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- PDB-5hz6: FABP4 in complex with 6-Chloro-2-isopropyl-4-(3-isopropyl-phenyl)... -

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Basic information

Entry
Database: PDB / ID: 5hz6
TitleFABP4 in complex with 6-Chloro-2-isopropyl-4-(3-isopropyl-phenyl)-quinoline-3-carboxylic acid
ComponentsFatty acid-binding protein, adipocyte
KeywordsTRANSPORT PROTEIN / LIPID BINDING PROTEIN / FATTY ACID BINDING PROTEIN / CYTOPLASM / LIPID-BINDING / PROTEIN BINDING / RO6806346_REFMAC
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 / long-chain fatty acid transport / brown fat cell differentiation / fatty acid transport / 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 / long-chain fatty acid transport / brown fat cell differentiation / fatty acid transport / 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 domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-65Y / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsEhler, A. / Rudolph, M.G.
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2016
Title: Design and synthesis of selective, dual fatty acid binding protein 4 and 5 inhibitors.
Authors: Kuhne, H. / Obst-Sander, U. / Kuhn, B. / Conte, A. / Ceccarelli, S.M. / Neidhart, W. / Rudolph, M.G. / Ottaviani, G. / Gasser, R. / So, S.S. / Li, S. / Zhang, X. / Gao, L. / Myers, M.
History
DepositionFeb 2, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: 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)14,8862
Polymers14,5191
Non-polymers3681
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.753, 53.256, 72.193
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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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 / fabp4


Mass: 14518.603 Da / Num. of mol.: 1 / Fragment: SOLUBLE FORM, RESIDUES 3-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15090
#2: Chemical ChemComp-65Y / 6-Chloro-2-isopropyl-4-(3-isopropyl-phenyl)-quinoline-3-carboxylic acid


Mass: 367.869 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22ClNO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.1 Å3/Da / Density % sol: 41.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.14→42.86 Å / Num. obs: 44583 / % possible obs: 97.9 % / Redundancy: 6.16 % / Biso Wilson estimate: 16.393 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0658 / Net I/σ(I): 10.27
Reflection shellResolution: 1.14→1.24 Å / Redundancy: 5.71 % / Rmerge(I) obs: 0.6068 / Mean I/σ(I) obs: 2.04 / Rsym value: 0.6068 / % possible all: 94.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
REFMAC5.6.0112refinement
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN-HOUSE STRUCTURE

Resolution: 1.14→42.86 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.261 / SU ML: 0.026 / Cross valid method: FREE R-VALUE / ESU R: 0.034 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17342 2183 5.1 %RANDOM
Rwork0.1358 ---
obs0.13772 41025 95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 59.42 Å2 / Biso mean: 14.728 Å2 / Biso min: 8.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20 Å2
2---0.18 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.14→42.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1017 0 26 226 1269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021117
X-RAY DIFFRACTIONr_bond_other_d0.0030.02757
X-RAY DIFFRACTIONr_angle_refined_deg1.9051.9891521
X-RAY DIFFRACTIONr_angle_other_deg1.38831870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.835149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8424.65143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84915218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.437156
X-RAY DIFFRACTIONr_chiral_restr0.1180.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021236
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02223
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr5.51931871
X-RAY DIFFRACTIONr_sphericity_free24.803552
X-RAY DIFFRACTIONr_sphericity_bonded10.85852030
LS refinement shellResolution: 1.14→1.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 140 -
Rwork0.294 2522 -
obs--83.74 %

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