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- PDB-5hz8: FABP4_3 in complex with 6,8-Dichloro-4-phenyl-2-piperidin-1-yl-qu... -

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Basic information

Entry
Database: PDB / ID: 5hz8
TitleFABP4_3 in complex with 6,8-Dichloro-4-phenyl-2-piperidin-1-yl-quinoline-3-carboxylic acid
ComponentsFatty acid-binding protein, adipocyte
KeywordsTRANSPORT PROTEIN / LIPID BINDING PROTEIN / FATTY ACID BINDING PROTEIN / CYTOPLASM / LIPID-BINDING / PROTEIN BINDING / _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-65Z / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.12 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 1.1Mar 8, 2017Group: Refinement description
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty acid-binding protein, adipocyte
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7746
Polymers15,0601
Non-polymers7145
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint10 kcal/mol
Surface area7240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.400, 55.768, 74.373
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: 15060.242 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-65Z / 6,8-dichloro-4-phenyl-2-(piperidin-1-yl)quinoline-3-carboxylic acid


Mass: 401.286 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18Cl2N2O2
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.44 Å3/Da / Density % sol: 49.53 %
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: 0.9999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.12→32 Å / Num. obs: 56631 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.81 % / Biso Wilson estimate: 15.086 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.0405 / Rsym value: 0.0405 / Net I/σ(I): 17.6
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.12-1.153.80.3863.1188.5
1.15-1.180.3284.51199.8
1.18-1.220.324.81199.8
1.22-1.250.285.55199.6
1.25-1.30.2247.02199.8
1.3-1.340.1888.39199.9
1.34-1.390.1719.44199.9
1.39-1.450.13511.54199.8
1.45-1.510.10415.42199.8
1.51-1.590.0819.561100
1.59-1.670.06423.2199.9
1.67-1.770.05427.06199.9
1.77-1.90.04135.39199.9
1.9-2.050.03541.63199.7
2.05-2.240.03345.41199.8
2.24-2.510.03146.35199.7
2.51-2.90.02853.49199.9
2.9-3.550.02656.4199.4
3.55-5.020.02555.76199.6
5.020.02458.29199.3

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Processing

Software
NameVersionClassification
SADABSdata scaling
PDB_EXTRACT3.2data extraction
REFMAC5refinement
XDSdata reduction
REFMAC5phasing
RefinementResolution: 1.12→31.96 Å / SU B: 1.017 / SU ML: 0.022 / Cross valid method: FREE R-VALUE / ESU R: 0.032 / ESU R Free: 0.033
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflection
Rfree0.17088 2857 5.2 %
Rwork0.14353 --
obs0.14499 51978 95.98 %
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 mean: 12.234 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å20 Å2
2---0.34 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.12→31.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1053 0 43 259 1355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221187
X-RAY DIFFRACTIONr_bond_other_d0.0020.02814
X-RAY DIFFRACTIONr_angle_refined_deg2.1472.0021608
X-RAY DIFFRACTIONr_angle_other_deg1.32632007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9035157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.64424.58348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.68615231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.88157
X-RAY DIFFRACTIONr_chiral_restr0.1330.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021297
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02233
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_restr4.80436728
X-RAY DIFFRACTIONr_sphericity_free14.0935259
X-RAY DIFFRACTIONr_sphericity_bonded5.32451978

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