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

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Basic information

Entry
Database: PDB / ID: 6ljw
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: 1.4 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)17,1873
Polymers16,9111
Non-polymers2752
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint4 kcal/mol
Surface area7210 Å2
Unit cell
Length a, b, c (Å)32.298, 53.888, 75.281
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: 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-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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 36.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.6M trisodium citrate, PH 6.5

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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: 1.35→50 Å / Num. obs: 29409 / % possible obs: 99 % / Redundancy: 12 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.015 / Rrim(I) all: 0.053 / Χ2: 0.999 / Net I/σ(I): 8 / Num. measured all: 353338
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.35-1.377.40.38612900.940.1440.4140.97789.3
1.37-1.48.80.3814310.9570.130.4030.97696.6
1.4-1.4310.80.35214300.9810.110.3690.98698.6
1.43-1.4511.60.3214310.9820.0960.3351.01399.1
1.45-1.4911.80.30714610.9840.0920.321.02799.5
1.49-1.52120.27514360.9870.0820.2871.02799.2
1.52-1.5611.90.23714710.990.0710.2471.04299.1
1.56-1.611.80.2114440.9920.0630.2191.09399.3
1.6-1.6513.10.19414630.9940.0550.2021.07699.5
1.65-1.713.30.18114740.9950.0510.1891.0599.6
1.7-1.7612.90.14514540.9960.0410.1511.04799.8
1.76-1.8312.60.12414720.9970.0360.131.05999.8
1.83-1.9212.10.09514990.9980.0280.0991.05599.9
1.92-2.0213.40.07714750.9990.0220.081.06599.9
2.02-2.1413.20.06514750.9990.0180.0681.079100
2.14-2.3112.80.05515080.9990.0160.0571.016100
2.31-2.5412.50.04814940.9990.0140.050.96100
2.54-2.9113.30.04115230.9990.0120.0430.886100
2.91-3.6612.20.03115380.9990.0090.0320.843100
3.66-5012.20.02616400.9990.0080.0270.70799.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.81 Å30.86 Å
Translation4.81 Å30.86 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: 1.4→30.858 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.76
RfactorNum. reflection% reflection
Rfree0.2316 1318 5 %
Rwork0.1976 --
obs0.1994 26374 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 39.87 Å2 / Biso mean: 17.2332 Å2 / Biso min: 8.29 Å2
Refinement stepCycle: final / Resolution: 1.4→30.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1060 0 36 108 1204
Biso mean--20.3 25.24 -
Num. residues----136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061111
X-RAY DIFFRACTIONf_angle_d0.7641488
X-RAY DIFFRACTIONf_chiral_restr0.075167
X-RAY DIFFRACTIONf_plane_restr0.004187
X-RAY DIFFRACTIONf_dihedral_angle_d4.044431
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4-1.45610.2451170.2127261294
1.4561-1.52230.25451420.2088274299
1.5223-1.60260.23521310.1981274599
1.6026-1.7030.22721160.20012809100
1.703-1.83450.22341420.20082763100
1.8345-2.01910.22341620.19362802100
2.0191-2.31110.22991660.19382788100
2.3111-2.91140.26031720.21012823100
2.9114-30.8580.2171700.18992972100

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