+Open data
-Basic information
Entry | Database: PDB / ID: 6peb | ||||||
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Title | Crystal Structure of human NAMPT in complex with NVP-LTM976 | ||||||
Components | Nicotinamide phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE | ||||||
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 / FOURIER SYNTHESIS / Resolution: 2.46 Å | ||||||
Authors | Weihofen, W.A. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2019 Title: Scaffold Morphing Identifies 3-Pyridyl Azetidine Ureas as Inhibitors of Nicotinamide Phosphoribosyltransferase (NAMPT). Authors: Palacios, D.S. / Meredith, E.L. / Kawanami, T. / Adams, C.M. / Chen, X. / Darsigny, V. / Palermo, M. / Baird, D. / George, E.L. / Guy, C. / Hewett, J. / Tierney, L. / Thigale, S. / Wang, L. / Weihofen, W.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6peb.cif.gz | 772.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6peb.ent.gz | 643.4 KB | Display | PDB format |
PDBx/mmJSON format | 6peb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/6peb ftp://data.pdbj.org/pub/pdb/validation_reports/pe/6peb | HTTPS FTP |
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-Related structure data
Related structure data | 6atbS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 56811.180 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 (E. coli) References: UniProt: P43490, nicotinamide phosphoribosyltransferase #2: Chemical | #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: 2.34 Å3/Da / Density % sol: 47.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.8 Details: 100 mM NaPO4, pH 8.8 34 % (w/v) PEG 3350 180 mM NaCl. Equal volumes (0.5 uL) of reservoir solution and protein. Compound was soaked overnight at 1 mM concentration in crystallization solution. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→246.84 Å / Num. obs: 78824 / % possible obs: 99.9 % / Observed criterion σ(I): 3.3 / Redundancy: 6.5 % / Biso Wilson estimate: 64.31 Å2 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.039 / Rrim(I) all: 0.073 / Rsym value: 0.061 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.46→2.59 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2145 / Rpim(I) all: 0.215 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6ATB Resolution: 2.46→34.94 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.399 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.428 / SU Rfree Blow DPI: 0.23 / SU Rfree Cruickshank DPI: 0.231
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Displacement parameters | Biso mean: 72.66 Å2
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Refine analyze | Luzzati coordinate error obs: 0.26 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.46→34.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.46→2.47 Å / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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