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- PDB-5u2n: Crystal structure of human NAMPT with A-1326133 -

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Basic information

Entry
Database: PDB / ID: 5u2n
TitleCrystal structure of human NAMPT with A-1326133
ComponentsNicotinamide phosphoribosyltransferase
KeywordsTransferase/Transferase Inhibitor / NAMPT inhibitor / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


nicotinamide phosphoribosyltransferase activity / nicotinamide phosphoribosyltransferase / 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 activity / nicotinamide phosphoribosyltransferase / 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-cell signaling / cell junction / 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-7TA / Nicotinamide phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.73 Å
AuthorsLongenecker, K.L. / Raich, D. / Korepanova, A.V.
CitationJournal: Mol. Cancer Ther. / Year: 2017
Title: Discovery and Characterization of Novel Nonsubstrate and Substrate NAMPT Inhibitors.
Authors: Wilsbacher, J.L. / Cheng, M. / Cheng, D. / Trammell, S.A.J. / Shi, Y. / Guo, J. / Koeniger, S.L. / Kovar, P.J. / He, Y. / Selvaraju, S. / Heyman, H.R. / Sorensen, B.K. / Clark, R.F. / ...Authors: Wilsbacher, J.L. / Cheng, M. / Cheng, D. / Trammell, S.A.J. / Shi, Y. / Guo, J. / Koeniger, S.L. / Kovar, P.J. / He, Y. / Selvaraju, S. / Heyman, H.R. / Sorensen, B.K. / Clark, R.F. / Hansen, T.M. / Longenecker, K.L. / Raich, D. / Korepanova, A.V. / Cepa, S. / Towne, D.L. / Abraham, V.C. / Tang, H. / Richardson, P.L. / McLoughlin, S.M. / Badagnani, I. / Curtin, M.L. / Michaelides, M.R. / Maag, D. / Buchanan, F.G. / Chiang, G.G. / Gao, W. / Rosenberg, S.H. / Brenner, C. / Tse, C.
History
DepositionNov 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Mar 21, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 1.3Oct 4, 2023Group: 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: Nicotinamide phosphoribosyltransferase
B: Nicotinamide phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,59810
Polymers108,2412
Non-polymers1,3578
Water15,061836
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10040 Å2
ΔGint-159 kcal/mol
Surface area32090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.166, 107.049, 83.135
Angle α, β, γ (deg.)90.000, 96.770, 90.000
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: 54120.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAMPT, PBEF, PBEF1 / Cell line (production host): HEK 293-6E / Production host: Mammalia (mammals)
References: UniProt: P43490, nicotinamide phosphoribosyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-7TA / N-{4-[1-(2-methylpropanoyl)piperidin-4-yl]phenyl}-2H-pyrrolo[3,4-c]pyridine-2-carboxamide


Mass: 390.478 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H26N4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 836 / 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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 3350, 0.2 M ammonium sulfate, and 0.1 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→107 Å / Num. obs: 109253 / % possible obs: 97.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 25.25 Å2 / Net I/σ(I): 15

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALAdata scaling
BUSTER2.11.7refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GVJ

2gvj


Resolution: 1.73→25.33 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.098 / SU Rfree Blow DPI: 0.094 / SU Rfree Cruickshank DPI: 0.093
RfactorNum. reflection% reflectionSelection details
Rfree0.192 5439 5.02 %RANDOM
Rwork0.164 ---
obs0.165 108403 98 %-
Displacement parametersBiso max: 122.31 Å2 / Biso mean: 27.67 Å2 / Biso min: 13.34 Å2
Baniso -1Baniso -2Baniso -3
1--3.122 Å20 Å20.369 Å2
2---4.4911 Å20 Å2
3---7.6131 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: final / Resolution: 1.73→25.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7431 0 88 836 8355
Biso mean--32.37 39.97 -
Num. residues----929
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2662SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes195HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1119HARMONIC5
X-RAY DIFFRACTIONt_it7695HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion973SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9730SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7695HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10436HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion3.76
X-RAY DIFFRACTIONt_other_torsion16.89
LS refinement shellResolution: 1.73→1.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 420 5.56 %
Rwork0.217 7132 -
all0.219 7552 -
obs--92.95 %

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