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- PDB-6ljx: Crystal structure of human FABP4 in complex with a novel inhibitor -

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Basic information

Entry
Database: PDB / ID: 6ljx
TitleCrystal structure of human FABP4 in complex with a novel inhibitor
ComponentsFatty acid-binding protein, adipocyte
KeywordsLIPID BINDING PROTEIN / FABP4 / inhibitor / complex
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 / cytosol / cytoplasm
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
2-phenylazanylbenzoic acid / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsSu, H.X. / Zhang, X.L. / Li, M.J. / Xu, Y.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: 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
DepositionDec 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 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)17,0922
Polymers16,8791
Non-polymers2131
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7080 Å2
Unit cell
Length a, b, c (Å)32.395, 53.701, 75.153
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 16879.203 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-EHO / 2-phenylazanylbenzoic acid


Mass: 213.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H11NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antiinflammatory*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.94 Å3/Da / Density % sol: 36.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.4 M trisodium citrate, PH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 19830 / % possible obs: 100 % / Redundancy: 12.3 % / Biso Wilson estimate: 14.21 Å2 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.036 / Rrim(I) all: 0.128 / Χ2: 0.976 / Net I/σ(I): 5.6 / Num. measured all: 243722
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.55-1.58101.4489730.7940.4751.5260.87100
1.58-1.6110.91.349680.7890.4241.4070.924100
1.61-1.6411.91.3859760.8590.4171.4470.911100
1.64-1.6712.51.2979510.9070.381.3520.888100
1.67-1.7112.51.1229990.8990.3291.170.949100
1.71-1.7512.60.9499660.930.2770.9890.989100
1.75-1.7912.50.9049800.9530.2650.9430.975100
1.79-1.84120.6719650.9570.2010.7011.067100
1.84-1.8911.80.5399680.9750.1640.5641.057100
1.89-1.9512.60.4269900.9810.1250.4441.152100
1.95-2.0213.20.3529850.9830.1010.3661.191100
2.02-2.113.20.2999750.9850.0850.3111.188100
2.1-2.212.90.2469840.9870.0710.2561.162100
2.2-2.3212.50.21210010.990.0620.2211.154100
2.32-2.46120.1859890.9890.0550.1931.083100
2.46-2.6513.40.1589960.9920.0450.1640.976100
2.65-2.9213.20.1310060.990.0370.1350.891100
2.92-3.3412.30.09810090.9950.0290.1020.78100
3.34-4.2112.40.07610410.9970.0220.080.626100
4.21-5011.60.08311080.9960.0240.0870.67299.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.81 Å30.79 Å
Translation4.81 Å30.79 Å

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NNT

4nnt


Resolution: 1.75→30.788 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.98
RfactorNum. reflection% reflection
Rfree0.2303 695 5.08 %
Rwork0.1865 --
obs0.1888 13681 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 57.79 Å2 / Biso mean: 16.7424 Å2 / Biso min: 3.88 Å2
Refinement stepCycle: final / Resolution: 1.75→30.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1059 0 32 103 1194
Biso mean--20.88 25.26 -
Num. residues----136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061116
X-RAY DIFFRACTIONf_angle_d0.7681499
X-RAY DIFFRACTIONf_chiral_restr0.058168
X-RAY DIFFRACTIONf_plane_restr0.004190
X-RAY DIFFRACTIONf_dihedral_angle_d3.214938
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.75-1.88510.25751100.2013247896
1.8851-2.07480.24261350.18252561100
2.0748-2.37490.23251530.18532575100
2.3749-2.99170.24871510.20512628100
2.9917-30.7880.20991460.17522744100

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