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- PDB-9j71: Crystal strcuture of Keap1_compound_7 -

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Basic information

Entry
Database: PDB / ID: 9j71
TitleCrystal strcuture of Keap1_compound_7
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 17, 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

Downloads & links

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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)128,9387
Polymers126,3334
Non-polymers2,6053
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)64,5763
Polymers63,1672
Non-polymers1,4101
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)109.473, 73.870, 123.081
Angle α, β, γ (deg.)90.000, 100.550, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 325 through 382 or resid 388 through 528 or resid 530 through 609))
d_2ens_1(chain "B" and (resid 325 through 382 or resid 388 through 528 or resid 530 through 609))
d_3ens_1(chain "C" and (resid 325 through 528 or resid 530 through 609))
d_4ens_1(chain "X" and (resid 325 through 382 or resid 388 through 528 or resid 530 through 609))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLYGLYASNASNAA325 - 3824 - 61
d_12THRTHRGLNGLNAA388 - 52867 - 207
d_13GLNGLNTHRTHRAA530 - 609209 - 288
d_21GLYGLYASNASNBB325 - 3824 - 61
d_22THRTHRGLNGLNBB388 - 52867 - 207
d_23GLNGLNTHRTHRBB530 - 609209 - 288
d_31GLYGLYGLNGLNCC325 - 5284 - 207
d_32GLNGLNTHRTHRCC530 - 609209 - 288
d_41GLYGLYASNASNXD325 - 3824 - 61
d_42THRTHRGLNGLNXD388 - 52867 - 207
d_43GLNGLNTHRTHRXD530 - 609209 - 288

NCS oper:
IDCodeMatrixVector
1given(0.380961222129, -0.591504708999, -0.710626995312), (0.636678285805, -0.389502916496, 0.665528540654), (-0.670454552985, -0.705981343431, 0.22821269708)42.0813124196, -59.9960488939, 79.850411981
2given(-0.997489506583, -0.0037582525383, 0.0707146363474), (-0.00368632923831, 0.999992547005, 0.00114756716891), (-0.0707184221588, 0.000884008777544, -0.997495926456)151.589550901, 5.28226636783, 77.0048979663
3given(-0.311997554703, -0.506720461519, 0.803674000909), (-0.614063363573, -0.537922821977, -0.577551056716), (0.724971524528, -0.673701277626, -0.143327865916)37.2463399813, 80.5425199574, -18.296568376

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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-A1EMI / ~{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-[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]propanamide


Mass: 1409.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C64H68N10O19S4 / 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: 3.87 Å3/Da / Density % sol: 68.24 %
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→44.45 Å / Num. obs: 75180 / % possible obs: 99.03 % / Redundancy: 6.6 % / Biso Wilson estimate: 75.45 Å2 / CC1/2: 0.991 / Net I/σ(I): 8.96
Reflection shellResolution: 2.993→3.1 Å / Num. unique obs: 3859 / CC1/2: 0.627

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
PHENIX1.17.1_3660phasing
Cootmodel building
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.993→44.45 Å / SU ML: 0.4729 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.8982
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2907 3843 5.11 %
Rwork0.2525 71337 -
obs0.2545 75180 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.68 Å2
Refinement stepCycle: LAST / Resolution: 2.993→44.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8757 0 179 0 8936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00449253
X-RAY DIFFRACTIONf_angle_d0.906512629
X-RAY DIFFRACTIONf_chiral_restr0.05491305
X-RAY DIFFRACTIONf_plane_restr0.00541659
X-RAY DIFFRACTIONf_dihedral_angle_d21.41723351
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.875070233427
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.06623840901
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.909299897032
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.993-3.030.44991200.41342259X-RAY DIFFRACTION84.24
3.03-3.070.36051500.36052728X-RAY DIFFRACTION99.65
3.07-3.110.4191430.35062623X-RAY DIFFRACTION99.71
3.11-3.160.36351470.33832686X-RAY DIFFRACTION99.86
3.16-3.20.34561420.33382726X-RAY DIFFRACTION99.76
3.2-3.250.35361420.31892640X-RAY DIFFRACTION99.86
3.25-3.310.3451400.3132687X-RAY DIFFRACTION99.93
3.31-3.370.32611460.30712674X-RAY DIFFRACTION99.93
3.37-3.430.40311410.35142652X-RAY DIFFRACTION98.69
3.43-3.490.46491410.40412592X-RAY DIFFRACTION96.3
3.49-3.560.30211440.312667X-RAY DIFFRACTION99.89
3.56-3.640.37851460.34392675X-RAY DIFFRACTION99.51
3.64-3.730.40711340.39332523X-RAY DIFFRACTION93.85
3.73-3.820.30771440.2652639X-RAY DIFFRACTION99.71
3.82-3.920.40641410.34922500X-RAY DIFFRACTION91.89
3.92-4.040.28181400.24282670X-RAY DIFFRACTION99.15
4.04-4.170.24751410.2012669X-RAY DIFFRACTION100
4.17-4.320.22361430.18292683X-RAY DIFFRACTION99.79
4.32-4.490.17831460.18632704X-RAY DIFFRACTION99.89
4.49-4.690.2611440.1822651X-RAY DIFFRACTION99.68
4.69-4.940.21931510.18182747X-RAY DIFFRACTION99.83
4.94-5.250.23281420.18592653X-RAY DIFFRACTION99.89
5.25-5.650.21621440.20572638X-RAY DIFFRACTION99.89
5.65-6.220.29981490.24262708X-RAY DIFFRACTION99.65
6.22-7.120.27691410.24042655X-RAY DIFFRACTION99.79
7.12-8.960.29721420.23492693X-RAY DIFFRACTION99.82
8.96-44.450.24141390.20192595X-RAY DIFFRACTION96.57

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