2GVJ

Crystal Structure of Human NMPRTase in complex with FK866

• PDB DOI: https://doi.org/10.2210/pdb2GVJ/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-05-02 Released: 2006-06-20 
• Deposition Author(s): Khan, J.A., Tao, X., Tong, L.

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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 

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

• PubMed: 16783377 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 112.25 kDa 
• Atom Count: 8,264 
• Modelled Residue Count: 929 
• Deposited Residue Count: 982 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinamide phosphoribosyltransferase	A, B	491	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGB	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
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Binding Affinity Annotations
ID	Source	Binding 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 = 60.78	α = 90
b = 105.896	β = 96.45
c = 83.427	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
COMO	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-20 
Deposition Author(s): Khan, J.A., Tao, X., Tong, L.

Revision History  

• 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