[English] 日本語
Yorodumi- PDB-6s6w: Crystal Structure of human ALDH1A3 in complex with 2,6-diphenylim... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s6w | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of human ALDH1A3 in complex with 2,6-diphenylimidazo[1,2-a]pyridine (compound GA11) and NAD+ | ||||||
Components | Aldehyde dehydrogenase family 1 member A3 | ||||||
Keywords | CYTOSOLIC PROTEIN / ALDH1A3 GA11 Glioma 2 / 6-diphenylimidazo[1 / 2-a]pyridine Retinaldehyde dehydrogenase inhinitor ALDHs | ||||||
Function / homology | Function and homology information nucleus accumbens development / optic cup morphogenesis involved in camera-type eye development / olfactory pit development / Harderian gland development / retinoic acid biosynthetic process / embryonic eye morphogenesis / retinal dehydrogenase / embryonic camera-type eye development / aldehyde dehydrogenase [NAD(P)+] activity / RA biosynthesis pathway ...nucleus accumbens development / optic cup morphogenesis involved in camera-type eye development / olfactory pit development / Harderian gland development / retinoic acid biosynthetic process / embryonic eye morphogenesis / retinal dehydrogenase / embryonic camera-type eye development / aldehyde dehydrogenase [NAD(P)+] activity / RA biosynthesis pathway / righting reflex / retinal metabolic process / aldehyde dehydrogenase (NAD+) activity / retinal dehydrogenase activity / retinol metabolic process / retinoic acid metabolic process / inner ear morphogenesis / face development / thyroid hormone binding / neuromuscular process controlling balance / NAD+ binding / locomotory behavior / protein homotetramerization / positive regulation of apoptotic process / apoptotic process / protein homodimerization activity / extracellular exosome / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.25 Å | ||||||
Authors | Gelardi, E.L.M. / Quattrini, L. / LaMotta, C. / Ferraris, D.M. / Garavaglia, S. | ||||||
Funding support | Italy, 1items
| ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: Imidazo[1,2-a]pyridine Derivatives as Aldehyde Dehydrogenase Inhibitors: Novel Chemotypes to Target Glioblastoma Stem Cells. Authors: Quattrini, L. / Gelardi, E.L.M. / Coviello, V. / Sartini, S. / Ferraris, D.M. / Mori, M. / Nakano, I. / Garavaglia, S. / La Motta, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6s6w.cif.gz | 201.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6s6w.ent.gz | 159.1 KB | Display | PDB format |
PDBx/mmJSON format | 6s6w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s6/6s6w ftp://data.pdbj.org/pub/pdb/validation_reports/s6/6s6w | HTTPS FTP |
---|
-Related structure data
Related structure data | 6te5C 5fhzS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 53813.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH1A3, ALDH6 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P47895, retinal dehydrogenase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-KXT / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.95 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 2.4M NaMalonate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07227 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2018 / Details: Rontec Xflash X-ray fluorescence detector | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.07227 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.25→48.017 Å / Num. all: 18877 / Num. obs: 18877 / % possible obs: 99.8 % / Redundancy: 4.7 % / Rpim(I) all: 0.064 / Rrim(I) all: 0.144 / Rsym value: 0.128 / Net I/av σ(I): 5.7 / Net I/σ(I): 9.8 / Num. measured all: 88980 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-Processing
Software |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FHZ Resolution: 3.25→48 Å / Cross valid method: THROUGHOUT
| ||||||||||||||||||
Displacement parameters | Biso max: 160.89 Å2 / Biso mean: 78.2344 Å2 / Biso min: 33.14 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.25→48 Å
|