2GVJ

Crystal Structure of Human NMPRTase in complex with FK866

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 

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This is version 1.4 of the entry. See complete history. 


Literature

Molecular basis for the inhibition of human NMPRTase, a novel target for anticancer agents.

Khan, J.A., Tao, X., Tong, L.

(2006) Nat Struct Mol Biol 13: 582-588

  • DOI: https://doi.org/10.1038/nsmb1105
  • Primary Citation of Related Structures:  
    2GVG, 2GVJ, 2GVL

  • PubMed Abstract: 

    Nicotinamide phosphoribosyltransferase (NMPRTase) has a crucial role in the salvage pathway of NAD+ biosynthesis, and a potent inhibitor of NMPRTase, FK866, can reduce cellular NAD+ levels and induce apoptosis in tumors. We have determined the crystal structures at up to 2.1-A resolution of human and murine NMPRTase, alone and in complex with the reaction product nicotinamide mononucleotide or the inhibitor FK866. The structures suggest that Asp219 is a determinant of substrate specificity of NMPRTase, which is confirmed by our mutagenesis studies. FK866 is bound in a tunnel at the interface of the NMPRTase dimer, and mutations in this binding site can abolish the inhibition by FK866. Contrary to current knowledge, the structures show that FK866 should compete directly with the nicotinamide substrate. Our structural and biochemical studies provide a starting point for the development of new anticancer agents.

    • Organizational Affiliation: 

    Department of Biological Sciences, Columbia University, New York, New York 10027, USA.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nicotinamide phosphoribosyltransferase
A, B
491Homo sapiensMutation(s): 3 
Gene Names: NAMPT
EC: 2.4.2.12
UniProt & NIH Common Fund Data Resources
Find proteins for P43490 (Homo sapiens)
Explore P43490 
Go to UniProtKB:  P43490
PHAROS:  P43490
GTEx:  ENSG00000105835 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43490
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGB
Query on DGB
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		(2E)-N-{4-[1-(benzenecarbonyl)piperidin-4-yl]butyl}-3-(pyridin-3-yl)prop-2-enamide
C24 H29 N3 O2
KPBNHDGDUADAGP-VAWYXSNFSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Binding Affinity Annotations 
IDSourceBinding Affinity
DGB BindingDB:  2GVJ Ki: min: 0.3, max: 3 (nM) from 2 assay(s)
IC50: min: 0.14, max: 35 (nM) from 12 assay(s)
PDBBind:  2GVJ Ki: 0.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.78α = 90
b = 105.896β = 96.45
c = 83.427γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-06-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2016-11-09
    Changes: Non-polymer description
  • Version 1.4: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary