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- PDB-9j7g: Crystal strcuture of Keap1_compound_8 -

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Basic information

Entry
Database: PDB / ID: 9j7g
TitleCrystal strcuture of Keap1_compound_8
ComponentsKelch-like ECH-associated protein 1
KeywordsLIGASE / E3 ubiquitin ligase
Function / homology
Function and homology information


regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / 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 ...regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / 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 / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / midbody / cellular response to oxidative stress / ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / in utero embryonic development / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / regulation of autophagy / Ub-specific processing proteases / protein ubiquitination / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Kelch-like ECH-associated protein 1 / : / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch motif / Kelch repeat type 1 ...Kelch-like ECH-associated protein 1 / : / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch motif / 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
: / Chem-GFD / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.993 Å
AuthorsXu, K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acta Pharm Sin B / Year: 2025
Title: Chemical knockdown of Keap1 and homoPROTAC-ing allergic rhinitis
Authors: Yan, J. / Wang, T. / Yu, R. / Xu, L. / Shao, H. / Li, T. / Wang, Z. / Cha, X. / Miao, Z. / Xing, C. / Xu, K. / Liu, H. / Zhuang, C.
History
DepositionAug 18, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)128,9827
Polymers126,3334
Non-polymers2,6493
Water00
1
A: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1812
Polymers31,5831
Non-polymers5981
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kelch-like ECH-associated protein 1
X: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6203
Polymers63,1672
Non-polymers1,4541
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1812
Polymers31,5831
Non-polymers5981
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.472, 74.149, 123.113
Angle α, β, γ (deg.)90.000, 100.861, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 31583.299 Da / Num. of mol.: 4
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-GFD / 2-[(4-aminophenyl)sulfonyl-[4-[(2-azanyl-2-oxidanylidene-ethyl)-(4-methoxyphenyl)sulfonyl-amino]naphthalen-1-yl]amino]ethanamide


Mass: 597.663 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H27N5O7S2
#3: Chemical ChemComp-A1EMM / ~{N}-[4-[(2-azanyl-2-oxidanylidene-ethyl)-[4-[(2-azanyl-2-oxidanylidene-ethyl)-(4-methoxyphenyl)sulfonyl-amino]naphthalen-1-yl]sulfamoyl]phenyl]-3-[2-[2-[2-[3-[[4-[(2-azanyl-2-oxidanylidene-ethyl)-[4-[(2-azanyl-2-oxidanylidene-ethyl)-(4-methoxyphenyl)sulfonyl-amino]naphthalen-1-yl]sulfamoyl]phenyl]amino]-3-oxidanylidene-propoxy]ethoxy]ethoxy]ethoxy]propanamide


Mass: 1453.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C66H72N10O20S4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: 3.93 Å3/Da / Density % sol: 68.73 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.05 M Zinc acetate dihydrate, 20% w/v polyethylene glycol 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.993→44.56 Å / Num. obs: 39327 / % possible obs: 99.44 % / Redundancy: 6.8 % / Biso Wilson estimate: 80.87 Å2 / CC1/2: 0.997 / Net I/σ(I): 14.08
Reflection shellResolution: 2.993→3.1 Å / Num. unique obs: 3901 / CC1/2: 0.997

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660phasing
Cootmodel building
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.993→44.56 Å / SU ML: 0.3991 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.726
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2501 3864 5.09 %
Rwork0.1993 72105 -
obs0.2019 39327 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.26 Å2
Refinement stepCycle: LAST / Resolution: 2.993→44.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8759 0 182 0 8941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01039256
X-RAY DIFFRACTIONf_angle_d1.251512631
X-RAY DIFFRACTIONf_chiral_restr0.06211305
X-RAY DIFFRACTIONf_plane_restr0.00691658
X-RAY DIFFRACTIONf_dihedral_angle_d16.45481353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.993-3.030.36571410.33692577X-RAY DIFFRACTION97.95
3.03-3.070.35681410.31072608X-RAY DIFFRACTION99.35
3.07-3.110.32051330.28182503X-RAY DIFFRACTION98.25
3.11-3.150.32791400.28682609X-RAY DIFFRACTION99.89
3.15-3.20.28551370.25662563X-RAY DIFFRACTION99.52
3.2-3.240.35071370.26682572X-RAY DIFFRACTION98.65
3.24-3.290.30771380.2632605X-RAY DIFFRACTION99.89
3.29-3.350.26171420.2312595X-RAY DIFFRACTION99.53
3.35-3.410.28631370.23232568X-RAY DIFFRACTION98.79
3.41-3.470.29141390.23332586X-RAY DIFFRACTION99.93
3.47-3.530.28731390.22392618X-RAY DIFFRACTION98.61
3.53-3.610.29821390.21812568X-RAY DIFFRACTION99.85
3.61-3.680.27551420.21082615X-RAY DIFFRACTION99.67
3.68-3.770.26011340.2112557X-RAY DIFFRACTION99.15
3.77-3.860.2671360.19462585X-RAY DIFFRACTION99.82
3.86-3.970.26261370.19632544X-RAY DIFFRACTION99.19
3.97-4.090.23721380.17572621X-RAY DIFFRACTION99.46
4.09-4.220.20211390.1562576X-RAY DIFFRACTION99.27
4.22-4.370.17391400.15292620X-RAY DIFFRACTION99.39
4.37-4.540.18281370.15592528X-RAY DIFFRACTION99.63
4.54-4.750.25081360.15872605X-RAY DIFFRACTION99.02
4.75-50.19591400.16642573X-RAY DIFFRACTION99.23
5-5.310.22331390.16482591X-RAY DIFFRACTION99.2
5.31-5.720.24831370.18422603X-RAY DIFFRACTION99.53
5.72-6.30.25241350.21722518X-RAY DIFFRACTION98.59
6.3-7.20.31151410.21572597X-RAY DIFFRACTION99.35
7.21-9.070.25191380.21522544X-RAY DIFFRACTION98.35
9.07-44.560.22841320.20362456X-RAY DIFFRACTION94.25

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