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- PDB-4o13: The crystal structure of NAMPT in complex with GNE-618 -

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Basic information

Entry
Database: PDB / ID: 4o13
TitleThe crystal structure of NAMPT in complex with GNE-618
ComponentsNicotinamide phosphoribosyltransferase
KeywordsTRANSFERASE/TRANSFERASE 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 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-2P1 / PHOSPHATE ION / Nicotinamide phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsOh, A. / Coons, M. / Brillantes, B. / Wang, W.
CitationJournal: Plos One / Year: 2014
Title: Structural Basis for Resistance to Diverse Classes of NAMPT Inhibitors.
Authors: Wang, W. / Elkins, K. / Oh, A. / Ho, Y.C. / Wu, J. / Li, H. / Xiao, Y. / Kwong, M. / Coons, M. / Brillantes, B. / Cheng, E. / Crocker, L. / Dragovich, P.S. / Sampath, D. / Zheng, X. / Bair, ...Authors: Wang, W. / Elkins, K. / Oh, A. / Ho, Y.C. / Wu, J. / Li, H. / Xiao, Y. / Kwong, M. / Coons, M. / Brillantes, B. / Cheng, E. / Crocker, L. / Dragovich, P.S. / Sampath, D. / Zheng, X. / Bair, K.W. / O'Brien, T. / Belmont, L.D.
History
DepositionDec 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)115,68216
Polymers113,8852
Non-polymers1,79714
Water16,736929
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11350 Å2
ΔGint-38 kcal/mol
Surface area32380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.556, 106.206, 82.949
Angle α, β, γ (deg.)90.00, 96.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 56942.375 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-2P1 / N-(4-{[3-(trifluoromethyl)phenyl]sulfonyl}benzyl)-2H-pyrazolo[3,4-b]pyridine-5-carboxamide


Mass: 460.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H15F3N4O3S
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 929 / 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: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: 0.1M Sodium phosphate, pH 8.6, 25% polyethylene glycol 3350, 0.2M NaCl and 1mM compound, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 14, 2013
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 105010 / Num. obs: 104905 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.75→1.81 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→34.863 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 23.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2274 5241 5 %
Rwork0.1969 --
obs0.1984 104744 99.11 %
all-105010 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.0762 Å20 Å2-0.6699 Å2
2--4.7549 Å20 Å2
3---2.1679 Å2
Refinement stepCycle: LAST / Resolution: 1.75→34.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7520 0 116 929 8565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077819
X-RAY DIFFRACTIONf_angle_d1.07810589
X-RAY DIFFRACTIONf_dihedral_angle_d12.9952867
X-RAY DIFFRACTIONf_chiral_restr0.0711148
X-RAY DIFFRACTIONf_plane_restr0.0051339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.76530.32771400.29622688X-RAY DIFFRACTION80
1.7653-1.78610.31941790.28153301X-RAY DIFFRACTION99
1.7861-1.80790.32771820.27443334X-RAY DIFFRACTION100
1.8079-1.83080.31151630.2483359X-RAY DIFFRACTION100
1.8308-1.85490.27751690.23223306X-RAY DIFFRACTION100
1.8549-1.88030.25371630.23273345X-RAY DIFFRACTION100
1.8803-1.90710.27451740.22413311X-RAY DIFFRACTION100
1.9071-1.93560.23711860.20843325X-RAY DIFFRACTION100
1.9356-1.96580.24341760.20913359X-RAY DIFFRACTION100
1.9658-1.99810.2191840.20113272X-RAY DIFFRACTION100
1.9981-2.03250.2311690.19873384X-RAY DIFFRACTION100
2.0325-2.06950.25841720.19833330X-RAY DIFFRACTION100
2.0695-2.10930.23961790.19723338X-RAY DIFFRACTION100
2.1093-2.15230.22761450.19863350X-RAY DIFFRACTION100
2.1523-2.19910.25851660.19533307X-RAY DIFFRACTION100
2.1991-2.25020.24161910.19863351X-RAY DIFFRACTION100
2.2502-2.30650.21361840.19493331X-RAY DIFFRACTION100
2.3065-2.36890.24661950.19453322X-RAY DIFFRACTION100
2.3689-2.43850.23251730.19243360X-RAY DIFFRACTION100
2.4385-2.51720.21971910.19123321X-RAY DIFFRACTION100
2.5172-2.60720.26371740.19613323X-RAY DIFFRACTION100
2.6072-2.71150.22451680.20083338X-RAY DIFFRACTION100
2.7115-2.83490.22031830.20513338X-RAY DIFFRACTION100
2.8349-2.98430.25481700.20663377X-RAY DIFFRACTION100
2.9843-3.17110.20631690.18773336X-RAY DIFFRACTION100
3.1711-3.41580.2221790.19323336X-RAY DIFFRACTION100
3.4158-3.75910.18651810.17733359X-RAY DIFFRACTION100
3.7591-4.30220.17811880.16563334X-RAY DIFFRACTION100
4.3022-5.41710.1971580.17193388X-RAY DIFFRACTION99
5.4171-34.86980.21641900.19963380X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 13.5207 Å / Origin y: 1.1456 Å / Origin z: 22.5765 Å
111213212223313233
T0.0916 Å2-0.0009 Å2-0.0041 Å2-0.1202 Å2-0.0083 Å2--0.1274 Å2
L0.1958 °20.0215 °2-0.0298 °2-0.3535 °2-0.0489 °2--0.4372 °2
S0.0158 Å °-0.0015 Å °0.0044 Å °-0.0241 Å °0.0176 Å °-0.0381 Å °0.0049 Å °0.0274 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 8:487 OR RESID 603:607 ) ) OR ( CHAIN B AND ( RESID 8:486 OR RESID 603:607 ) )A8 - 487
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 8:487 OR RESID 603:607 ) ) OR ( CHAIN B AND ( RESID 8:486 OR RESID 603:607 ) )A603 - 607
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 8:487 OR RESID 603:607 ) ) OR ( CHAIN B AND ( RESID 8:486 OR RESID 603:607 ) )B8 - 486
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 8:487 OR RESID 603:607 ) ) OR ( CHAIN B AND ( RESID 8:486 OR RESID 603:607 ) )B603 - 607

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