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- PDB-4l2o: Crystal structure of human ALDH3A1 with its selective inhibitor 1... -

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Basic information

Entry
Database: PDB / ID: 4l2o
TitleCrystal structure of human ALDH3A1 with its selective inhibitor 1-(4-fluorophenyl)sulfonyl-2-methylbenzimidazole
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 / 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 / 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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-1DD / ACETATE ION / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Aldehyde dehydrogenase, dimeric NADP-preferring
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.937 Å
AuthorsHurley, T.D. / Parajuli, B.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Crystal structure of human ALDH3A1 with its selective inhibitor 1-(4-fluorophenyl)sulfonyl-2-methylbenzimidazole
Authors: Parajuli, B. / Hurley, T.D.
History
DepositionJun 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 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_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.pdbx_dist_value / _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_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

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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
E: Aldehyde dehydrogenase
G: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,30823
Polymers208,9834
Non-polymers4,32519
Water16,358908
1
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,67312
Polymers104,4912
Non-polymers2,18210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11610 Å2
ΔGint-48 kcal/mol
Surface area30950 Å2
MethodPISA
2
E: Aldehyde dehydrogenase
G: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,63411
Polymers104,4912
Non-polymers2,1439
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11400 Å2
ΔGint-47 kcal/mol
Surface area31340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.221, 90.916, 117.925
Angle α, β, γ (deg.)90.00, 112.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABEG

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


Mass: 52245.738 Da / Num. of mol.: 4
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)+]

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Non-polymers , 5 types, 927 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical
ChemComp-1DD / 1-[(4-fluorophenyl)sulfonyl]-2-methyl-1H-benzimidazole


Mass: 290.313 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H11FN2O2S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 908 / 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: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Potassium acetate, 20% PEG 3350, (4 microlitres of 4 mg/mL of ALDH3A1 + 4 microlitres of mother liquor), 1 mM NAD+, 1 mM compound solution, 1 DMSO, pH 7.5, VAPOR DIFFUSION, SITTING ...Details: 0.2 M Potassium acetate, 20% PEG 3350, (4 microlitres of 4 mg/mL of ALDH3A1 + 4 microlitres of mother liquor), 1 mM NAD+, 1 mM compound solution, 1 DMSO, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9869 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 27, 2013 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9869 Å / Relative weight: 1
ReflectionResolution: 1.937→50 Å / Num. all: 132178 / Num. obs: 127287 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0.2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.34 / Rsym value: 0.072 / Net I/σ(I): 10.9
Reflection shellResolution: 1.937→1.98 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.5 / Num. unique all: 6331 / % possible all: 92.6

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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: 1.937→40 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.411 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25047 6642 5 %RANDOM
Rwork0.21456 ---
obs0.21636 125475 95.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.032 Å2
Baniso -1Baniso -2Baniso -3
1--2 Å2-0 Å2-0.51 Å2
2--3.44 Å2-0 Å2
3----1.83 Å2
Refinement stepCycle: LAST / Resolution: 1.937→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13947 0 279 908 15134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0214659
X-RAY DIFFRACTIONr_angle_refined_deg1.0321.99719946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.93251823
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5124.525621
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.649152536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2811582
X-RAY DIFFRACTIONr_chiral_restr0.0640.22231
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02111006
LS refinement shellResolution: 1.937→1.987 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 434 -
Rwork0.245 8096 -
obs--85.15 %

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