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Yorodumi- PDB-5tpg: Optimization of spirocyclic proline tryptophanhydroxylase-1 inhibitors -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tpg | ||||||
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Title | Optimization of spirocyclic proline tryptophanhydroxylase-1 inhibitors | ||||||
Components | Tryptophan 5-hydroxylase 1Tryptophan hydroxylase | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE inhibitor / TPH1 / Iron / acyl / quanidine / OXIDOREDUCTASE-INHIBITOR complex / OXIDOREDUCTASE-OXIDOREDUCTASE inhibitor complex | ||||||
Function / homology | Function and homology information regulation of hemostasis / tryptophan 5-monooxygenase / tryptophan 5-monooxygenase activity / Serotonin and melatonin biosynthesis / serotonin biosynthetic process / aromatic amino acid metabolic process / platelet degranulation / bone remodeling / NGF-stimulated transcription / negative regulation of ossification ...regulation of hemostasis / tryptophan 5-monooxygenase / tryptophan 5-monooxygenase activity / Serotonin and melatonin biosynthesis / serotonin biosynthetic process / aromatic amino acid metabolic process / platelet degranulation / bone remodeling / NGF-stimulated transcription / negative regulation of ossification / response to immobilization stress / positive regulation of fat cell differentiation / mammary gland alveolus development / circadian rhythm / neuron projection / iron ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å | ||||||
Authors | Stein, A.J. / Goldberg, D.R. / De Lombaert, S. / Holt, M.C. | ||||||
Citation | Journal: Bioorg. Med. Chem. Lett. / Year: 2017 Title: Optimization of spirocyclic proline tryptophan hydroxylase-1 inhibitors. Authors: Goldberg, D.R. / De Lombaert, S. / Aiello, R. / Bourassa, P. / Barucci, N. / Zhang, Q. / Paralkar, V. / Stein, A.J. / Holt, M. / Valentine, J. / Zavadoski, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tpg.cif.gz | 76.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tpg.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 5tpg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/5tpg ftp://data.pdbj.org/pub/pdb/validation_reports/tp/5tpg | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 35471.332 Da / Num. of mol.: 1 / Fragment: UNP residues 104-402 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TPH1, TPH, TPRH, TRPH / Production host: Escherichia coli (E. coli) / References: UniProt: P17752, tryptophan 5-monooxygenase |
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-Non-polymers , 5 types, 181 molecules
#2: Chemical | ChemComp-FE / | ||||
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#3: Chemical | ChemComp-TRS / | ||||
#4: Chemical | #5: Chemical | ChemComp-7H5 / ( | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20% PEG 3350, 0.1 Na Citrate, pH 5.5, 4% Acetonitrile |
-Data collection
Diffraction | Mean temperature: 190 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 16, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→50 Å / Num. obs: 44280 / % possible obs: 99.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.066 / Χ2: 1.146 / Net I/av σ(I): 23.463 / Net I/σ(I): 8 / Num. measured all: 162965 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→33.67 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.803 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 26.679 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→33.67 Å
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Refine LS restraints |
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