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- PDB-5y0g: Crystal structure of human FABP4 complexed with ligand 4-Fluoro-3... -

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Basic information

Entry
Database: PDB / ID: 5y0g
TitleCrystal structure of human FABP4 complexed with ligand 4-Fluoro-3-((4-methoxynaphthalene)-1-sulfonamido) benzoic acid
ComponentsFatty acid-binding protein, adipocyte
KeywordsLIPID BINDING PROTEIN / FABP4 / inhibitor
Function / homology
Function and homology information


hormone receptor binding / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / cellular response to lithium ion / Triglyceride catabolism / white fat cell differentiation / long-chain fatty acid transport / fatty acid transport / brown fat cell differentiation / lipid droplet ...hormone receptor binding / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / cellular response to lithium ion / Triglyceride catabolism / white fat cell differentiation / long-chain fatty acid transport / fatty acid transport / brown fat cell differentiation / lipid droplet / cholesterol homeostasis / fatty acid binding / response to bacterium / Transcriptional regulation of white adipocyte differentiation / positive regulation of inflammatory response / cellular response to tumor necrosis factor / positive regulation of cold-induced thermogenesis / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / negative regulation of DNA-templated transcription / extracellular exosome / nucleus / cytoplasm / cytosol
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-8JL / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.542 Å
AuthorsSu, H.X. / Liu, Q.F. / Xu, Y.C.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: Eur J Med Chem / Year: 2018
Title: From hit to lead: Structure-based discovery of naphthalene-1-sulfonamide derivatives as potent and selective inhibitors of fatty acid binding protein 4
Authors: Gao, D.D. / Dou, H.X. / Su, H.X. / Zhang, M.M. / Wang, T. / Liu, Q.F. / Cai, H.Y. / Ding, H.P. / Yang, Z. / Zhu, W.L. / Xu, Y.C. / Wang, H.Y. / Li, Y.X.
History
DepositionJul 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fatty acid-binding protein, adipocyte
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2872
Polymers16,9111
Non-polymers3751
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7180 Å2
Unit cell
Length a, b, c (Å)32.380, 53.670, 75.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fatty acid-binding protein, adipocyte / Adipocyte lipid-binding protein / ALBP / Adipocyte-type fatty acid-binding protein / AFABP / Fatty ...Adipocyte lipid-binding protein / ALBP / Adipocyte-type fatty acid-binding protein / AFABP / Fatty acid-binding protein 4


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
#2: Chemical ChemComp-8JL / 4-fluoranyl-3-[(4-methoxynaphthalen-1-yl)sulfonylamino]benzoic acid


Mass: 375.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H14FNO5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 1.93 Å3/Da / Density % sol: 36.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.6 M sodium citrate, pH 6.5 / PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9775 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 1.54→43.7 Å / Num. obs: 36585 / % possible obs: 98 % / Redundancy: 3.29 % / Net I/σ(I): 15.08
Reflection shellResolution: 1.54→1.58 Å / Redundancy: 2.54 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.75 / Num. unique obs: 2467 / CC1/2: 0.899 / Rpim(I) all: 0.41 / % possible all: 89.8

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NNS

4nns


Resolution: 1.542→43.697 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.07
RfactorNum. reflection% reflection
Rfree0.2046 1102 3.01 %
Rwork0.174 --
obs0.175 36580 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.542→43.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1060 0 26 100 1186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131106
X-RAY DIFFRACTIONf_angle_d1.1931490
X-RAY DIFFRACTIONf_dihedral_angle_d2.922932
X-RAY DIFFRACTIONf_chiral_restr0.072168
X-RAY DIFFRACTIONf_plane_restr0.008186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.542-1.61220.261370.21414237X-RAY DIFFRACTION94
1.6122-1.69720.22841340.18484448X-RAY DIFFRACTION99
1.6972-1.80350.17471390.16984477X-RAY DIFFRACTION99
1.8035-1.94280.23911390.16474462X-RAY DIFFRACTION99
1.9428-2.13830.21321350.16934449X-RAY DIFFRACTION99
2.1383-2.44770.20281400.17384486X-RAY DIFFRACTION99
2.4477-3.08370.19211330.1894450X-RAY DIFFRACTION99
3.0837-43.71450.19841450.16454469X-RAY DIFFRACTION99

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