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- PDB-6e68: NAMPT co-crystal with inhibitor compound 2 -

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Basic information

Entry
Database: PDB / ID: 6.0E+68
TitleNAMPT co-crystal with inhibitor compound 2
ComponentsNicotinamide phosphoribosyltransferase
KeywordsTRANSFERASE/INHIBITOR / nicotinamide phosphoribosyltransferase / cytotoxic / Antibody-drug conjugates / Anti-tumor / CYTOSOLIC PROTEIN / TRANSFERASE-INHIBITOR complex
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-HVM / PHOSPHATE ION / Nicotinamide phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWaight, A.B. / Neumann, C.S.
CitationJournal: to be published
Title: NAMPT co-crystal with inhibitor compound 2
Authors: Neumann, C.S. / Olivas, K.C. / Anderson, M.E. / Cochran, J.H. / Jin, S. / Li, F. / Loftus, L.V. / Meyer, D.W. / Neale, J. / Nix, J.C. / Pittman, P.G. / Simmons, J.K. / Ulrich, M.L. / Waight, ...Authors: Neumann, C.S. / Olivas, K.C. / Anderson, M.E. / Cochran, J.H. / Jin, S. / Li, F. / Loftus, L.V. / Meyer, D.W. / Neale, J. / Nix, J.C. / Pittman, P.G. / Simmons, J.K. / Ulrich, M.L. / Waight, A.B. / Wong, A. / Zaval, M.C. / Zeng, W. / Lyon, R.P. / Senter, P.D.
History
DepositionJul 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)109,9866
Polymers108,9832
Non-polymers1,0034
Water20,7711153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-56 kcal/mol
Surface area32650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.464, 106.410, 82.745
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: 54491.734 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-HVM / (2E)-N-{4-[1-(3-aminobenzene-1-carbonyl)piperidin-4-yl]butyl}-3-(pyridin-3-yl)prop-2-enamide


Mass: 406.521 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H30N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1153 / 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: 2.47 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium phosphate, pH 9.0, 28% polyethylene glycol 3350, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9762 Å
DetectorType: NOIR-1 / Detector: CCD / Date: May 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.5→65.054 Å / Num. all: 160628 / Num. obs: 160628 / % possible obs: 97 % / Redundancy: 3.5 % / Rpim(I) all: 0.074 / Rrim(I) all: 0.139 / Rsym value: 0.117 / Net I/av σ(I): 5.9 / Net I/σ(I): 9.3 / Num. measured all: 555921
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.5-1.582.81.1080.754222197120.7891.3681.1080.982.2
1.58-1.683.40.8550.975839225770.5471.0180.8551.498.7
1.68-1.793.50.5861.374913213280.3660.6920.5862.399.3
1.79-1.943.30.3571.966302199200.2310.4260.3573.999.6
1.94-2.123.50.2053.365002183820.1270.2410.2057.199.7
2.12-2.373.80.1275.262759166490.0760.1480.12711.299.8
2.37-2.743.80.0877.855309147000.0520.1020.08715.399.8
2.74-3.353.70.05312.946390124430.0320.0620.05322.399.7
3.35-4.743.70.03318.73543695700.020.0390.03333.899.4
4.74-65.0543.70.03119.51974953470.0190.0360.03131.699.4

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O28

4o28


Resolution: 1.5→65.054 Å / FOM work R set: 0.8997 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.167 8065 5.02 %
Rwork0.1597 152498 -
obs0.1601 160563 96.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.81 Å2 / Biso mean: 17.07 Å2 / Biso min: 5.29 Å2
Refinement stepCycle: final / Resolution: 1.5→65.054 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7520 0 130 1153 8803
Biso mean--13.58 29.87 -
Num. residues----940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0197768
X-RAY DIFFRACTIONf_angle_d1.82510520
X-RAY DIFFRACTIONf_chiral_restr0.1231148
X-RAY DIFFRACTIONf_plane_restr0.0121334
X-RAY DIFFRACTIONf_dihedral_angle_d14.2242880
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.51710.31352040.32253763396772
1.5171-1.53490.34032380.31023996423477
1.5349-1.55360.31972270.30694324455183
1.5536-1.57330.29212220.2894686490889
1.5733-1.5940.29372790.28715011529095
1.594-1.61580.28432740.27335141541599
1.6158-1.63890.28482810.25375213549499
1.6389-1.66340.25312560.24075219547599
1.6634-1.68940.23832840.23375210549499
1.6894-1.71710.24842520.22185186543899
1.7171-1.74670.21522830.21535176545999
1.7467-1.77840.2022590.20035243550299
1.7784-1.81270.21182670.194152055472100
1.8127-1.84970.19182930.186752315524100
1.8497-1.88990.18712960.180852305526100
1.8899-1.93380.1692660.162451975463100
1.9338-1.98220.1592860.153451995485100
1.9822-2.03580.16012900.145952405530100
2.0358-2.09570.16062750.14115203547899
2.0957-2.16340.14593000.131452435543100
2.1634-2.24070.12662720.129752545526100
2.2407-2.33040.14972570.12652365493100
2.3304-2.43650.12612450.123452865531100
2.4365-2.56490.1332690.125752565525100
2.5649-2.72560.13472780.126452345512100
2.7256-2.93610.14083000.137252355535100
2.9361-3.23150.13362650.132852585523100
3.2315-3.69910.13042630.13215265552899
3.6991-4.66030.13642800.12095264554499
4.6603-65.11540.14783040.15985294559899

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