5LMK

Structure of phopsho-CDK2-cyclin A in complex with an ATP-competitive inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

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Literature

Explicit treatment of active-site waters enhances quantum mechanical/implicit solvent scoring: Inhibition of CDK2 by new pyrazolo[1,5-a]pyrimidines.

Hylsova, M., Carbain, B., Fanfrlik, J., Musilova, L., Haldar, S., Kopruluoglu, C., Ajani, H., Brahmkshatriya, P.S., Jorda, R., Krystof, V., Hobza, P., Echalier, A., Paruch, K., Lepsik, M.

(2016) Eur J Med Chem 126: 1118-1128

  • DOI: 10.1016/j.ejmech.2016.12.023
  • Primary Citation of Related Structures:  
    5LMK

  • PubMed Abstract: 

    • We present comprehensive testing of solvent representation in quantum mechanics (QM)-based scoring of protein-ligand affinities. To this aim, we prepared 21 new inhibitors of cyclin-dependent kinase 2 (CDK2) with the pyrazolo[1,5-a]pyrimidine core, whose activities spanned three orders of magnitude ...

    We present comprehensive testing of solvent representation in quantum mechanics (QM)-based scoring of protein-ligand affinities. To this aim, we prepared 21 new inhibitors of cyclin-dependent kinase 2 (CDK2) with the pyrazolo[1,5-a]pyrimidine core, whose activities spanned three orders of magnitude. The crystal structure of a potent inhibitor bound to the active CDK2/cyclin A complex revealed that the biphenyl substituent at position 5 of the pyrazolo[1,5-a]pyrimidine scaffold was located in a previously unexplored pocket and that six water molecules resided in the active site. Using molecular dynamics, protein-ligand interactions and active-site water H-bond networks as well as thermodynamics were probed. Thereafter, all the inhibitors were scored by the QM approach utilizing the COSMO implicit solvent model. Such a standard treatment failed to produce a correlation with the experiment (R 2  = 0.49). However, the addition of the active-site waters resulted in significant improvement (R 2  = 0.68). The activities of the compounds could thus be interpreted by taking into account their specific noncovalent interactions with CDK2 and the active-site waters. In summary, using a combination of several experimental and theoretical approaches we demonstrate that the inclusion of explicit solvent effects enhance QM/COSMO scoring to produce a reliable structure-activity relationship with physical insights. More generally, this approach is envisioned to contribute to increased accuracy of the computational design of novel inhibitors.

    Organizational Affiliation: 

    Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic. Electronic address: lepsik@uochb.cas.cz.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-dependent kinase 2A299Homo sapiensMutation(s): 0 
Gene Names: CDK2, CDKN2
EC: 2.7.11.22
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
PHAROS:  P24941
Entity Groups  
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UniProt GroupP24941
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-A2B, D258Homo sapiensMutation(s): 0 
Gene Names: CCNA2, CCN1, CCNA
UniProt & NIH Common Fund Data Resources
Find proteins for P20248 (Homo sapiens)
Explore P20248 
Go to UniProtKB:  P20248
PHAROS:  P20248
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UniProt GroupP20248
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-dependent kinase 2C297Homo sapiensMutation(s): 0 
Gene Names: CDK2, CDKN2
EC: 2.7.11.22
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
PHAROS:  P24941
Entity Groups  
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UniProt GroupP24941
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6ZK
Query on 6ZK
Download Ideal Coordinates CCD File 
E [auth A],
H [auth C]		4-[4-[3-bromanyl-7-(pyridin-3-ylmethylamino)pyrazolo[1,5-a]pyrimidin-5-yl]phenyl]benzamide
C25 H19 Br N6 O
BNCZSQHEMDOHNQ-UHFFFAOYSA-N		 Ligand Interaction
SGM
Query on SGM
Download Ideal Coordinates CCD File 
F [auth B],
I [auth D]		MONOTHIOGLYCEROL
C3 H8 O2 S
PJUIMOJAAPLTRJ-GSVOUGTGSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
G [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO		A L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Binding Affinity Annotations 
IDSourceBinding Affinity
6ZK BindingDB:  5LMK IC50: 37 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.466α = 90
b = 134.395β = 90
c = 149.481γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2016-08-01 
  • Released Date: 2017-01-25 
    • Deposition Author(s): Echalier, A.

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection