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- PDB-5y13: Crystal structure of human FABP4 complexed with ligand 5-((4-brom... -

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Basic information

Entry
Database: PDB / ID: 5y13
TitleCrystal structure of human FABP4 complexed with ligand 5-((4-bromonaphthalene)-1-sulfonamido)pentanoic acid
ComponentsFatty acid-binding protein, adipocyte
KeywordsLIPID BINDING PROTEIN / FABP4 / inhibitor
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-8K0 / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsSu, H.X. / Liu, Q.F. / Xu, Y.C.
CitationJournal: Eur J Med Chem / Year: 2018
Title: From hit to lead: Structure-based discovery of naphthalene-1-sulfonamide derivatives as potent and selective inhibitors of fatty acid binding protein 4
Authors: Gao, D.D. / Dou, H.X. / Su, H.X. / Zhang, M.M. / Wang, T. / Liu, Q.F. / Cai, H.Y. / Ding, H.P. / Yang, Z. / Zhu, W.L. / Xu, Y.C. / Wang, H.Y. / Li, Y.X.
History
DepositionJul 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)17,2982
Polymers16,9111
Non-polymers3861
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7220 Å2
Unit cell
Length a, b, c (Å)32.690, 53.640, 75.360
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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P15090
#2: Chemical ChemComp-8K0 / 5-[(4-bromanylnaphthalen-1-yl)sulfonylamino]pentanoic acid


Mass: 386.261 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16BrNO4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 1.95 Å3/Da / Density % sol: 37.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.6M trisodium citrate, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→29.99 Å / Num. obs: 25254 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.655 % / Biso Wilson estimate: 14.76 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.033 / Rrim(I) all: 0.039 / Χ2: 1.012 / Net I/σ(I): 27.22 / Num. measured all: 92294 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.75-1.83.4830.07313.646399191518370.9960.08695.9
1.8-1.843.7820.0617.086924183318310.9960.07199.9
1.84-1.93.7550.05318.986815181818150.9970.06299.8
1.9-1.963.760.04621.446685177917780.9980.05399.9
1.96-2.023.7420.04323.396324169016900.9980.05100
2.02-2.093.7290.03925.496093163516340.9980.04699.9
2.09-2.173.7080.03827.135959160916070.9980.04499.9
2.17-2.263.7240.03628.255608150615060.9980.042100
2.26-2.363.7320.03529.245482147014690.9980.0499.9
2.36-2.473.7180.03330.945231140914070.9980.03999.9
2.47-2.613.730.03232.384920132213190.9980.03799.8
2.61-2.773.6470.03233.144621126812670.9980.03799.9
2.77-2.963.6450.03134.484319118611850.9980.03699.9
2.96-3.23.6290.03135.893995110411010.9980.03799.7
3.2-3.53.5560.0337.183567102010030.9980.03598.3
3.5-3.913.4850.0337.430779178830.9970.03596.3
3.91-4.523.2980.02936.0624248187350.9970.03589.9
4.52-5.533.2690.02936.4818476725650.9970.03484.1
5.53-7.833.3180.0336.0916095334850.9970.03591
7.83-29.992.8830.02933.873952861370.9970.03547.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 1.75→29.99 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 20.37
RfactorNum. reflection% reflection
Rfree0.2191 2530 10.02 %
Rwork0.1757 --
obs0.1801 25251 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 52.95 Å2 / Biso mean: 18.39 Å2 / Biso min: 6.15 Å2
Refinement stepCycle: final / Resolution: 1.75→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1049 0 22 90 1161
Biso mean--25.45 24.3 -
Num. residues----136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061094
X-RAY DIFFRACTIONf_angle_d1.0751473
X-RAY DIFFRACTIONf_chiral_restr0.067168
X-RAY DIFFRACTIONf_plane_restr0.003184
X-RAY DIFFRACTIONf_dihedral_angle_d14.742412
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7501-1.78370.2251370.16931179131695
1.7837-1.82010.2511460.168913191465100
1.8201-1.85970.23741390.167812711410100
1.8597-1.9030.21721450.174913071452100
1.903-1.95050.2121440.169512591403100
1.9505-2.00330.21411450.16712991444100
2.0033-2.06220.25151440.163412941438100
2.0622-2.12880.22541390.169612741413100
2.1288-2.20480.22721460.170613031449100
2.2048-2.29310.21821470.175112731420100
2.2931-2.39740.22971430.176712961439100
2.3974-2.52370.20471460.181813041450100
2.5237-2.68170.23641400.19912721412100
2.6817-2.88870.27681470.209912871434100
2.8887-3.17910.23621380.181813001438100
3.1791-3.63840.18771420.15871283142598
3.6384-4.58140.15541280.15821170129892
4.5814-29.99430.24771140.19111031114580

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