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- PDB-5wi1: Crystal structure of human NAMPT with fragment 5: (3E)-3-[(phenyl... -

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Basic information

Entry
Database: PDB / ID: 5wi1
TitleCrystal structure of human NAMPT with fragment 5: (3E)-3-[(phenylamino)methylidene]oxan-2-one
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 / : / 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 / : / 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
(3E)-3-[(phenylamino)methylidene]oxan-2-one / Nicotinamide phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsLongenecker, K.L. / Raich, D. / Korepanova, A.V.
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2018
Title: Fragment-based discovery of a potent NAMPT inhibitor.
Authors: Korepanova, A. / Longenecker, K.L. / Pratt, S.D. / Panchal, S.C. / Clark, R.F. / Lake, M. / Gopalakrishnan, S.M. / Raich, D. / Sun, C. / Petros, A.M.
History
DepositionJul 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 1.2May 1, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
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:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)111,7886
Polymers111,1902
Non-polymers5994
Water9,692538
1
A: Nicotinamide phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8943
Polymers55,5951
Non-polymers2992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nicotinamide phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8943
Polymers55,5951
Non-polymers2992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-73 kcal/mol
Surface area32560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.815, 106.759, 83.359
Angle α, β, γ (deg.)90.000, 96.550, 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: 55594.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAMPT, PBEF, PBEF1 / Cell (production host): HEK 293-6E / Production host: Homo sapiens (human)
References: UniProt: P43490, nicotinamide phosphoribosyltransferase
#2: Chemical ChemComp-AOY / (3E)-3-[(phenylamino)methylidene]oxan-2-one


Mass: 203.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H13NO2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 2.39 Å3/Da / Density % sol: 48.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 10K, sodium chloride, glycerol, Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→51.697 Å / Num. obs: 63067 / % possible obs: 87 % / Redundancy: 3.7 % / Biso Wilson estimate: 21.21 Å2 / Rmerge(I) obs: 0.228 / Rsym value: 0.228 / Net I/σ(I): 7.7
Reflection shellResolution: 1.99→1.996 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.831 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.831 / % possible all: 97.2

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Processing

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

2gvj


Resolution: 1.99→22.98 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.894 / SU R Cruickshank DPI: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.201 / SU Rfree Blow DPI: 0.167 / SU Rfree Cruickshank DPI: 0.169
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3239 5.15 %RANDOM
Rwork0.189 ---
obs0.191 62927 86.9 %-
Displacement parametersBiso max: 103.28 Å2 / Biso mean: 20.89 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--6.007 Å20 Å2-1.1034 Å2
2--1.1364 Å20 Å2
3---4.8706 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 1.99→22.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7422 0 40 538 8000
Biso mean--21.18 28.52 -
Num. residues----928
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2642SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes194HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1100HARMONIC5
X-RAY DIFFRACTIONt_it7638HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion972SEMIHARMONIC5
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_contact9118SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7638HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10350HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion3.27
X-RAY DIFFRACTIONt_other_torsion17.15
LS refinement shellResolution: 1.99→2.04 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2634 249 4.66 %
Rwork0.2321 5098 -
all0.2335 5347 -
obs--99.8 %

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