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- PDB-5fnt: Structure of the Keap1 Kelch domain in complex with a small molec... -

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Basic information

Entry
Database: PDB / ID: 5fnt
TitleStructure of the Keap1 Kelch domain in complex with a small molecule inhibitor.
ComponentsKELCH-LIKE ECH-ASSOCIATED PROTEIN 1
KeywordsTRANSCRIPTION / KEAP1 / NRF2 / OXIDATIVE STRESS
Function / homology
Function and homology information


cellular response to carbohydrate stimulus / KEAP1-NFE2L2 pathway / regulation of epidermal cell differentiation / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity ...cellular response to carbohydrate stimulus / KEAP1-NFE2L2 pathway / regulation of epidermal cell differentiation / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity / cellular response to interleukin-4 / inclusion body / regulation of autophagy / actin filament / adherens junction / disordered domain specific binding / cellular response to oxidative stress / midbody / ubiquitin-dependent protein catabolic process / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / protein ubiquitination / negative regulation of gene expression / focal adhesion / regulation of DNA-templated transcription / endoplasmic reticulum / protein-containing complex / 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-0PL / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsDavies, T.G. / Wixted, W.E. / Coyle, J.E. / Griffiths-Jones, C. / Hearn, K. / McMenamin, R. / Norton, D. / Rich, S.J. / Richardson, C. / Saxty, G. ...Davies, T.G. / Wixted, W.E. / Coyle, J.E. / Griffiths-Jones, C. / Hearn, K. / McMenamin, R. / Norton, D. / Rich, S.J. / Richardson, C. / Saxty, G. / Willems, H.M.G. / Woolford, A.J. / Cottom, J.E. / Kou, J. / Yonchuk, J.G. / Feldser, H.G. / Sanchez, Y. / Foley, J.P. / Bolognese, B.J. / Logan, G. / Podolin, P.L. / Yan, H. / Callahan, J.F. / Heightman, T.D. / Kerns, J.K.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Mono-Acidic Inhibitors of the Kelch-Like Ech-Associated Protein 1 : Nuclear Factor Erythroid 2-Related Factor 2 (Keap1:Nrf2) Protein-Protein Interaction with High Cell Potency Identified by ...Title: Mono-Acidic Inhibitors of the Kelch-Like Ech-Associated Protein 1 : Nuclear Factor Erythroid 2-Related Factor 2 (Keap1:Nrf2) Protein-Protein Interaction with High Cell Potency Identified by Fragment-Based Discovery.
Authors: Davies, T.G. / Wixted, W.E. / Coyle, J.E. / Griffiths-Jones, C. / Hearn, K. / Mcmenamin, R.L. / Norton, D. / Rich, S.J. / Richardson, C. / Saxty, G. / Willems, H.M.G. / Woolford, A.J. / ...Authors: Davies, T.G. / Wixted, W.E. / Coyle, J.E. / Griffiths-Jones, C. / Hearn, K. / Mcmenamin, R.L. / Norton, D. / Rich, S.J. / Richardson, C. / Saxty, G. / Willems, H.M.G. / Woolford, A.J. / Cottom, J.E. / Kou, J. / Yonchuk, J.G. / Feldser, H.G. / Sanchez, Y. / Foley, J.P. / Bolognese, B.J. / Logan, G.A. / Podolin, P.L. / Yan, H. / Callahan, J.F. / Heightman, T.D. / Kerns, J.K.
History
DepositionNov 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 2.0Apr 4, 2018Group: Atomic model / Data collection / Category: atom_site / diffrn_source
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _diffrn_source.type
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)33,8973
Polymers33,3621
Non-polymers5342
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.349, 103.349, 56.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein KELCH-LIKE ECH-ASSOCIATED PROTEIN 1 / CYTOSOLIC INHIBITOR OF NRF2 / INRF2 / KEAP1


Mass: 33362.297 Da / Num. of mol.: 1 / Fragment: KELCH DOMAIN, RESIDUES 322-624
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9Z2X8
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-0PL / (3S)-3-{4-Chloro-3-[(N-methylbenzenesulfonamido) methyl]phenyl}-3-(1-methyl-1H-1,2,3-benzotriazol-5-yl)propanoic acid


Mass: 498.982 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H23ClN4O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 52.77 % / Description: NONE
Crystal growpH: 7
Details: 0.3-0.6 (NH4)2SO4, 0.4-1.4 M LI2SO4 AND 0.1 M NA3CITRATE-HCL PH 5.6

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ / Wavelength: 1.54187
DetectorType: RIGAKU CCD / Detector: CCD / Date: May 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.79→89.5 Å / Num. obs: 29094 / % possible obs: 90.6 % / Redundancy: 2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.3
Reflection shellResolution: 1.79→1.83 Å / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 2.6 / % possible all: 51.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X2J

1x2j


Resolution: 1.79→90.6 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.09 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20219 1478 5.1 %RANDOM
Rwork0.17037 ---
obs0.172 27616 90.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.696 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0.14 Å20 Å2
2---0.29 Å20 Å2
3---0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.79→90.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2219 0 35 353 2607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192338
X-RAY DIFFRACTIONr_bond_other_d0.0020.02222
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9283197
X-RAY DIFFRACTIONr_angle_other_deg0.2040.84547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3365300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80222.752109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04415.087344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7951521
X-RAY DIFFRACTIONr_chiral_restr0.1030.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0211848
X-RAY DIFFRACTIONr_gen_planes_other00.01511
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7891.6941167
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5892.1161171
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.794→1.841 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 54 -
Rwork0.266 1126 -
obs--49.43 %
Refinement TLS params.Method: refined / Origin x: 22.6818 Å / Origin y: 61.5301 Å / Origin z: 37.9264 Å
111213212223313233
T0.0263 Å20.0057 Å2-0.0105 Å2-0.0072 Å20.0018 Å2--0.0275 Å2
L2.16 °2-0.164 °2-0.6099 °2-2.6723 °20.5151 °2--1.0926 °2
S-0.033 Å °-0.0505 Å °-0.06 Å °0.1551 Å °0.0226 Å °0.1043 Å °0.0265 Å °0.0328 Å °0.0103 Å °

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