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- PDB-4l1o: Crystal structure of human ALDH3A1 with inhibitor 1-{[4-(1,3-benz... -

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Basic information

Entry
Database: PDB / ID: 4l1o
TitleCrystal structure of human ALDH3A1 with inhibitor 1-{[4-(1,3-benzodioxol-5-ylmethyl)piperazin-1-yl]methyl}-1H-indole-2,3-dione
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE/Inhibitor / Catalyzes benzaldehyde / Rossmann fold / Dehydrogenase / NADP+ binding / OXIDOREDUCTASE-Inhibitor complex
Function / homology
Function and homology information


aldehyde dehydrogenase [NAD(P)+] / 3-chloroallyl aldehyde dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) activity / alcohol dehydrogenase (NADP+) activity / aldehyde dehydrogenase [NAD(P)+] activity / cellular aldehyde metabolic process / aldehyde dehydrogenase (NAD+) activity / Phase I - Functionalization of compounds / xenobiotic metabolic process / lipid metabolic process ...aldehyde dehydrogenase [NAD(P)+] / 3-chloroallyl aldehyde dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) activity / alcohol dehydrogenase (NADP+) activity / aldehyde dehydrogenase [NAD(P)+] activity / cellular aldehyde metabolic process / aldehyde dehydrogenase (NAD+) activity / Phase I - Functionalization of compounds / xenobiotic metabolic process / lipid metabolic process / endoplasmic reticulum / extracellular space / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Aldehyde dehydrogenase NAD(P)-dependent / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / 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 NAD(P)-dependent / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-1VL / ACETATE ION / : / Aldehyde dehydrogenase, dimeric NADP-preferring
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHurley, T.D. / Parajuli, B.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Development of selective inhibitors for aldehyde dehydrogenases based on substituted indole-2,3-diones.
Authors: Kimble-Hill, A.C. / Parajuli, B. / Chen, C.H. / Mochly-Rosen, D. / Hurley, T.D.
History
DepositionJun 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Structure summary
Revision 1.2Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Jun 5, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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 / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,52910
Polymers104,4912
Non-polymers1,0378
Water11,674648
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9520 Å2
ΔGint-32 kcal/mol
Surface area32740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.257, 86.396, 170.225
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aldehyde dehydrogenase / ALDHIII / Aldehyde dehydrogenase 3 / Aldehyde dehydrogenase family 3 member A1


Mass: 52245.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH3, ALDH3A1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
References: UniProt: P30838, aldehyde dehydrogenase [NAD(P)+]
#2: Chemical ChemComp-1VL / (3S)-1-{[4-(1,3-benzodioxol-5-ylmethyl)piperazin-1-yl]methyl}-3-hydroxy-1,3-dihydro-2H-indol-2-one


Mass: 381.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H23N3O4
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 648 / Source method: isolated from a natural source / Formula: H2O

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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: 2.16 Å3/Da / Density % sol: 42.93 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Potassium Acetate, 20% PEG 3350, (3 microlitres of 3mg/ml of ALDH3A1+ 3 microlitres of mother liquor), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 2, 2011 / Details: OSMIC CONFOCAL BLUE
RadiationMonochromator: OSMIC CONFOCAL BLUE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 37399 / % possible obs: 90.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0.2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.146 / Rsym value: 0.06 / Net I/σ(I): 16.26
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 6.7 / Num. unique all: 2921 / % possible all: 88.1

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Processing

Software
NameVersionClassification
HKL-3000data collection
AMoREphasing
REFMAC5refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3SZA

3sza


Resolution: 2.3→47.95 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.901 / SU B: 6.435 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.483 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22513 1990 5.1 %RANDOM
Rwork0.17686 ---
obs0.17936 37399 95.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å2-0 Å20 Å2
2--0.37 Å2-0 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7019 0 48 648 7715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0197366
X-RAY DIFFRACTIONr_bond_other_d0.0030.027128
X-RAY DIFFRACTIONr_angle_refined_deg1.0891.97810011
X-RAY DIFFRACTIONr_angle_other_deg0.724316468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4945937
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.16124.479317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65151297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9171542
X-RAY DIFFRACTIONr_chiral_restr0.0560.21116
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218349
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021613
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 129 -
Rwork0.201 2529 -
obs--88.66 %

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