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Yorodumi- PDB-6ljv: Crystal structure of human FABP4 in complex with a novel inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ljv | ||||||
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Title | Crystal structure of human FABP4 in complex with a novel inhibitor | ||||||
Components | Fatty acid-binding protein, adipocyte | ||||||
Keywords | LIPID BINDING PROTEIN / FABP4 / inhibitor / complex | ||||||
Function / homology | Function and homology information hormone receptor binding / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / Triglyceride catabolism / white fat cell differentiation / long-chain fatty acid transport / brown fat cell differentiation / fatty acid transport / lipid droplet ...hormone receptor binding / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / Triglyceride catabolism / white fat cell differentiation / long-chain fatty acid transport / brown fat cell differentiation / fatty acid transport / lipid droplet / cholesterol homeostasis / fatty acid binding / response to bacterium / Transcriptional regulation of white adipocyte differentiation / positive regulation of inflammatory response / positive regulation of cold-induced thermogenesis / cellular response to tumor necrosis factor / negative regulation of DNA-templated transcription / extracellular exosome / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.401 Å | ||||||
Authors | Su, H.X. / Zhang, X.L. / Li, M.J. / Xu, Y.C. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Med.Chem. / Year: 2020 Title: Exploration of Fragment Binding Poses Leading to Efficient Discovery of Highly Potent and Orally Effective Inhibitors of FABP4 for Anti-inflammation. Authors: Su, H. / Zou, Y. / Chen, G. / Dou, H. / Xie, H. / Yuan, X. / Zhang, X. / Zhang, N. / Li, M. / Xu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ljv.cif.gz | 74 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ljv.ent.gz | 51.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ljv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ljv_validation.pdf.gz | 839.4 KB | Display | wwPDB validaton report |
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Full document | 6ljv_full_validation.pdf.gz | 839.5 KB | Display | |
Data in XML | 6ljv_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 6ljv_validation.cif.gz | 10.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/6ljv ftp://data.pdbj.org/pub/pdb/validation_reports/lj/6ljv | HTTPS FTP |
-Related structure data
Related structure data | 6ljsC 6ljtC 6ljuC 6ljwC 6ljxC 4nntS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16911.268 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FABP4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P15090 |
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#2: Chemical | ChemComp-EHC / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.6M trisodium citrate, PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→50 Å / Num. obs: 26653 / % possible obs: 99.5 % / Redundancy: 11.5 % / Biso Wilson estimate: 17.12 Å2 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.02 / Rrim(I) all: 0.07 / Χ2: 1.433 / Net I/σ(I): 11.7 / Num. measured all: 306442 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NNT Resolution: 1.401→29.869 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.44
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.12 Å2 / Biso mean: 22.7034 Å2 / Biso min: 11.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.401→29.869 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 7.556 Å / Origin y: -9.7769 Å / Origin z: -14.928 Å
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Refinement TLS group |
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