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- PDB-5lx5: CRYSTAL STRUCTURE OF VISFATIN IN COMPLEX WITH SAR154782-RP. -

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Basic information

Entry
Database: PDB / ID: 5lx5
TitleCRYSTAL STRUCTURE OF VISFATIN IN COMPLEX WITH SAR154782-RP.
ComponentsNicotinamide phosphoribosyltransferase
KeywordsTRANSFERASE / NAMPT / INHIBITOR / DRUG DESIGN / CANCER
Function / homology
Function and homology information


nicotinamide phosphoribosyltransferase / nicotinamide phosphoribosyltransferase activity / NAD biosynthesis via nicotinamide riboside salvage pathway / Nicotinamide salvaging / NAD biosynthetic process / positive regulation of nitric-oxide synthase biosynthetic process / NPAS4 regulates expression of target genes / BMAL1:CLOCK,NPAS2 activates circadian gene expression / cytokine activity / circadian regulation of gene expression ...nicotinamide phosphoribosyltransferase / nicotinamide phosphoribosyltransferase activity / NAD biosynthesis via nicotinamide riboside salvage pathway / Nicotinamide salvaging / NAD biosynthetic process / positive regulation of nitric-oxide synthase biosynthetic process / NPAS4 regulates expression of target genes / BMAL1:CLOCK,NPAS2 activates circadian gene expression / cytokine activity / circadian regulation of gene expression / cell junction / cell-cell signaling / nuclear speck / positive regulation of cell population proliferation / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / cytosol
Similarity search - Function
Nicotinamide phosphoribosyl transferase / Nicotinamide phosphoribosyltransferase, N-terminal domain / Nicotinamide phosphoribosyltransferase, N-terminal domain / Nicotinate/nicotinamide phosphoribosyltransferase / Nicotinate phosphoribosyltransferase (NAPRTase) family / Nicotinate phosphoribosyltransferase-like, C-terminal / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-7A0 / DIPHOSPHATE / Nicotinamide phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsBertrand, T. / Marquette, J.P.
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF VISFATIN IN COMPLEX WITH SAR154782-RP
Authors: Bertrand, T. / Marquette, J.P.
History
DepositionSep 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nicotinamide phosphoribosyltransferase
B: Nicotinamide phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,2896
Polymers111,4462
Non-polymers1,8434
Water16,934940
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9250 Å2
ΔGint-34 kcal/mol
Surface area31960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.710, 106.690, 83.460
Angle α, β, γ (deg.)90.00, 96.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nicotinamide phosphoribosyltransferase / Nampt / Pre-B-cell colony-enhancing factor 1 / Pre-B cell-enhancing factor / Visfatin


Mass: 55723.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAMPT, PBEF, PBEF1 / Production host: Escherichia coli (E. coli)
References: UniProt: P43490, nicotinamide phosphoribosyltransferase
#2: Chemical ChemComp-7A0 / [(2~{R},3~{S},4~{R},5~{R})-5-[2-azanyl-5-[[[4-[6-(ethylamino)-5-(2-piperidin-1-ylethylcarbamoyl)pyridin-2-yl]-2-fluoranyl-phenyl]carbamoylamino]methyl]pyridin-1-ium-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate


Mass: 747.731 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H45FN8O9P
#3: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 940 / 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: 2.41 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: CHES 100mM - PEG8000 14% - Malonate Na 200mM - pH8.8
PH range: 8.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.88→82.76 Å / Num. obs: 84857 / % possible obs: 98.6 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 7.3
Reflection shellResolution: 1.88→1.93 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 2.1 / % possible all: 95.8

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Processing

Software
NameClassification
BUSTER-TNTrefinement
XDSdata reduction
Aimlessdata scaling
BUSTER-TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→65.51 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.196 8508 10.03 %RANDOM
Rwork0.163 ---
all-84822 --
obs-13465 98.31 %-
Refinement stepCycle: LAST / Resolution: 1.88→65.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7406 0 122 940 8468

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