Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 112254.26 
• Atom Count: 7489 
• Residue Count: 982 
• Unique protein chains: 1

2GVJ

Crystal Structure of Human NMPRTase in complex with FK866

• DOI: 10.2210/pdb2GVJ/pdb

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


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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.298 
• R-Value Work: 0.247 

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: 10.1038/nsmb1105
• Primary Citation of Related Structures:  
  2GVL, 2GVG


• 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: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Nicotinamide phosphoribosyltransferase	A, B	491	Homo sapiens	Mutation(s): 0  Gene Names: NAMPT (PBEF, PBEF1) EC: 2.4.2.12
Find proteins for P43490 (Homo sapiens) Go to Gene View: NAMPT Go to UniProtKB:  P43490

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
DGB	A, B	(2E)-N-{4-[1-(benzenecarbonyl)piperidin-4-yl]butyl}-3-(pyridin-3-yl)prop-2-enamide FK-866 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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DGB	IC50: 0.1 - 3 nM (100) BINDINGDB
DGB	Ki: 0.3 nM (100) BINDINGDB
DGB	Ki: 0.3 nM BINDINGMOAD
DGB	Ki: 0.3 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.298 
• R-Value Work: 0.247 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 60.780	α = 90.00
b = 105.896	β = 96.45
c = 83.427	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-05-02 
• 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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2016-11-09
  Type: Non-polymer description