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- PDB-5d47: Crystal Structure of FABP4 in complex with 3-[5-cyclopropyl-3-(3-... -

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Basic information

Entry
Database: PDB / ID: 5d47
TitleCrystal Structure of FABP4 in complex with 3-[5-cyclopropyl-3-(3-methoxypyridin-4-yl)-2-phenyl-1H-indol-1-yl] propanoic acid
ComponentsFatty acid-binding protein, adipocyte
KeywordsLIPID BINDING PROTEIN / FATTY ACID BINDING PROTEIN
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
Chem-L19 / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTagami, U. / Takahashi, K. / Igarashi, S. / Ejima, C. / Yoshida, T. / Takeshita, S. / Miyanaga, W. / Sugiki, M. / Tokumasu, M. / Hatanaka, T. ...Tagami, U. / Takahashi, K. / Igarashi, S. / Ejima, C. / Yoshida, T. / Takeshita, S. / Miyanaga, W. / Sugiki, M. / Tokumasu, M. / Hatanaka, T. / Kashiwagi, T. / Ishikawa, K. / Miyano, H. / Mizukoshi, T.
CitationJournal: Acs Med.Chem.Lett. / Year: 2016
Title: Interaction Analysis of FABP4 Inhibitors by X-ray Crystallography and Fragment Molecular Orbital Analysis
Authors: Tagami, U. / Takahashi, K. / Igarashi, S. / Ejima, C. / Yoshida, T. / Takeshita, S. / Miyanaga, W. / Sugiki, M. / Tokumasu, M. / Hatanaka, T. / Kashiwagi, T. / Ishikawa, K. / Miyano, H. / Mizukoshi, T.
History
DepositionAug 7, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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)17,3242
Polymers16,9111
Non-polymers4121
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7050 Å2
Unit cell
Length a, b, c (Å)32.300, 53.830, 74.860
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 (E. coli) / References: UniProt: P15090
#2: Chemical ChemComp-L19 / 3-[5-cyclopropyl-3-(3-methoxypyridin-4-yl)-2-phenyl-1H-indol-1-yl]propanoic acid


Mass: 412.480 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H24N2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 1.92 Å3/Da / Density % sol: 36.08 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: 2.4 M NaH2PO4/K2HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 14733 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 17.7 % / Biso Wilson estimate: 22.424 Å2 / Rmerge F obs: 0.049 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.049 / Net I/σ(I): 29.23 / Num. measured all: 104930
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.7-1.80.2050.2627.6416385230222480.28297.7
1.8-20.1170.13914.0523792334732880.1598.2
2-2.50.0480.06426.7531523444843960.06998.8
2.5-30.0280.0439.7614081199619800.04399.2
3-40.0150.02857.5811122160115940.0399.6
4-50.0120.02366.2139075875750.02598
5-100.0120.02363.5636655745650.02598.4
100.0130.02460.0445595870.02691.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREP11.0.02phasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HNX

2hnx


Resolution: 1.7→43.7 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.2026 / WRfactor Rwork: 0.174 / FOM work R set: 0.8736 / SU B: 1.982 / SU ML: 0.067 / SU R Cruickshank DPI: 0.1112 / SU Rfree: 0.1082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 747 5.1 %RANDOM
Rwork0.1769 ---
obs0.1786 13985 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.97 Å2 / Biso mean: 18.327 Å2 / Biso min: 7.22 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20 Å2
2---0.55 Å20 Å2
3----0.97 Å2
Refinement stepCycle: final / Resolution: 1.7→43.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1050 0 31 119 1200
Biso mean--28.36 32.09 -
Num. residues----135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.021099
X-RAY DIFFRACTIONr_angle_refined_deg2.3021.9841480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6235134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.14124.54544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.80115205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.395156
X-RAY DIFFRACTIONr_chiral_restr0.1780.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02800
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 56 -
Rwork0.196 893 -
all-949 -
obs--97.13 %

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