+Open data
-Basic information
Entry | Database: PDB / ID: 8ivu | ||||||
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Title | Crystal Structure of Human NAMPT in complex with A4276 | ||||||
Components | Nicotinamide phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / NAMPT / Inhibitor / Complex / Cancer | ||||||
Function / homology | Function and homology information nicotinamide phosphoribosyltransferase / nicotinamide phosphoribosyltransferase activity / NAD biosynthesis via nicotinamide riboside salvage pathway / Nicotinamide salvaging / NAD biosynthetic process / positive regulation of nitric-oxide synthase biosynthetic process / NPAS4 regulates expression of target genes / BMAL1:CLOCK,NPAS2 activates circadian gene expression / cytokine activity / circadian regulation of gene expression ...nicotinamide phosphoribosyltransferase / nicotinamide phosphoribosyltransferase activity / NAD biosynthesis via nicotinamide riboside salvage pathway / Nicotinamide salvaging / NAD biosynthetic process / positive regulation of nitric-oxide synthase biosynthetic process / NPAS4 regulates expression of target genes / BMAL1:CLOCK,NPAS2 activates circadian gene expression / cytokine activity / circadian regulation of gene expression / cell junction / cell-cell signaling / nuclear speck / positive regulation of cell population proliferation / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09000922463 Å | ||||||
Authors | Kang, B.G. / Cha, S.S. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Theranostics / Year: 2023 Title: Discovery of a novel NAMPT inhibitor that selectively targets NAPRT-deficient EMT-subtype cancer cells and alleviates chemotherapy-induced peripheral neuropathy. Authors: Kim, M. / Kim, H. / Kang, B.G. / Lee, J. / Kim, T. / Lee, H. / Jung, J. / Oh, M.J. / Seo, S. / Ryu, M.J. / Sung, Y. / Lee, Y. / Yeom, J. / Han, G. / Cha, S.S. / Jung, H. / Kim, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ivu.cif.gz | 453.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ivu.ent.gz | 318.7 KB | Display | PDB format |
PDBx/mmJSON format | 8ivu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ivu_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8ivu_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8ivu_validation.xml.gz | 69.8 KB | Display | |
Data in CIF | 8ivu_validation.cif.gz | 97.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/8ivu ftp://data.pdbj.org/pub/pdb/validation_reports/iv/8ivu | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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-Components
#1: Protein | Mass: 55594.938 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NAMPT, PBEF, PBEF1 / Production host: Escherichia coli B (bacteria) References: UniProt: P43490, nicotinamide phosphoribosyltransferase #2: Chemical | ChemComp-SJ6 / #3: Chemical | ChemComp-PO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.16 % |
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Crystal grow | Temperature: 283.15 K / Method: microbatch / pH: 7 Details: 0.1M sodium phosphate pH 7.0, 0.2M sodium chloride, 25% (w/v) polyethylene glycol (PEG) 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→29.71 Å / Num. obs: 132238 / % possible obs: 99.9 % / Redundancy: 13.8 % / Biso Wilson estimate: 40.4049994066 Å2 / Rrim(I) all: 0.203 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.09→2.15 Å / Num. unique obs: 12302 / CC1/2: 0.594 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09000922463→29.7083970676 Å / SU ML: 0.268400200344 / Cross valid method: NONE / σ(F): 1.34752066661 / Phase error: 25.7579814875 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.5320590098 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09000922463→29.7083970676 Å
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Refine LS restraints |
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LS refinement shell |
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