 | Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title |
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Revision 1.2 | Sep 4, 2019 | Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last |
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Revision 1.3 | Nov 6, 2024 | Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id |
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