6INL | pdb_00006inl

Crystal structure of CDK2 IN complex with Inhibitor CVT-313

• PDB DOI: https://doi.org/10.2210/pdb6INL/pdb

• Classification: CELL CYCLE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
• Mutation(s): No 


• Deposited: 2018-10-25 Released: 2019-10-30 
• Deposition Author(s): Talapati, S.R., Krishnamurthy, N.R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.250 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Structure of cyclin-dependent kinase 2 (CDK2) in complex with the specific and potent inhibitor CVT-313.

Talapati, S.R., Nataraj, V., Pothuganti, M., Gore, S., Ramachandra, M., Antony, T., More, S.S., Krishnamurthy, N.R.

(2020) Acta Crystallogr F Struct Biol Commun 76: 350-356

• PubMed: 32744246 
• DOI: https://doi.org/10.1107/S2053230X20009243
• Primary Citation Related Structures: 
  6INL


• PubMed Abstract: 
  

  CVT-313 is a potent CDK2 inhibitor that was identified by screening a purine-analogue library and is currently in preclinical studies. Since this molecule has the potential to be developed as a CDK2 inhibitor for cancer therapy, the potency of CVT-313 to bind and stabilize CDK2 was evaluated, together with its ability to inhibit aberrant cell proliferation. CVT-313 increased the melting temperature of CDK2 by 7°C in thermal stabilization studies, thus indicating its protein-stabilizing effect. CVT-313 inhibited the growth of human lung carcinoma cell line A549 in a dose-dependent manner, with an IC ₅₀ of 1.2 µM, which is in line with the reported biochemical potency of 0.5 µM. To support the further chemical modification of CVT-313 and to improve its biochemical and cellular potency, a crystal structure was elucidated in order to understand the molecular interaction of CVT-313 and CDK2. The crystal structure of CDK2 bound to CVT-313 was determined to a resolution of 1.74 Å and clearly demonstrated that CVT-313 binds in the ATP-binding pocket, interacting with Leu83, Asp86 and Asp145 directly, and the binding was further stabilized by a water-mediated interaction with Asn132. Based on the crystal structure, further modifications of CVT-313 are proposed to provide additional interactions with CDK2 in the active site, which may significantly increase the biochemical and cellular potency of CVT-313.

---

Organizational Affiliation: 
• Aurigene Discovery Technologies Ltd, 39-40 KIADB Industrial Area, Electronic City Phase II, Hosur Road, Bangalore 560 100, India.
School of Basic and Applied Sciences, Dayananada Sagar University, Shavige Malleshawara Hills, Kumaraswamy Layout, Bangalore 560 078, India.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.46 kDa 
• Atom Count: 2,376 
• Modeled Residue Count: 272 
• Deposited Residue Count: 299 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 2	A	299	Homo sapiens	Mutation(s): 0  Gene Names: CDK2 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 GTEx:  ENSG00000123374

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AJR	B [auth A]	2,2'-{[6-{[(4-methoxyphenyl)methyl]amino}-9-(propan-2-yl)-9H-purin-2-yl]azanediyl}di(ethan-1-ol) C20 H28 N6 O3 NQVIIUBWMBHLOZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AJR	BindingDB:  6INL	IC50: min: 176, max: 500 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.250 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.645	α = 90
b = 71.994	β = 90
c = 72.075	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-30 
Deposition Author(s): Talapati, S.R., Krishnamurthy, N.R.

Revision History  

• Version 1.0: 2019-10-30
  Type: Initial release
  
• Version 1.1: 2020-08-12
  Changes: Database references, Structure summary
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description