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- PDB-4xjt: Human CD38 complexed with inhibitor 2 [4-[(2,6-dimethylbenzyl)ami... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xjt | ||||||
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Title | Human CD38 complexed with inhibitor 2 [4-[(2,6-dimethylbenzyl)amino]-2-methylquinoline-8-carboxamide] | ||||||
![]() | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | ||||||
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Function / homology | ![]() 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / artery smooth muscle contraction / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Shewchuk, L.M. / Deaton, D.N. / Stewart, E. | ||||||
![]() | ![]() Title: Discovery of 4-Amino-8-quinoline Carboxamides as Novel, Submicromolar Inhibitors of NAD-Hydrolyzing Enzyme CD38. Authors: Becherer, J.D. / Boros, E.E. / Carpenter, T.Y. / Cowan, D.J. / Deaton, D.N. / Haffner, C.D. / Jeune, M.R. / Kaldor, I.W. / Poole, J.C. / Preugschat, F. / Rheault, T.R. / Schulte, C.A. / ...Authors: Becherer, J.D. / Boros, E.E. / Carpenter, T.Y. / Cowan, D.J. / Deaton, D.N. / Haffner, C.D. / Jeune, M.R. / Kaldor, I.W. / Poole, J.C. / Preugschat, F. / Rheault, T.R. / Schulte, C.A. / Shearer, B.G. / Shearer, T.W. / Shewchuk, L.M. / Smalley, T.L. / Stewart, E.L. / Stuart, J.D. / Ulrich, J.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.4 KB | Display | ![]() |
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PDB format | ![]() | 86.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4xjsC ![]() 1yh3S C: citing same article ( S: Starting model for refinement |
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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: 30317.318 Da / Num. of mol.: 1 / Mutation: N100D, N164A, N209D, N219D, E226Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P28907, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase, 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase |
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#2: Chemical | ChemComp-41Z / |
#3: Chemical | ChemComp-NA7 / [( |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.77 % |
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Protein concentration 7mgs/ml. Crystals were grown from 23% PEG3350, 0.1mM BisTrisPropane at 22 deg C (2+2uL drops over a 500uL well). Crystals were soaked with 5mM inhibitor for 24 hours ...Details: Protein concentration 7mgs/ml. Crystals were grown from 23% PEG3350, 0.1mM BisTrisPropane at 22 deg C (2+2uL drops over a 500uL well). Crystals were soaked with 5mM inhibitor for 24 hours prior to data collection. Crystals were flash frozen in PFO. |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 10, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.6→36.1 Å / Num. obs: 7323 / % possible obs: 99 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 26 |
Reflection shell | Resolution: 2.6→2.66 Å / Redundancy: 7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 4.7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1YH3 Resolution: 2.6→36.1 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.908 / SU B: 27.095 / SU ML: 0.285 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 117.6 Å2 / Biso mean: 48.013 Å2 / Biso min: 20.89 Å2
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Refinement step | Cycle: final / Resolution: 2.6→36.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -7.448 Å / Origin y: -14.692 Å / Origin z: 15.2297 Å
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