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- PDB-6te5: Crystal structure of human Aldehyde dehydrogenase 1A3 in complex ... -

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Basic information

Entry
Database: PDB / ID: 6te5
TitleCrystal structure of human Aldehyde dehydrogenase 1A3 in complex with LQ43 inhibitor compound
ComponentsAldehyde dehydrogenase family 1 member A3
KeywordsOXIDOREDUCTASE / Dehydrogenase isoenzyme ALDH1A3 Selective Inhibitor High grade Glioma
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 / retinoic acid metabolic process / retinol metabolic process / inner ear morphogenesis / thyroid hormone binding / face development / 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
Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
Chem-N4Q / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Retinaldehyde dehydrogenase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsGelardi, E.L.M. / Garavaglia, S.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of Education Italy
CitationJournal: 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
DepositionNov 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde dehydrogenase family 1 member A3
B: Aldehyde dehydrogenase family 1 member A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,4947
Polymers112,3552
Non-polymers2,1405
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-31 kcal/mol
Surface area34100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.184, 89.338, 159.208
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Aldehyde dehydrogenase family 1 member A3 / Aldehyde dehydrogenase 6 / Retinaldehyde dehydrogenase 3 / RalDH3


Mass: 56177.289 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 ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-N4Q / 6-(3,5-dimethoxyphenyl)-2-(4-methoxyphenyl)imidazo[1,2-a]pyridine


Mass: 360.406 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H20N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.13 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / Details: Sodium Malonate 2.4M pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.967 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 3.25→47.956 Å / Num. all: 18856 / Num. obs: 18856 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rpim(I) all: 0.076 / Rrim(I) all: 0.185 / Rsym value: 0.168 / Net I/av σ(I): 4.3 / Net I/σ(I): 8.9 / Num. measured all: 105886
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
3.25-3.435.90.77211570526740.3390.8460.7722.499.9
3.43-3.635.80.4761.61484125720.2110.5220.4763.899.9
3.63-3.885.60.3152.41360124360.1420.3470.3155.599.9
3.88-4.25.30.2083.61176622280.0970.2310.2087.5100
4.2-4.64.70.1255.7966620770.0630.1410.12510.299.8
4.6-5.146.10.1166.21150119000.050.1270.11612.5100
5.14-5.9360.1295.71025817000.0550.140.12911.3100
5.93-7.275.90.1136.4854514470.0490.1240.11311.8100
7.27-10.285.70.05112.6657911520.0220.0560.05122100
10.28-47.9565.10.04611.634246700.0220.0510.04622.698.6

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.14-3260-000refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FHZ

5fhz


Resolution: 3.25→47.956 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2376 --
Rwork0.1867 --
obs-18829 99.71 %
Displacement parametersBiso max: 138.55 Å2 / Biso mean: 57.2162 Å2 / Biso min: 22.26 Å2
Refinement stepCycle: LAST / Resolution: 3.25→47.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7446 0 148 20 7614

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