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- PDB-9hwv: Crystal structure of the Keap1 Kelch domain in complex with the s... -

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Basic information

Entry
Database: PDB / ID: 9hwv
TitleCrystal structure of the Keap1 Kelch domain in complex with the small molecule UCAB#1010 at 1.50 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
: / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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)34,58612
Polymers33,3621
Non-polymers1,22311
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-31 kcal/mol
Surface area12320 Å2
Unit cell
Length a, b, c (Å)103.128, 103.128, 54.923
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

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 171 molecules

#2: Chemical ChemComp-A1IXZ / (3~{S})-3-(1,3-benzodioxol-5-yl)-3-[7-[2-[[(1~{R})-cyclohex-2-en-1-yl]amino]-2-oxidanylidene-ethoxy]naphthalen-2-yl]propanoic acid


Mass: 473.517 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H27NO6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.5 M AMMONIUM SULFATE, 0.1 M SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.6 AND 1.0 M LITHIUM SULFATE MONOHYDRATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 23, 2022
RadiationMonochromator: Si (111), double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.5→46.78 Å / Num. obs: 53714 / % possible obs: 99.9 % / Redundancy: 20.4 % / Biso Wilson estimate: 17.77 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.211 / Rpim(I) all: 0.048 / Rrim(I) all: 0.217 / Χ2: 1.01 / Net I/σ(I): 11.9 / Num. measured all: 1097416
Reflection shellResolution: 1.5→1.52 Å / % possible obs: 97.3 % / Redundancy: 19.3 % / Rmerge(I) obs: 3.401 / Num. measured all: 49122 / Num. unique obs: 2548 / CC1/2: 0.451 / Rpim(I) all: 0.784 / Rrim(I) all: 3.493 / Χ2: 1.05 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
XDS20220604data reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
PHENIX1.20.1_4487refinement
PDB_EXTRACTV4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→44.66 Å / SU ML: 0.1418 / Cross valid method: FREE R-VALUE / σ(F): 0.58 / Phase error: 18.6394
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1824 2647 4.93 %
Rwork0.1647 51001 -
obs0.1656 53648 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.41 Å2
Refinement stepCycle: LAST / Resolution: 1.5→44.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2235 0 72 160 2467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912489
X-RAY DIFFRACTIONf_angle_d1.09233410
X-RAY DIFFRACTIONf_chiral_restr0.1004353
X-RAY DIFFRACTIONf_plane_restr0.0093452
X-RAY DIFFRACTIONf_dihedral_angle_d7.0303378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.28931560.2642555X-RAY DIFFRACTION97.34
1.52-1.550.24871360.24162683X-RAY DIFFRACTION99.82
1.55-1.580.23491110.22022696X-RAY DIFFRACTION99.79
1.58-1.620.21451450.21842677X-RAY DIFFRACTION99.82
1.62-1.660.20961640.19942631X-RAY DIFFRACTION99.86
1.66-1.70.24251390.19042678X-RAY DIFFRACTION99.89
1.7-1.740.20961490.17692661X-RAY DIFFRACTION99.93
1.74-1.80.19421450.16572681X-RAY DIFFRACTION100
1.8-1.850.18041500.162668X-RAY DIFFRACTION99.89
1.85-1.920.17411170.15292695X-RAY DIFFRACTION99.93
1.92-20.17441300.13822680X-RAY DIFFRACTION100
2-2.090.15451370.13732701X-RAY DIFFRACTION100
2.09-2.20.13871410.14032690X-RAY DIFFRACTION100
2.2-2.340.17281450.14582690X-RAY DIFFRACTION99.96
2.34-2.520.19421180.15282712X-RAY DIFFRACTION100
2.52-2.770.20531380.16582695X-RAY DIFFRACTION100
2.77-3.170.16011280.16662717X-RAY DIFFRACTION99.96
3.17-3.990.16971500.16382714X-RAY DIFFRACTION100
3.99-44.660.18431480.16482777X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.540379104424-0.02814467024850.1355442519570.312700503793-0.420507880020.4270838252780.2117039225410.09805862006950.262072344218-0.155940797323-0.190881721573-0.326421594371-0.0281381336820.0537475326319-0.001482202377860.207119235150.04580662250170.05284371341630.1989299874010.04314760393270.22547872595145.24789500618.6141479413-10.5494516588
20.09635127538650.106432759271-0.008843855128880.0984255004462-0.02447125281490.06046343187460.08177323384750.1039501048260.141484672007-0.10482163077-0.06632299297990.0447068510299-0.0364715865366-0.135397829525-9.35824802488E-60.2090038324990.03551796185030.00804717694660.1635837173380.0003200073340110.16099705235133.475192634217.3750928575-8.5337582263
30.9299636476390.102259756881-0.1557434791370.232846926682-0.3656879995910.2811017823990.1676436310670.1018220894070.329405930101-0.118254142315-0.03591658800150.104637721113-0.266198433792-0.158299742890.005621346899820.2197460193370.04185862245780.02490716326320.157199674820.01970829552310.16712613173231.377180609922.0769809575-8.18763663938
40.279604458353-0.140701696793-0.01235147578740.571285219266-0.367928651450.2749856439250.05344274150820.05152277317830.00790520756376-0.04879752489080.02966585993850.150259268103-0.0257484967065-0.09237841338940.003519421841880.1511759526640.0168246475483-0.009105053869040.150947722717-0.02377883408220.17012822504425.327782996711.1163358724-0.413990195576
50.9289939853780.1156532888630.1912870202380.594009672326-0.2626429134960.253389804374-0.0342548310267-0.0907242174382-0.1449923757060.07149038962740.02497671368950.07083284451960.0222978423493-0.017570117838-0.0001665249142790.1594979741540.00280944469404-0.002449964665370.136622134415-0.01454703954160.15041723451634.92684112722.230804738467.42159758705
60.528542368684-0.228183624123-0.07505131871460.280776152376-0.3363451124950.42738195960.0787231936852-0.247307267877-0.02565535314670.0911662132821-0.13121003572-0.02943551986620.004666516958650.07178984117-0.002111168791760.149337051644-0.00822386130346-0.02427075084590.153437387897-0.01165687580990.14797480187146.3201424492.6107713747610.1761356538
70.610057118492-0.139805940265-0.004819488868940.408414852516-0.5863692373020.6352881536470.02066280423210.0756330366040.182266785610.0204838044836-0.0920371755206-0.210831789333-0.1595938418390.196218147502-0.0001045124281660.184387025979-0.00113878783025-0.004518899664720.164327970977-0.002947190546470.15783277178251.463371908611.43917995970.386226756098
80.2795147958390.146867748352-0.1522995137090.133866910361-0.09171113805750.1657948301670.03608125344620.2256998749790.146121455464-0.149256287954-0.106239251468-0.128024925919-0.05696613879720.1607731934984.18343883689E-50.2070765785060.01535735157580.03575965223080.2282181578770.01502656321280.19965679480848.523918063515.1380492261-7.48078473061
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 323 through 355 )323 - 3551 - 33
22chain 'A' and (resid 356 through 377 )356 - 37734 - 55
33chain 'A' and (resid 378 through 405 )378 - 40556 - 83
44chain 'A' and (resid 406 through 453 )406 - 45384 - 131
55chain 'A' and (resid 454 through 522 )454 - 522132 - 200
66chain 'A' and (resid 523 through 547 )523 - 547201 - 225
77chain 'A' and (resid 548 through 589 )548 - 589226 - 267
88chain 'A' and (resid 590 through 613 )590 - 613268 - 291

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