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- PDB-5d48: Crystal Structure of FABP4 in complex with 3-{5-cyclopropyl-3-(3,... -

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Basic information

Entry
Database: PDB / ID: 5d48
TitleCrystal Structure of FABP4 in complex with 3-{5-cyclopropyl-3-(3,5-dimethyl-1H-pyrazol-4-yl)-2-[3-(propan-2-yloxy) 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-L96 / PHOSPHATE ION / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)17,5594
Polymers16,9111
Non-polymers6483
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-8 kcal/mol
Surface area7270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.080, 53.730, 74.740
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-L96 / 3-{5-cyclopropyl-3-(3,5-dimethyl-1H-pyrazol-4-yl)-2-[3-(propan-2-yloxy)phenyl]-1H-indol-1-yl}propanoic acid


Mass: 457.564 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H31N3O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.9 Å3/Da / Density % sol: 35.41 %
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: Jan 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. obs: 12310 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 18.4 % / Biso Wilson estimate: 25.359 Å2 / Rmerge F obs: 0.061 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.072 / Net I/σ(I): 18.92 / Num. measured all: 85078
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
1.81-1.950.2180.2447.9217125241724150.26399.9
1.95-2.20.0980.12813.5720816295229500.13899.9
2.2-2.70.0650.08119.0221712313131210.08899.7
2.7-3.50.0290.05227.6613816201920150.05699.8
3.5-50.0230.04732.877624115811530.05199.6
5-70.0250.05432.4226094074050.05899.5
7-100.0290.05931.759501621610.06599.4
100.0290.05528.6442694900.06295.7

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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: 1.81→43.63 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.248 / WRfactor Rwork: 0.1861 / FOM work R set: 0.8411 / SU B: 2.877 / SU ML: 0.09 / SU R Cruickshank DPI: 0.1404 / SU Rfree: 0.1435 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2445 588 4.8 %RANDOM
Rwork0.1843 ---
obs0.187 11721 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.54 Å2 / Biso mean: 21.749 Å2 / Biso min: 10.62 Å2
Baniso -1Baniso -2Baniso -3
1-1.95 Å20 Å20 Å2
2---0.24 Å20 Å2
3----1.71 Å2
Refinement stepCycle: final / Resolution: 1.81→43.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1061 0 44 86 1191
Biso mean--21.59 30.66 -
Num. residues----136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021121
X-RAY DIFFRACTIONr_angle_refined_deg2.531.9951512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3655135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63624.22245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.24115208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.897157
X-RAY DIFFRACTIONr_chiral_restr0.1530.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02810
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 39 -
Rwork0.232 762 -
all-801 -
obs--99.63 %

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