+Open data
-Basic information
Entry | Database: PDB / ID: 8otv | ||||||
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Title | Crystal structure of NUDT14 complexed with novel compound | ||||||
Components | Uridine diphosphate glucose pyrophosphatase NUDT14 | ||||||
Keywords | HYDROLASE / HYDROLASE INHIBITOR / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information Synthesis of dolichyl-phosphate-glucose / UDP-sugar diphosphatase / UDP-sugar diphosphatase activity / ADP-ribose diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / protein N-linked glycosylation via asparagine / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | ||||||
Authors | Balikci, E. / Feyerherm, C. / Bradshaw, W. / Seupel, R. / Brennan, P.E. / Bountra, C. / von Delft, F. / Huber, K. / Structural Genomics Consortium (SGC) | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: J.Med.Chem. / Year: 2024 Title: Unexpected Noncovalent Off-Target Activity of Clinical BTK Inhibitors Leads to Discovery of a Dual NUDT5/14 Antagonist. Authors: Balikci, E. / Marques, A.M.C. / Bauer, L.G. / Seupel, R. / Bennett, J. / Raux, B. / Buchan, K. / Simelis, K. / Singh, U. / Rogers, C. / Ward, J. / Cheng, C. / Szommer, T. / Schutzenhofer, K. ...Authors: Balikci, E. / Marques, A.M.C. / Bauer, L.G. / Seupel, R. / Bennett, J. / Raux, B. / Buchan, K. / Simelis, K. / Singh, U. / Rogers, C. / Ward, J. / Cheng, C. / Szommer, T. / Schutzenhofer, K. / Elkins, J.M. / Sloman, D.L. / Ahel, I. / Fedorov, O. / Brennan, P.E. / Huber, K.V.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8otv.cif.gz | 183.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8otv.ent.gz | 144 KB | Display | PDB format |
PDBx/mmJSON format | 8otv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8otv_validation.pdf.gz | 1015.3 KB | Display | wwPDB validaton report |
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Full document | 8otv_full_validation.pdf.gz | 1017 KB | Display | |
Data in XML | 8otv_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 8otv_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/8otv ftp://data.pdbj.org/pub/pdb/validation_reports/ot/8otv | HTTPS FTP |
-Related structure data
Related structure data | 8rdzC 8riyC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24228.287 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: CN(CC1)CCC1N2C3=NC=NC(N)=C3C(C4=CC=C(OC5=CC=CC=C5)C=C4)=N2 Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT14, UGPP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O95848, UDP-sugar diphosphatase #2: Chemical | Mass: 400.476 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H24N6O / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | ChemComp-DMS / | #4: Chemical | ChemComp-MG / | #5: 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: 2.6 Å3/Da / Density % sol: 52.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M sodium chloride, 25% PEG3350, 0.1M Bis-Tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→54.05 Å / Num. obs: 556903 / % possible obs: 99.5 % / Redundancy: 6.4 % / Biso Wilson estimate: 36.09 Å2 / CC1/2: 0.999 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.82→1.85 Å / Num. unique obs: 17936 / CC1/2: 0.295 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→54.05 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.15 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82→54.05 Å
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Refine LS restraints |
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LS refinement shell |
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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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