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- PDB-7um9: Human ALDH1A1 with bound compound CM38 -

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Basic information

Entry
Database: PDB / ID: 7um9
TitleHuman ALDH1A1 with bound compound CM38
ComponentsRetinal dehydrogenase 1
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE inhibitor / Inhibitor / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE inhibitor complex
Function / homology
Function and homology information


fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / benzaldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency / retinal dehydrogenase / gamma-aminobutyric acid biosynthetic process / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / Fructose catabolism ...fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / benzaldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency / retinal dehydrogenase / gamma-aminobutyric acid biosynthetic process / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / Fructose catabolism / Ethanol oxidation / aldehyde metabolic process / RA biosynthesis pathway / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / cellular detoxification of aldehyde / androgen binding / aldehyde dehydrogenase (NAD+) activity / retinal dehydrogenase activity / retinol metabolic process / negative regulation of cold-induced thermogenesis / retinoid metabolic process / GTPase activator activity / NAD binding / axon / synapse / 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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-NQR / YTTERBIUM (III) ION / Aldehyde dehydrogenase 1A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHurley, T.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA214567 United States
CitationJournal: Cancers (Basel) / Year: 2022
Title: A Novel ALDH1A1 Inhibitor Blocks Platinum-Induced Senescence and Stemness in Ovarian Cancer.
Authors: Muralikrishnan, V. / Fang, F. / Given, T.C. / Podicheti, R. / Chtcherbinine, M. / Metcalfe, T.X. / Sriramkumar, S. / O'Hagan, H.M. / Hurley, T.D. / Nephew, K.P.
History
DepositionApr 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 8, 2023Group: 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.journal_volume / _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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4377
Polymers54,9251
Non-polymers1,5126
Water3,855214
1
A: Retinal dehydrogenase 1
hetero molecules

A: Retinal dehydrogenase 1
hetero molecules

A: Retinal dehydrogenase 1
hetero molecules

A: Retinal dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,74828
Polymers219,6984
Non-polymers6,04924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_555x,-y,-z1
Buried area28420 Å2
ΔGint-213 kcal/mol
Surface area57720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.108, 109.108, 83.077
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number89
Space group name H-MP422
Space group name HallP42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Retinal dehydrogenase 1 / RalDH1 / ALDH-E1 / ALHDII / Aldehyde dehydrogenase family 1 member A1 / Aldehyde dehydrogenase / cytosolic


Mass: 54924.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH1A1, ALDC, ALDH1, PUMB1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P00352, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor, retinal dehydrogenase

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Non-polymers , 5 types, 220 molecules

#2: Chemical ChemComp-NQR / (4-methylfuro[3,2-c]quinolin-2-yl)(piperidin-1-yl)methanone


Mass: 294.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-YB / YTTERBIUM (III) ION


Mass: 173.040 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Yb
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.25 Å3/Da / Density % sol: 45.35 % / Description: plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 10% PEG 3350, 100 mM Bis-Tris, pH 6.2, 200 mM NaCl, 5 mM YbCl3, 500 uM CM38

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.8→48.79 Å / Num. obs: 44719 / % possible obs: 95.6 % / Redundancy: 12.9 % / Biso Wilson estimate: 22.21 Å2 / CC1/2: 0.926 / CC star: 0.981 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.026 / Rrim(I) all: 0.096 / Χ2: 1.007 / Net I/σ(I): 24.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1783 / CC1/2: 0.926 / CC star: 0.981 / Rpim(I) all: 0.155 / Rrim(I) all: 0.528 / Χ2: 0.856 / % possible all: 77.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JWU

7jwu


Resolution: 1.8→48.79 Å / SU ML: 0.1937 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.7236
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2156 2000 4.47 %Random
Rwork0.1782 42700 --
obs0.1799 44700 95.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.45 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3816 0 70 214 4100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00644041
X-RAY DIFFRACTIONf_angle_d0.89515499
X-RAY DIFFRACTIONf_chiral_restr0.0518604
X-RAY DIFFRACTIONf_plane_restr0.0052708
X-RAY DIFFRACTIONf_dihedral_angle_d10.2827574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.31791140.25232432X-RAY DIFFRACTION77.67
1.85-1.90.29781200.23772565X-RAY DIFFRACTION82.11
1.9-1.950.26021300.22122760X-RAY DIFFRACTION87.52
1.95-2.020.24711360.22012897X-RAY DIFFRACTION92.08
2.02-2.090.23541430.20643080X-RAY DIFFRACTION98.2
2.09-2.170.26381490.20213161X-RAY DIFFRACTION100
2.17-2.270.26571480.19223161X-RAY DIFFRACTION99.97
2.27-2.390.23371480.18783161X-RAY DIFFRACTION99.94
2.39-2.540.25181480.1893177X-RAY DIFFRACTION99.7
2.54-2.740.23651500.18833183X-RAY DIFFRACTION99.97
2.74-3.010.22931490.18663199X-RAY DIFFRACTION99.97
3.01-3.450.21031510.18123219X-RAY DIFFRACTION99.82
3.45-4.340.19621530.15093262X-RAY DIFFRACTION100
4.35-48.790.15521610.14753443X-RAY DIFFRACTION99.64
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)
11.501790681450.175772229620.7081909696940.6565393891030.08697754718110.979676662695-0.0775380653045-0.0163298631252-0.3020901946540.103722997126-0.09270985720180.182659534510.3638889360650.08846246205090.03106200824220.3189849106740.06126365983310.1837011895680.2503532198920.1659628613670.40474558265654.5520036156-33.806776190723.6970344414
20.8791859244180.230297492817-0.1825516681240.397754351241-0.1324740211370.652077440442-0.134838423124-0.245561464987-0.3224544726880.101266151658-0.02977432640850.06890558684060.1111085094790.08378776213780.1049804740520.2602190828030.06653617681520.1015302962230.2362568844270.1209471271810.28897401374259.2941974991-23.690818468826.5399616031
30.7919086311560.0891219732049-0.2889850421790.523380225785-0.1024387041330.439281211231-0.12747021457-0.108925475109-0.1521780875260.06264554282760.01007421356150.1060727409770.05464484982730.01199516077650.08355429122740.1801208029550.03740615519670.06916656155340.1674368515670.03687407722040.19360965396654.4458070268-17.00279906417.1809761367
40.7608983603210.01085041245980.2451787605290.741686517517-0.286952227011.07877203428-0.139976455827-0.0899108100838-0.08177085404580.08738698746950.06971093098990.3599292785350.0995655159383-0.209888103570.04438074004150.200633743156-0.0006302734910360.1015659660780.2518987768940.02611391625240.38485587266623.1923211668-11.226169606317.4924295079
50.855670402954-0.1717682633420.006840133923270.5965883241610.1605644572040.436919894989-0.117216365435-0.193343401951-0.404826201180.1467027590280.090376034171-0.007584957921970.0970212011291-0.07250940644560.04870968415530.3288326030190.03846945775780.2284159098040.2883353128960.09306541070910.45332679916627.1732462363-22.120347598731.009499547
60.4432375865380.319355623756-0.3230912455630.798642471446-0.4314360339460.938007562908-0.0449008789671-0.1214734469030.08070606822320.2411089774340.1171209942420.348817641539-0.096166213638-0.0827190142048-0.04662188575980.2239722979990.04728186110.07844576981950.233449361160.01529902340360.28230378279827.3241191346-2.1264520345920.0432402934
70.220280305656-0.000357179024380.01231433305930.05041567745850.03894916253020.0218060207714-0.135769641791-0.0457802409939-0.02758530914680.03869370928730.02833978651170.0008679189896910.0386481524221-0.0003825094617480.08235854483070.2003910768720.008758506476310.02096071397250.207881950450.008243501485680.18905705026354.0517567131-2.388590160979.70726254842
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 81 )
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 269 )
4X-RAY DIFFRACTION4chain 'A' and (resid 270 through 329 )
5X-RAY DIFFRACTION5chain 'A' and (resid 330 through 384 )
6X-RAY DIFFRACTION6chain 'A' and (resid 385 through 454 )
7X-RAY DIFFRACTION7chain 'A' and (resid 455 through 501 )

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