2BZS

Binding of anti-cancer prodrug CB1954 to the activating enzyme NQO2 revealed by the crystal structure of their complex.

• PDB DOI: https://doi.org/10.2210/pdb2BZS/pdb

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


• Deposited: 2005-08-22 Released: 2005-09-23 
• Deposition Author(s): Abu Khader, M.M., Heap, J.T., De Matteis, C., Kellam, B., Doughty, S.W., Minton, N., Paoli, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.247 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 

Literature

Binding of the Anticancer Prodrug Cb1954 to the Activating Enzyme Nqo2 Revealed by the Crystal Structure of Their Complex.

Abu Khader, M.M., Heap, J.T., De Matteis, C., Kellam, B., Doughty, S.W., Minton, N., Paoli, M.

(2005) J Med Chem 48: 7714

• PubMed: 16302811 
• DOI: https://doi.org/10.1021/jm050730n
• Primary Citation of Related Structures:  
  2BZS


• PubMed Abstract: 
  

  CB1954 is an attractive prodrug for directed-enzyme prodrug therapy (DEPT) and a conventional prodrug against tumors in which the enzyme NQO2 is highly expressed. We have determined the crystal structure of the NQO2-CB1954 complex to 2.0 A resolution. The binding of the prodrug is governed by hydrophobic forces, while two key electrostatic contacts determine the specific orientation of the ligand. The structure also reveals an unfavorable interaction, therefore suggesting possible avenues for DEPT-tailored engineering studies.

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Organizational Affiliation: 

School of Pharmacy and The Institute of Infection, Immunity and Inflammation, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.

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 PQS (software)

Macromolecule Content

• Total Structure Weight: 55.13 kDa 
• Atom Count: 4,091 
• Modelled Residue Count: 460 
• Deposited Residue Count: 472 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NRH DEHYDROGENASE [QUINONE] 2	A, B	236	Homo sapiens	Mutation(s): 0  EC: 1.6.99
UniProt & NIH Common Fund Data Resources
Find proteins for P16083 (Homo sapiens) Explore P16083  Go to UniProtKB:  P16083
PHAROS:  P16083 GTEx:  ENSG00000124588

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
CB1	E [auth A], H [auth B]	5-(AZIRIDIN-1-YL)-2,4-DINITROBENZAMIDE C9 H8 N4 O5 WOCXQMCIOTUMJV-UHFFFAOYSA-N
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.247 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.83	α = 90
b = 106.11	β = 90
c = 61.65	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-23 
Deposition Author(s): Abu Khader, M.M., Heap, J.T., De Matteis, C., Kellam, B., Doughty, S.W., Minton, N., Paoli, M.

Revision History  

• Version 1.0: 2005-09-23
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-12-12
  Changes: Advisory, Data collection, Structure summary
• Version 1.4: 2023-12-13
  Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary