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- PDB-5fnu: Structure of the Keap1 Kelch domain in complex with a small molec... -
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Basic information
Entry | Database: PDB / ID: 5fnu | |||||||||
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Title | Structure of the Keap1 Kelch domain in complex with a small molecule inhibitor. | |||||||||
![]() | KELCH-LIKE ECH-ASSOCIATED PROTEIN 1 | |||||||||
![]() | TRANSCRIPTION / KEAP1 / NRF2 / OXIDATIVE STRESS | |||||||||
Function / homology | ![]() 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 | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | 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. ...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. | |||||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133.6 KB | Display | ![]() |
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PDB format | ![]() | 105.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5fnqC ![]() 5fnrC ![]() 5fnsC ![]() 5fntC ![]() 5fzjC ![]() 5fznC ![]() 1x2jS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33362.297 Da / Num. of mol.: 1 / Fragment: KELCH DOMAIN, UNP RESIDUES 322-624 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-L6I / ( |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.79 % / Description: NONE |
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Crystal grow | pH: 7 Details: 0.3-0.6 (NH4)2SO4, 0.4-1.4 M LI2SO4 AND 0.1 M NA3CITRATE-HCL PH 5.6 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU CCD / Detector: CCD / Date: Apr 30, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→51.65 Å / Num. obs: 28698 / % possible obs: 87.5 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.78→1.84 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.5 / % possible all: 44.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1X2J Resolution: 1.78→51.65 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.751 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.563 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→51.65 Å
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Refine LS restraints |
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