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- PDB-9hwq: Crystal structure of the Keap1 Kelch domain in complex with the X... -

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Basic information

Entry
Database: PDB / ID: 9hwq
TitleCrystal structure of the Keap1 Kelch domain in complex with the XChem fragment Z19735904 at 1.14 Angstrom resolution.
ComponentsKelch-like ECH-associated protein 1
KeywordsPEPTIDE BINDING PROTEIN / Keap1 / Nrf2 / Oxidative stress / Inhibitor
Function / homology
Function and homology information


regulation of epidermal cell differentiation / Neddylation / Ub-specific processing proteases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / transcription regulator inhibitor activity / inclusion body ...regulation of epidermal cell differentiation / Neddylation / Ub-specific processing proteases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / transcription regulator inhibitor activity / inclusion body / cellular response to interleukin-4 / actin filament / centriolar satellite / disordered domain specific binding / cellular response to oxidative stress / midbody / ubiquitin-dependent protein catabolic process / in utero embryonic development / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / protein ubiquitination / regulation of autophagy / regulation of DNA-templated transcription / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Kelch-like ECH-associated protein 1 / : / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch motif / Kelch / Kelch repeat type 1 / 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 motif / Kelch / Kelch repeat type 1 / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
~{N}-cyclohexyl-2-phenoxy-ethanamide / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsNarayanan, D. / Bach, A. / Gajhede, M.
Funding support Denmark, 1items
OrganizationGrant numberCountry
LundbeckfondenR366-2021-270 Denmark
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Fragment-Based Drug Discovery of Novel High-affinity, Selective, and Anti-inflammatory Inhibitors of the Keap1-Nrf2 Protein-Protein Interaction.
Authors: Lin, C. / Narayanan, D. / Barreca, M. / Poulsen, C. / da Costa, L.S. / Chen, X. / Wichman, K.G. / Charley, C.A. / Lindsay, J.L. / Dezfouli, M. / Vlissari, D. / Mortensen, T.S. / Chan, C.B. / ...Authors: Lin, C. / Narayanan, D. / Barreca, M. / Poulsen, C. / da Costa, L.S. / Chen, X. / Wichman, K.G. / Charley, C.A. / Lindsay, J.L. / Dezfouli, M. / Vlissari, D. / Mortensen, T.S. / Chan, C.B. / Wang, J. / Richardson, W. / Manning, C.E. / Chen, Z. / Zang, J. / Kack, H. / Gajhede, M. / Bullock, A.N. / Blake, D.J. / Olagnier, D. / Bach, A.
History
DepositionJan 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 8, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)34,77916
Polymers33,3621
Non-polymers1,41715
Water6,593366
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-60 kcal/mol
Surface area12070 Å2
Unit cell
Length a, b, c (Å)103.146, 103.146, 55.225
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

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


Mass: 33362.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Keap1, Inrf2, Kiaa0132
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9Z2X8
#2: Chemical ChemComp-B0A / ~{N}-cyclohexyl-2-phenoxy-ethanamide


Mass: 233.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.69 Å3/Da / Density % sol: 54.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.5 M AMMONIUM SULFATE, 0.1 M SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.6 AND 0.9 M LITHIUM SULFATE MONOHYDRATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.14→89.33 Å / Num. obs: 121832 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 11.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.038 / Rrim(I) all: 0.117 / Χ2: 0.85 / Net I/σ(I): 12.2
Reflection shellResolution: 1.14→1.17 Å / % possible obs: 100 % / Redundancy: 7.9 % / Rmerge(I) obs: 2.477 / Num. measured all: 70866 / Num. unique obs: 9027 / CC1/2: 0.494 / Rpim(I) all: 0.945 / Rrim(I) all: 2.655 / Χ2: 0.82 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.20.1_4487refinement
PDB_EXTRACTV4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.14→89.33 Å / SU ML: 0.1087 / Cross valid method: FREE R-VALUE / σ(F): 0.38 / Phase error: 17.1036
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1638 6298 5.17 %
Rwork0.1447 115465 -
obs0.1457 121763 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.18 Å2
Refinement stepCycle: LAST / Resolution: 1.14→89.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2220 0 78 366 2664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072412
X-RAY DIFFRACTIONf_angle_d1.02163288
X-RAY DIFFRACTIONf_chiral_restr0.0929342
X-RAY DIFFRACTIONf_plane_restr0.0102429
X-RAY DIFFRACTIONf_dihedral_angle_d6.9733355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.150.27632040.25453681X-RAY DIFFRACTION95.5
1.15-1.170.24192010.24723842X-RAY DIFFRACTION99.93
1.17-1.180.27071910.23123887X-RAY DIFFRACTION100
1.18-1.20.25351990.22323839X-RAY DIFFRACTION99.98
1.2-1.210.23782280.223777X-RAY DIFFRACTION99.98
1.21-1.230.23671840.22563935X-RAY DIFFRACTION99.95
1.23-1.240.23221930.2233811X-RAY DIFFRACTION99.98
1.24-1.260.26322070.20663833X-RAY DIFFRACTION100
1.26-1.280.22052190.2033846X-RAY DIFFRACTION99.98
1.28-1.30.19722130.18613846X-RAY DIFFRACTION99.95
1.3-1.330.20122050.17473817X-RAY DIFFRACTION99.98
1.33-1.350.18492100.16593839X-RAY DIFFRACTION100
1.35-1.380.20252280.15433853X-RAY DIFFRACTION99.98
1.38-1.40.17462010.14793801X-RAY DIFFRACTION99.98
1.41-1.440.18031950.1443880X-RAY DIFFRACTION100
1.44-1.470.18322030.14233852X-RAY DIFFRACTION99.98
1.47-1.510.15642500.13813784X-RAY DIFFRACTION100
1.51-1.550.15092130.13483857X-RAY DIFFRACTION100
1.55-1.590.14861940.11813876X-RAY DIFFRACTION99.98
1.59-1.640.15252020.11323869X-RAY DIFFRACTION100
1.64-1.70.14482370.11163808X-RAY DIFFRACTION100
1.7-1.770.12112090.11233855X-RAY DIFFRACTION100
1.77-1.850.13961950.11393879X-RAY DIFFRACTION100
1.85-1.950.16631860.13073919X-RAY DIFFRACTION100
1.95-2.070.12722120.11433823X-RAY DIFFRACTION100
2.07-2.230.13622460.11893833X-RAY DIFFRACTION99.98
2.23-2.450.15132260.13773872X-RAY DIFFRACTION100
2.45-2.810.15732320.13973863X-RAY DIFFRACTION100
2.81-3.540.1661880.13523928X-RAY DIFFRACTION99.98
3.54-89.330.1552270.15373960X-RAY DIFFRACTION99.86

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