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- PDB-4m6q: Identification of Amides Derived From 1H-Pyrazolo[3,4-b]pyridine-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4m6q | ||||||
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Title | Identification of Amides Derived From 1H-Pyrazolo[3,4-b]pyridine-5-carboxylic Acid as Potent Inhibitors of Human Nicotinamide Phosphoribosyltransferase (NAMPT) | ||||||
![]() | Nicotinamide phosphoribosyltransferase | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / Transferase / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Giannetti, A.M. / Zheng, X. / Skelton, N. / Wang, W. / Bravo, B. / Feng, Y. / Gunzner-Toste, J. / Ho, Y. / Hua, R. / Wang, C. ...Giannetti, A.M. / Zheng, X. / Skelton, N. / Wang, W. / Bravo, B. / Feng, Y. / Gunzner-Toste, J. / Ho, Y. / Hua, R. / Wang, C. / Zhao, Q. / Liederer, B.M. / Liu, Y. / O'Brien, T. / Oeh, J. / Sampath, D. / Shen, Y. / Wang, L. / Wu, H. / Xiao, Y. / Yuen, P. / Zak, M. / Zhao, G. / Dragovich, P.S. | ||||||
![]() | ![]() Title: Identification of amides derived from 1H-pyrazolo[3,4-b]pyridine-5-carboxylic acid as potent inhibitors of human nicotinamide phosphoribosyltransferase (NAMPT). Authors: Zheng, X. / Bair, K.W. / Bauer, P. / Baumeister, T. / Bowman, K.K. / Buckmelter, A.J. / Caligiuri, M. / Clodfelter, K.H. / Feng, Y. / Han, B. / Ho, Y.C. / Kley, N. / Li, H. / Liang, X. / ...Authors: Zheng, X. / Bair, K.W. / Bauer, P. / Baumeister, T. / Bowman, K.K. / Buckmelter, A.J. / Caligiuri, M. / Clodfelter, K.H. / Feng, Y. / Han, B. / Ho, Y.C. / Kley, N. / Li, H. / Liang, X. / Liederer, B.M. / Lin, J. / Ly, J. / O'Brien, T. / Oeh, J. / Oh, A. / Reynolds, D.J. / Sampath, D. / Sharma, G. / Skelton, N. / Smith, C.C. / Tremayne, J. / Wang, L. / Wang, W. / Wang, Z. / Wu, H. / Wu, J. / Xiao, Y. / Yang, G. / Yuen, P.W. / Zak, M. / Dragovich, P.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 383.1 KB | Display | ![]() |
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PDB format | ![]() | 313.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4lv9C ![]() 4lvaC ![]() 4lvbC ![]() 4lvdC ![]() 4lvfC ![]() 4lvgC ![]() 4m6pC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 56942.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P43490, nicotinamide phosphoribosyltransferase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.3 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: 0.2uL + 0.2uL drops containing 6mg/mL Nampt, 0.1M Sodium phosphate, 25-29% polyethylene glycol 3350, 0.2M NaCl, 1mM compound, followed by in-situ adduct formation , pH 8.6, VAPOR DIFFUSION, ...Details: 0.2uL + 0.2uL drops containing 6mg/mL Nampt, 0.1M Sodium phosphate, 25-29% polyethylene glycol 3350, 0.2M NaCl, 1mM compound, followed by in-situ adduct formation , pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2012 |
Radiation | Monochromator: Liquid Nitrogen cooled Dual Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999993 Å / Relative weight: 1 |
Reflection | Resolution: 2.406→65.239 Å / Num. all: 40583 / Num. obs: 40096 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.406→2.414 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 |
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Refinement step | Cycle: LAST / Resolution: 2.406→65.239 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 13.4373 Å / Origin y: 1.0726 Å / Origin z: 22.5569 Å
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Refinement TLS group | Selection details: chain A or chain B |