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

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Basic information

Entry
Database: PDB / ID: 5fnq
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 / Cul3-RING ubiquitin ligase complex / ubiquitin ligase-substrate adaptor activity / centriolar satellite / inclusion body ...cellular response to carbohydrate stimulus / KEAP1-NFE2L2 pathway / regulation of epidermal cell differentiation / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / Cul3-RING ubiquitin ligase complex / ubiquitin ligase-substrate adaptor activity / centriolar satellite / inclusion body / cellular response to interleukin-4 / regulation of autophagy / actin filament / adherens junction / disordered domain specific binding / cellular response to oxidative stress / ubiquitin-dependent protein catabolic process / midbody / 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
3-(4-CHLOROPHENYL)PROPANOIC ACID / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.91 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 18, 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 / _atom_site.pdbx_formal_charge / _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)33,5472
Polymers33,3621
Non-polymers1851
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.625, 103.625, 56.027
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-S0W / 3-(4-CHLOROPHENYL)PROPANOIC ACID


Mass: 184.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9ClO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 52.74 % / Description: NONE
Crystal growpH: 7
Details: 0.3-0.6 M (NH4)2SO4, 0.4-1.4 M LI2SO4, 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: Apr 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.91→44.87 Å / Num. obs: 26103 / % possible obs: 97.7 % / Redundancy: 3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.3
Reflection shellResolution: 1.91→1.95 Å / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 4.8 / % possible all: 90.1

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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
Resolution: 1.91→44.87 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.477 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21524 1317 5 %RANDOM
Rwork0.17765 ---
obs0.17957 24786 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0.13 Å20 Å2
2---0.26 Å20 Å2
3---0.84 Å2
Refinement stepCycle: LAST / Resolution: 1.91→44.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2226 0 12 311 2549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192302
X-RAY DIFFRACTIONr_bond_other_d0.0010.0228
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9323136
X-RAY DIFFRACTIONr_angle_other_deg0.050.95618
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3025293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49322.685108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2815.044340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2651521
X-RAY DIFFRACTIONr_chiral_restr0.0990.2333
X-RAY DIFFRACTIONr_gen_planes_refined00.0211817
X-RAY DIFFRACTIONr_gen_planes_other00.0144
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_it1.0282.3031163
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9622.7451139
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: 1.911→1.961 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 77 -
Rwork0.229 1630 -
obs--85.78 %
Refinement TLS params.Method: refined / Origin x: 22.7977 Å / Origin y: 61.6775 Å / Origin z: 37.8825 Å
111213212223313233
T0.031 Å20.0062 Å2-0.0208 Å2-0.0058 Å20.0032 Å2--0.0629 Å2
L2.5411 °2-0.4132 °2-0.7548 °2-3.5661 °20.4014 °2--1.389 °2
S-0.038 Å °-0.0259 Å °-0.0846 Å °0.1627 Å °0.0459 Å °0.217 Å °0.0325 Å °0.0098 Å °-0.0079 Å °

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