Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 34.49 kDa 
• Atom Count: 2317 
• Residue Count: 268 
• Unique protein chains: 1

2BRN

Structure-based Design of Novel Chk1 Inhibitors: Insights into Hydrogen Bonding and Protein-Ligand Affinity

• DOI: 10.2210/pdb2BRN/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2005-05-09 Released: 2005-05-12 
• Deposition Author(s): Foloppe, N., Fisher, L.M., Howes, R., Kierstan, P., Potter, A., Robertson, A.G.S., Surgenor, A.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.285 
• R-Value Work: 0.203 
• R-Value Observed: 0.207 

Literature

Structure-Based Design of Novel Chk1 Inhibitors: Insights Into Hydrogen Bonding and Protein-Ligand Affinity.

Foloppe, N., Fisher, L.M., Howes, R., Kierstan, P., Potter, A., Robertson, A.G.S., Surgenor, A.E.

(2005) J Med Chem 48: 4332

• PubMed: 15974586 
• DOI: 10.1021/jm049022c
• Primary Citation of Related Structures:  
  2BR1, 2BRH, 2BRG, 2BRB, 2BRO, 2BRN, 2BRM


• PubMed Abstract: 
  

We report the discovery, synthesis, and crystallographic binding mode of novel furanopyrimidine and pyrrolopyrimidine inhibitors of the Chk1 kinase, an oncology target. These inhibitors are synthetically tractable and inhibit Chk1 by competing for its ATP site. A chronological account allows an objective comparison of modeled compound docking modes to the subsequently obtained crystal structures. The comparison provides insights regarding the interpretation of modeling results, in relationship to the multiple reasonable docking modes which may be obtained in a kinase-ATP site. The crystal structures were used to guide medicinal chemistry efforts. This led to a thorough characterization of a pair of ligand-protein complexes which differ by a single hydrogen bond. An analysis indicates that this hydrogen bond is expected to contribute a fraction of the 10-fold change in binding affinity, adding a valuable observation to the debate about the energetic role of hydrogen bonding in molecular recognition.

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Organizational Affiliation: 

Vernalis (R&D) Limited, Granta Park, Abington, Cambridge CB1 6GB, UK. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN KINASE CHK1	A	297	Homo sapiens	Mutation(s): 0  Gene Names: CHEK1, CHK1 EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (UniProt)
Find proteins for O14757 (Homo sapiens) Explore O14757  Go to UniProtKB:  O14757
NIH Common Fund Data Resources
PHAROS:  O14757 GTEx:  ENSG00000149554

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DF1	A	(2R)-1-[(5,6-DIPHENYL-7H-PYRROLO[2,3-D]PYRIMIDIN-4-YL)AMINO]PROPAN-2-OL C21 H20 N4 O VBASHTSSQNDDAS-CQSZACIVSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DF1	IC50:  5500   nM  BindingDB
DF1	IC50 :  5500   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.285 
• R-Value Work: 0.203 
• R-Value Observed: 0.207 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.907	α = 90
b = 65.692	β = 101.81
c = 54.429	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-05-09 
• Released Date: 2005-05-12 
Deposition Author(s): Foloppe, N., Fisher, L.M., Howes, R., Kierstan, P., Potter, A., Robertson, A.G.S., Surgenor, A.E.

Revision History 

• Version 1.0: 2005-05-12
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance