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- PDB-4xmb: Crystal structure of 2,2'-(naphthalene-1,4-diylbis(((4-methoxyphe... -

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Basic information

Entry
Database: PDB / ID: 4xmb
TitleCrystal structure of 2,2'-(naphthalene-1,4-diylbis(((4-methoxyphenyl)sulfonyl)azanediyl))diacetamide bound to human Keap1 Kelch domain
ComponentsKelch-like ECH-associated protein 1
KeywordsPROTEIN BINDING / nrf2 activators / cul3 / cullin3 / btb
Function / homology
Function and homology information


regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / inclusion body / cellular response to interleukin-4 / regulation of autophagy / actin filament / negative regulation of DNA-binding transcription factor activity ...regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / inclusion body / cellular response to interleukin-4 / regulation of autophagy / actin filament / negative regulation of DNA-binding transcription factor activity / KEAP1-NFE2L2 pathway / disordered domain specific binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / cellular response to oxidative stress / Neddylation / midbody / ubiquitin-dependent protein catabolic process / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / protein ubiquitination / Ub-specific processing proteases / endoplasmic reticulum / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Kelch-type beta propeller / Kelch-like ECH-associated protein 1 / : / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch repeat type 1 / Kelch motif ...Kelch-type beta propeller / Kelch-like ECH-associated protein 1 / : / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch repeat type 1 / Kelch motif / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / 6 Propeller / Neuraminidase / SKP1/BTB/POZ domain superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-41P / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.428 Å
AuthorsLuciano, J.P. / Ryuzoji, A.F. / Mesecar, A.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Walter Cancer Foundation - Purdue UniversityP30 CA023168 United States
CitationJournal: Eur.J.Med.Chem. / Year: 2015
Title: Probing the structural requirements of non-electrophilic naphthalene-based Nrf2 activators.
Authors: Jain, A.D. / Potteti, H. / Richardson, B.G. / Kingsley, L. / Luciano, J.P. / Ryuzoji, A.F. / Lee, H. / Krunic, A. / Mesecar, A.D. / Reddy, S.P. / Moore, T.W.
History
DepositionJan 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2672
Polymers31,6541
Non-polymers6131
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.470, 51.521, 67.238
Angle α, β, γ (deg.)90.00, 101.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Kelch-like ECH-associated protein 1 / Cytosolic inhibitor of Nrf2 / INrf2 / Kelch-like protein 19 / Keap1


Mass: 31654.373 Da / Num. of mol.: 1 / Fragment: Kelch domain (UNP residues 321-609)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1, INRF2, KIAA0132, KLHL19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14145
#2: Chemical ChemComp-41P / 2,2'-(naphthalene-1,4-diylbis(((4-methoxyphenyl)sulfonyl)azanediyl))diacetamide


Mass: 612.674 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H28N4O8S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.42 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium chloride, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.547 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.547 Å / Relative weight: 1
ReflectionResolution: 2.4275→32.971 Å / Num. obs: 9899 / % possible obs: 94.99 % / Redundancy: 3.4 % / Net I/σ(I): 6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4IN4

4in4


Resolution: 2.428→27.771 Å / SU ML: 0.26 / Cross valid method: NONE / σ(F): 1.4 / Phase error: 23.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2287 940 10 %
Rwork0.1707 --
obs0.1765 9401 94.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.428→27.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2201 0 42 143 2386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022303
X-RAY DIFFRACTIONf_angle_d0.6563143
X-RAY DIFFRACTIONf_dihedral_angle_d13.908840
X-RAY DIFFRACTIONf_chiral_restr0.041329
X-RAY DIFFRACTIONf_plane_restr0.002414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4275-2.55540.30211300.20041176X-RAY DIFFRACTION92
2.5554-2.71540.25421340.20911203X-RAY DIFFRACTION96
2.7154-2.92490.29041360.19731214X-RAY DIFFRACTION96
2.9249-3.21880.26681340.20481205X-RAY DIFFRACTION95
3.2188-3.68370.19721320.15151191X-RAY DIFFRACTION95
3.6837-4.63750.1951330.13871199X-RAY DIFFRACTION93
4.6375-27.77290.20171410.16431273X-RAY DIFFRACTION97

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