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

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Basic information

Entry
Database: PDB / ID: 6ljs
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 / cellular response to lithium ion / long-chain fatty acid binding / Triglyceride catabolism / white fat cell differentiation / fatty acid transport / long-chain fatty acid transport / brown fat cell differentiation / 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 / fatty acid transport / long-chain 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 / 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 / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
2-[(2-phenylphenyl)amino]benzoic 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)17,2633
Polymers16,9111
Non-polymers3512
Water1,76598
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 area7010 Å2
Unit cell
Length a, b, c (Å)32.291, 53.814, 75.177
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-EHR / 2-[(2-phenylphenyl)amino]benzoic acid


Mass: 289.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H15NO2 / Feature type: SUBJECT OF INVESTIGATION
#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.: 98 / 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: 1.93 Å3/Da / Density % sol: 36.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.6M trisodium citrate, PH6.5

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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: 19784 / % possible obs: 100 % / Redundancy: 11.9 % / Biso Wilson estimate: 13.16 Å2 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.042 / Rrim(I) all: 0.147 / Χ2: 0.98 / Net I/σ(I): 6.1 / Num. measured all: 235877
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.55-1.589.51.1239840.7560.3781.1880.824100
1.58-1.6110.21.0489840.8110.3421.1040.85100
1.61-1.6411.51.0469410.8510.3211.0960.854100
1.64-1.6711.80.9819510.8840.2981.0260.852100
1.67-1.7111.80.8710110.8750.2630.910.907100
1.71-1.7512.10.7529500.9230.2250.7860.934100
1.75-1.7911.90.7189950.9210.2170.7510.94100
1.79-1.8411.60.5559470.9560.170.5811.01100
1.84-1.8911.40.5179870.9650.160.5421.045100
1.89-1.9512.30.419660.9810.1210.4281.136100
1.95-2.0212.70.369880.9720.1050.3751.163100
2.02-2.112.80.3129670.9820.090.3251.182100
2.1-2.212.60.2769820.9830.0810.2871.179100
2.2-2.3212.20.249980.9870.0710.251.15100
2.32-2.4611.80.2119860.9860.0640.2211.156100
2.46-2.6513.10.1889910.9910.0540.1961.072100
2.65-2.92130.16210090.9910.0470.1680.99100
2.92-3.3412.10.12810030.9910.0390.1340.911100
3.34-4.2112.20.10310390.9960.030.1070.799100
4.21-5011.60.08611050.9960.0260.090.58199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.8 Å30.82 Å
Translation4.8 Å30.82 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→30.816 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.18
RfactorNum. reflection% reflection
Rfree0.2238 689 5.11 %
Rwork0.1825 --
obs0.1846 13474 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.28 Å2 / Biso mean: 16.7631 Å2 / Biso min: 5.37 Å2
Refinement stepCycle: final / Resolution: 1.75→30.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1060 0 26 98 1184
Biso mean--24.43 25.57 -
Num. residues----136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051101
X-RAY DIFFRACTIONf_angle_d0.7591476
X-RAY DIFFRACTIONf_chiral_restr0.057167
X-RAY DIFFRACTIONf_plane_restr0.004185
X-RAY DIFFRACTIONf_dihedral_angle_d3.936673
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.75-1.88510.27151070.199231490
1.8851-2.07480.23521330.1811255299
2.0748-2.37490.2251510.17642567100
2.3749-2.99170.23911520.20142624100
2.9917-30.8160.20151460.1718272899
Refinement TLS params.Method: refined / Origin x: 7.4962 Å / Origin y: -9.7816 Å / Origin z: -14.7717 Å
111213212223313233
T0.0555 Å2-0.0022 Å2-0.012 Å2-0.0668 Å20.0007 Å2--0.0677 Å2
L1.0508 °2-0.2607 °2-0.2378 °2-1.4233 °2-0.1806 °2--0.7535 °2
S0.0021 Å °0.0058 Å °0.0217 Å °-0.0628 Å °0.0473 Å °0.0247 Å °-0.0039 Å °0.0073 Å °-0.0462 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-4 - 131
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allS1 - 98
4X-RAY DIFFRACTION1allC1

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