Biological Assembly 1  

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

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

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

Macromolecule Content

• Total Structure Weight: 33.97 kDa 
• Atom Count: 2388 
• Modelled Residue Count: 269 
• Deposited Residue Count: 294 
• Unique protein chains: 2

1NVS

The Complex Structure Of Checkpoint Kinase Chk1/SB218078

• DOI: 10.2210/pdb1NVS/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2003-02-04 Released: 2003-04-08 
• Deposition Author(s): Zhao, B., Bower, M.J., McDevitt, P.J., Zhao, H., Davis, S.T., Johanson, K.O., Green, S.M., Concha, N.O., Zhou, B.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.255 
• R-Value Work: 0.232 

Literature

Structural Basis for Chk1 Inhibition by UCN-01

Zhao, B., Bower, M.J., McDevitt, P.J., Zhao, H., Davis, S.T., Johanson, K.O., Green, S.M., Concha, N.O., Zhou, B.B.

(2002) J Biol Chem 277: 46609-46615

• PubMed: 12244092 
• DOI: 10.1074/jbc.M201233200
• Primary Citation of Related Structures:  
  1NVQ, 1NVR, 1NVS


• PubMed Abstract: 
  

Chk1 is a serine-threonine kinase that plays an important role in the DNA damage response, including G(2)/M cell cycle control. UCN-01 (7-hydroxystaurosporine), currently in clinical trials, has recently been shown to be a potent Chk1 inhibitor that abrogates the G(2)/M checkpoint induced by DNA-damaging agents. To understand the structural basis of Chk1 inhibition by UCN-01, we determined the crystal structure of the Chk1 kinase domain in complex with UCN-01. Chk1 structures with staurosporine and its analog SB-218078 were also determined. All three compounds bind in the ATP-binding pocket of Chk1, producing only slight changes in the protein conformation. Selectivity of UCN-01 toward Chk1 over cyclin-dependent kinases can be explained by the presence of a hydroxyl group in the lactam moiety interacting with the ATP-binding pocket. Hydrophobic interactions and hydrogen-bonding interactions were observed in the structures between UCN-01 and the Chk1 kinase domain. The high structural complementarity of these interactions is consistent with the potency and selectivity of UCN-01.

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Organizational Affiliation: 

Department of Structural Biology, GlaxoSmithKline, King of Prussia, Pennsylvania 19406, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase Chk1	A	289	Homo sapiens	Mutation(s): 0  Gene Names: CHEK1, CHK1 EC: 2.7.1 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O14757 (Homo sapiens) Explore O14757  Go to UniProtKB:  O14757
PHAROS:  O14757 GTEx:  ENSG00000149554

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide ASVSA	B	5	N/A	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UCM (Subject of Investigation/LOI)	D [auth A]	REL-(9R,12S)-9,10,11,12-TETRAHYDRO-9,12-EPOXY-1H-DIINDOLO[1,2,3-FG:3',2',1'-KL]PYRROLO[3,4-I][1,6]BENZODIAZOCINE-1,3(2H)-DIONE C24 H15 N3 O3 OTPNDVKVEAIXTI-IYBDPMFKSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
UCM	PDBBind:  1NVS	Ki: 15 (nM) from 1 assay(s)
	Binding MOAD:  1NVS	Ki: 15 (nM) from 1 assay(s)
	BindingDB:  1NVS	IC50: 15 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.255 
• R-Value Work: 0.232 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.032	α = 90
b = 65.897	β = 94.21
c = 58.156	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
X-PLOR	model building
CNS	refinement
HKL-2000	data reduction
X-PLOR	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2003-02-04 
• Released Date: 2003-04-08 
Deposition Author(s): Zhao, B., Bower, M.J., McDevitt, P.J., Zhao, H., Davis, S.T., Johanson, K.O., Green, S.M., Concha, N.O., Zhou, B.B.

Revision History  

• Version 1.0: 2003-04-08
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance