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- PDB-3hk1: Identification and Characterization of a Small Molecule Inhibitor... -

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Basic information

Entry
Database: PDB / ID: 3hk1
TitleIdentification and Characterization of a Small Molecule Inhibitor of Fatty Acid Binding Proteins
ComponentsFatty acid-binding protein, adipocyte
KeywordsPROTEIN BINDING / lipid binding protein / fatty acid binding protein / Cytoplasm / Lipid-binding / Nucleus / Phosphoprotein / Transport
Function / homology
Function and homology information


Triglyceride catabolism / hormone receptor binding / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / white fat cell differentiation / fatty acid transport / long-chain fatty acid transport / brown fat cell differentiation / fatty acid metabolic process ...Triglyceride catabolism / hormone receptor binding / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / white fat cell differentiation / fatty acid transport / long-chain fatty acid transport / brown fat cell differentiation / fatty acid metabolic process / cholesterol homeostasis / fatty acid binding / response to bacterium / positive regulation of inflammatory response / cellular response to tumor necrosis factor / positive regulation of cold-induced thermogenesis / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / nucleoplasm / nucleus / cytoplasm / cytosol
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
Chem-B64 / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHertzel, A.V. / Hellberg, K. / Reynolds, J.M. / Kruse, A.C. / Juhlmann, B.E. / Smith, A.J. / Sanders, M.A. / Ohlendorf, D.H. / Suttles, J. / Bernlohr, D.A.
CitationJournal: J.Med.Chem. / Year: 2009
Title: Identification and characterization of a small molecule inhibitor of Fatty Acid binding proteins.
Authors: Hertzel, A.V. / Hellberg, K. / Reynolds, J.M. / Kruse, A.C. / Juhlmann, B.E. / Smith, A.J. / Sanders, M.A. / Ohlendorf, D.H. / Suttles, J. / Bernlohr, D.A.
History
DepositionMay 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)14,8772
Polymers14,5401
Non-polymers3371
Water4,053225
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.017, 94.113, 49.662
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Fatty acid-binding protein, adipocyte / A-FABP / AFABP / Fatty acid-binding protein 4 / Adipocyte lipid-binding protein / ALBP / P2 ...A-FABP / AFABP / Fatty acid-binding protein 4 / Adipocyte lipid-binding protein / ALBP / P2 adipocyte protein / Myelin P2 protein homolog / 3T3-L1 lipid-binding protein / Protein 422 / P15


Mass: 14539.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: adipocyte, Ap2, Fabp4, fatty acid binding protein 4 / Plasmid: Modified pRSETb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P04117
#2: Chemical ChemComp-B64 / 4-{[2-(methoxycarbonyl)-5-(2-thienyl)-3-thienyl]amino}-4-oxo-2-butenoic acid / (2Z)-4-{[5-(methoxycarbonyl)-2,2'-bithiophen-4-yl]amino}-4-oxobut-2-enoic acid


Mass: 337.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H11NO5S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 3.09 Å3/Da / Density % sol: 60.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.5 M sodium/potassium phosphate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 125 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 9, 2008 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→24.77 Å / Num. all: 20158 / Num. obs: 20158 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rsym value: 0.035 / Net I/σ(I): 49.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 6.5 / Num. unique all: 969 / Rsym value: 0.277 / % possible all: 98.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREP9.4.09phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LIB

1lib


Resolution: 1.7→24.77 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.582 / SU ML: 0.054 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.195 1028 5.1 %RANDOM
Rwork0.175 ---
obs0.176 19117 99.77 %-
all-19117 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.1 Å2 / Biso mean: 20.148 Å2 / Biso min: 10.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→24.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1022 0 22 225 1269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221058
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.9811423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1865132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.98724.41943
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61615201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.182157
X-RAY DIFFRACTIONr_chiral_restr0.0880.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02774
X-RAY DIFFRACTIONr_nbd_refined0.1910.2452
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2727
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2150
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3850.225
X-RAY DIFFRACTIONr_mcbond_it1.3541.5671
X-RAY DIFFRACTIONr_mcangle_it1.44121051
X-RAY DIFFRACTIONr_scbond_it2.3593463
X-RAY DIFFRACTIONr_scangle_it4.0384.5371
LS refinement shellResolution: 1.7→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 76 -
Rwork0.26 1369 -
all-1445 -
obs-1445 98.3 %

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