Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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: 54.13 kDa 
• Atom Count: 4217 
• Modelled Residue Count: 460 
• Deposited Residue Count: 462 
• Unique protein chains: 1

3GAM

Synthesis of Casimiroin and Optimization of Its Quinone Reductase 2 and Aromatase Inhibitory activity

• PDB DOI: 10.2210/pdb3GAM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-17 Released: 2009-03-24 
• Deposition Author(s): Sturdy, M., Pegan, S.D., Maiti, A., Marler, L., Mesecar, A.D., Pezzuto, J.M., Cushman, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.239 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 

Literature

Synthesis of casimiroin and optimization of its quinone reductase 2 and aromatase inhibitory activities.

Maiti, A., Reddy, P.V., Sturdy, M., Marler, L., Pegan, S.D., Mesecar, A.D., Pezzuto, J.M., Cushman, M.

(2009) J Med Chem 52: 1873-1884

• PubMed: 19265439 
• DOI: 10.1021/jm801335z
• Primary Citation of Related Structures:  
  3G5M, 3GAM


• PubMed Abstract: 
  

An efficient method has been developed to synthesize casimiroin (1), a component of the edible fruit of Casimiroa edulis, on a multigram scale in good overall yield. The route was versatile enough to provide an array of compound 1 analogues that were evaluated as QR2 and aromatase inhibitors. In addition, X-ray crystallography studies of QR2 in complex with compound 1 and one of its more potent analogues has provided insight into the mechanism of action of this new series of QR2 inhibitors. The initial biological investigations suggest that compound 1 and its analogues merit further investigation as potential chemopreventive or chemotherapeutic agents.

---

Organizational Affiliation: 

Department of Medicinal Chemistry and Molecular Pharmacology, School of Pharmacy and Pharmaceutical Sciences, and the Purdue Cancer Center, Purdue University, West Lafayette, Indiana 47907, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosyldihydronicotinamide dehydrogenase [quinone]	A, B	231	Homo sapiens	Mutation(s): 0  Gene Names: NQO2, NMOR2 EC: 1.10.99.2 (PDB Primary Data), 1.10.5.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P16083 (Homo sapiens) Explore P16083  Go to UniProtKB:  P16083
PHAROS:  P16083

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	D [auth A], G [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
MXX	C [auth A], F [auth B]	5,8-dimethoxy-1,4-dimethylquinolin-2(1H)-one C13 H15 N O3 FTGZPMFPUDKJBX-UHFFFAOYSA-N
ZN	E [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MXX	Binding MOAD:  3GAM	IC50: 4100 (nM) from 1 assay(s)
	BindingDB:  3GAM	IC50: 4100 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.239 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.346	α = 90
b = 83.889	β = 90
c = 106.696	γ = 90

Software Package:

Software Name	Purpose
SERGUI	data collection
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-02-17 
• Released Date: 2009-03-24 
Deposition Author(s): Sturdy, M., Pegan, S.D., Maiti, A., Marler, L., Mesecar, A.D., Pezzuto, J.M., Cushman, M.

Revision History  

• Version 1.0: 2009-03-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance