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Yorodumi- PDB-7nd1: First-in-class small molecule inhibitors of Polycomb Repressive C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nd1 | ||||||
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Title | First-in-class small molecule inhibitors of Polycomb Repressive Complex 1 (PRC1) RING domain | ||||||
Components |
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Keywords | GENE REGULATION / Polycomb Repressive Complex 1 (PRC1) / Inhibitor | ||||||
Function / homology | Function and homology information histone H2AK119 ubiquitin ligase activity / regulation of adaxial/abaxial pattern formation / RING-like zinc finger domain binding / PRC1 complex / sex chromatin / segment specification / rostrocaudal neural tube patterning / ubiquitin-protein transferase activator activity / somatic stem cell division / embryonic skeletal system morphogenesis ...histone H2AK119 ubiquitin ligase activity / regulation of adaxial/abaxial pattern formation / RING-like zinc finger domain binding / PRC1 complex / sex chromatin / segment specification / rostrocaudal neural tube patterning / ubiquitin-protein transferase activator activity / somatic stem cell division / embryonic skeletal system morphogenesis / PcG protein complex / positive regulation of immature T cell proliferation in thymus / SUMOylation of DNA methylation proteins / gastrulation with mouth forming second / SUMOylation of RNA binding proteins / positive regulation of ubiquitin-protein transferase activity / anterior/posterior axis specification / negative regulation of gene expression, epigenetic / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / germ cell development / humoral immune response / hemopoiesis / negative regulation of apoptotic signaling pathway / MLL1 complex / heterochromatin / SUMOylation of DNA damage response and repair proteins / ubiquitin ligase complex / positive regulation of B cell proliferation / epigenetic regulation of gene expression / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / promoter-specific chromatin binding / apoptotic signaling pathway / RING-type E3 ubiquitin transferase / euchromatin / brain development / negative regulation of DNA-binding transcription factor activity / ubiquitin protein ligase activity / positive regulation of fibroblast proliferation / mitotic cell cycle / gene expression / regulation of gene expression / Oxidative Stress Induced Senescence / in utero embryonic development / nuclear body / protein ubiquitination / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Authors | Cierpicki, T. / Lund, G. / Jaremko, L. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2021 Title: Small-molecule inhibitors targeting Polycomb repressive complex 1 RING domain. Authors: Shukla, S. / Ying, W. / Gray, F. / Yao, Y. / Simes, M.L. / Zhao, Q. / Miao, H. / Cho, H.J. / Gonzalez-Alonso, P. / Winkler, A. / Lund, G. / Purohit, T. / Kim, E. / Zhang, X. / Ray, J.M. / ...Authors: Shukla, S. / Ying, W. / Gray, F. / Yao, Y. / Simes, M.L. / Zhao, Q. / Miao, H. / Cho, H.J. / Gonzalez-Alonso, P. / Winkler, A. / Lund, G. / Purohit, T. / Kim, E. / Zhang, X. / Ray, J.M. / He, S. / Nikolaidis, C. / Ndoj, J. / Wang, J. / Jaremko, L. / Jaremko, M. / Ryan, R.J.H. / Guzman, M.L. / Grembecka, J. / Cierpicki, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nd1.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7nd1.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 7nd1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/7nd1 ftp://data.pdbj.org/pub/pdb/validation_reports/nd/7nd1 | HTTPS FTP |
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-Related structure data
Related structure data | 6wi7C 6wi8C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 12766.979 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RNF2, BAP1, DING, HIPI3, RING1B / Production host: Escherichia coli (E. coli) References: UniProt: Q99496, RING-type E3 ubiquitin transferase | ||||
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#2: Protein | Mass: 11727.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BMI1, PCGF4, RNF51 / Production host: Escherichia coli (E. coli) / References: UniProt: P35226 | ||||
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-U9E / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 0.12 mM [U-2H; U-13C; U-15N; CH3 ILV] Ring1B-BMI1, 95% H2O/5% D2O Label: sample1 / Solvent system: 95% H2O/5% D2O |
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Sample | Conc.: 0.12 mM / Component: Ring1B-BMI1 / Isotopic labeling: [U-2H; U-13C; U-15N; CH3 ILV] |
Sample conditions | Details: 50 mM sodium phosphate, pH 6.8, 150 mM NaCl, 1 mM TCEP, 10 uM ZnCl2, 5% DMSO Ionic strength: 150 mM / Label: conditions1 / pH: 6.8 / Pressure: 1 atm / Temperature: 303.3 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |