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- PDB-6b5g: ALDH1A2 liganded with NAD and (3-ethoxythiophen-2-yl){4-[4-nitro-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6b5g | |||||||||
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Title | ALDH1A2 liganded with NAD and (3-ethoxythiophen-2-yl){4-[4-nitro-3-(pyrrolidin-1-yl)phenyl]piperazin-1-yl}methanone (compound 6-118) | |||||||||
![]() | Retinal dehydrogenase 2 | |||||||||
![]() | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / retinoic acid signaling / male contraception / drug discovery / drug development / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | |||||||||
Function / homology | ![]() determination of bilateral symmetry / : / regulation of vascular endothelial cell proliferation / 9-cis-retinoic acid biosynthetic process / 3-chloroallyl aldehyde dehydrogenase activity / retinoic acid biosynthetic process / retinal dehydrogenase / ureter maturation / embryonic camera-type eye development / morphogenesis of embryonic epithelium ...determination of bilateral symmetry / : / regulation of vascular endothelial cell proliferation / 9-cis-retinoic acid biosynthetic process / 3-chloroallyl aldehyde dehydrogenase activity / retinoic acid biosynthetic process / retinal dehydrogenase / ureter maturation / embryonic camera-type eye development / morphogenesis of embryonic epithelium / pituitary gland development / RA biosynthesis pathway / proximal/distal pattern formation / vitamin A metabolic process / neural crest cell development / retinal metabolic process / hindbrain development / embryonic digestive tract development / aldehyde dehydrogenase (NAD+) activity / retinal binding / response to vitamin A / cardiac muscle tissue development / embryonic forelimb morphogenesis / pancreas development / retinal dehydrogenase activity / neural tube development / retinol metabolic process / retinoic acid metabolic process / midgut development / blood vessel development / face development / heart morphogenesis / cellular response to retinoic acid / response to retinoic acid / liver development / response to cytokine / kidney development / lung development / neuron differentiation / response to estradiol / protein homotetramerization / cell population proliferation / positive regulation of apoptotic process / negative regulation of cell population proliferation / positive regulation of cell population proliferation / positive regulation of gene expression / perinuclear region of cytoplasm / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Chen, Y. / Zhu, J.-Y. / Schonbrunn, E. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis of ALDH1A2 Inhibition by Irreversible and Reversible Small Molecule Inhibitors. Authors: Chen, Y. / Zhu, J.Y. / Hong, K.H. / Mikles, D.C. / Georg, G.I. / Goldstein, A.S. / Amory, J.K. / Schonbrunn, E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 401.5 KB | Display | ![]() |
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PDB format | ![]() | 325.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 77.6 KB | Display | |
Data in CIF | ![]() | 106 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6aljSC ![]() 6b5hC ![]() 6b5iC S: Starting model for refinement 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: 54170.602 Da / Num. of mol.: 4 / Fragment: UNP residues 26-518 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-CQY / ( #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.52 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 40 mg/mL ALDH1A2, 0.2 M sodium citrate tribasic dehydrate, 20% w/v PEG3350, 1.3 mM 6-118, 4 mM NAD, 10% DMSO |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 22, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rosenbaum-Rock double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→51.112 Å / Num. obs: 98817 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 7.395 % / Biso Wilson estimate: 27.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.116 / Χ2: 0.986 / Net I/σ(I): 13.89 / Num. measured all: 730750 / Scaling rejects: 235 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 6ALJ Resolution: 2.2→51.112 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.6 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.66 Å2 / Biso mean: 30.8121 Å2 / Biso min: 13.22 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→51.112 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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