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- PDB-9r6n: Crystal structure of ALDH1A2 in complex with KyA33 -

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Basic information

Entry
Database: PDB / ID: 9r6n
TitleCrystal structure of ALDH1A2 in complex with KyA33
ComponentsRetinal dehydrogenase 2
KeywordsOXIDOREDUCTASE / Inhibitor
Function / homology
Function and homology information


determination of bilateral symmetry / regulation of vascular endothelial cell proliferation / 3-chloroallyl aldehyde dehydrogenase activity / 9-cis-retinoic acid biosynthetic process / retinoic acid biosynthetic process / retinal dehydrogenase / ureter maturation / embryonic camera-type eye development / midgut development / pituitary gland development ...determination of bilateral symmetry / regulation of vascular endothelial cell proliferation / 3-chloroallyl aldehyde dehydrogenase activity / 9-cis-retinoic acid biosynthetic process / retinoic acid biosynthetic process / retinal dehydrogenase / ureter maturation / embryonic camera-type eye development / midgut development / pituitary gland development / morphogenesis of embryonic epithelium / RA biosynthesis pathway / proximal/distal pattern formation / vitamin A metabolic process / neural crest cell development / hindbrain development / retinal metabolic process / embryonic digestive tract development / aldehyde dehydrogenase (NAD+) activity / retinal binding / pancreas development / retinal dehydrogenase (NAD+) activity / embryonic forelimb morphogenesis / response to vitamin A / retinoic acid metabolic process / retinol metabolic process / anterior/posterior pattern specification / cardiac muscle tissue development / neural tube development / blood vessel development / face development / response to retinoic acid / heart morphogenesis / retinoic acid receptor signaling pathway / cellular response to retinoic acid / response to cytokine / lung development / kidney development / liver 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 / 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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
: / Retinal dehydrogenase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsFang, C. / Esposito, M. / Huang, J. / Kang, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Immunol. / Year: 2026
Title: Targeting autocrine retinoic acid signaling by ALDH1A2 inhibition enhances antitumor dendritic cell vaccine efficacy.
Authors: Fang, C. / Esposito, M. / Hars, U. / Byrne, R.T. / Song, B. / Huang, J. / Roichman, A. / Shue, L. / Cheng, X. / Proudfoot, J. / Zhao, D. / Wei, Y. / Cristea, I.M. / Rabinowitz, J.D. / Kang, Y.
History
DepositionMay 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinal dehydrogenase 2
B: Retinal dehydrogenase 2
C: Retinal dehydrogenase 2
D: Retinal dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,54541
Polymers217,2594
Non-polymers3,28637
Water57,5403194
1
A: Retinal dehydrogenase 2
C: Retinal dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,36522
Polymers108,6292
Non-polymers1,73620
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8520 Å2
ΔGint23 kcal/mol
Surface area34350 Å2
2
B: Retinal dehydrogenase 2
D: Retinal dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,17919
Polymers108,6292
Non-polymers1,55017
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint19 kcal/mol
Surface area34630 Å2
Unit cell
Length a, b, c (Å)81.639, 140.045, 84.775
Angle α, β, γ (deg.)90.00, 93.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Retinal dehydrogenase 2 / RALDH 2 / RalDH2 / Aldehyde dehydrogenase family 1 member A2 / ALDH1A2 / Retinaldehyde-specific ...RALDH 2 / RalDH2 / Aldehyde dehydrogenase family 1 member A2 / ALDH1A2 / Retinaldehyde-specific dehydrogenase type 2 / RALDH(II)


Mass: 54314.730 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH1A2, RALDH2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: O94788, retinal dehydrogenase
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-A1IDQ / 3-ethyl-~{N}-(8-methyl-2-oxidanylidene-3,4-dihydro-1~{H}-quinolin-6-yl)pyridine-4-carboxamide


Mass: 309.362 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H19N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3194 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.23 Å3/Da / Density % sol: 44.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M L-Proline, 0.1 M HEPES-NaOH pH 7.50, 10% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 365896 / % possible obs: 98.5 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.043 / Rrim(I) all: 0.113 / Net I/σ(I): 9.3 / Num. measured all: 2497266
Reflection shellResolution: 1.4→1.48 Å / % possible obs: 97 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.635 / Num. measured all: 370489 / Num. unique obs: 52541 / CC1/2: 0.801 / Rpim(I) all: 0.258 / Rrim(I) all: 0.686 / Net I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
DIALS3.8.0data reduction
SCALA3.3.22data scaling
REFMAC5.8.0352phasing
REFMAC5.8.0352refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.4→29.82 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.029 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1767 18629 5.1 %RANDOM
Rwork0.15573 ---
obs0.15682 346817 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.619 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å2-0.07 Å2
2--0.06 Å20 Å2
3----0.86 Å2
Refinement stepCycle: 1 / Resolution: 1.4→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15250 0 224 3194 18668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01216283
X-RAY DIFFRACTIONr_bond_other_d0.0010.01615032
X-RAY DIFFRACTIONr_angle_refined_deg1.0191.65422093
X-RAY DIFFRACTIONr_angle_other_deg0.3671.56135157
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44952118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.2135107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.517102772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0540.22391
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219168
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023252
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6040.9248044
X-RAY DIFFRACTIONr_mcbond_other0.6040.9248045
X-RAY DIFFRACTIONr_mcangle_it0.9661.38610087
X-RAY DIFFRACTIONr_mcangle_other0.9661.38610088
X-RAY DIFFRACTIONr_scbond_it1.1951.1078239
X-RAY DIFFRACTIONr_scbond_other1.1951.1078240
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8281.58811929
X-RAY DIFFRACTIONr_long_range_B_refined5.72923.03620195
X-RAY DIFFRACTIONr_long_range_B_other4.98114.13818629
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å
RfactorNum. reflection% reflection
Rfree0.24 1317 -
Rwork0.224 24730 -
obs--94.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.05570.03340.09060.1442-0.03970.26030.0238-0.0117-0.00190.0166-0.02020.00110.0096-0.0055-0.00360.0236-0.00580.00430.02130.00590.0266435.875-138.404130.427
20.0809-0.0120.02460.25760.06080.11890.02060.0199-0.0243-0.0376-0.02680.05690.0041-0.00720.00610.01760.0068-0.02040.0182-0.01730.0482408.981-150.91690.577
30.08620.0001-0.01870.1993-0.01840.11730.0033-0.02460.01270.02230.00280.0512-0.0231-0.0166-0.00620.0130.00790.01830.0269-0.00940.0548405.981-118.501121.878
40.0697-0.0484-0.09180.1157-0.0120.21050.03520.00940.0023-0.0302-0.0267-0.0057-0.02960.0001-0.00850.03490.0120.00840.02240.00740.0214439.055-129.73886.357
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 999
2X-RAY DIFFRACTION2B20 - 999
3X-RAY DIFFRACTION3C20 - 999
4X-RAY DIFFRACTION4D20 - 999

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