4FKQ | pdb_00004fkq

Crystal structure of the cdk2 in complex with oxindole inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4FKQ/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2012-06-13 Released: 2013-05-08 
• Deposition Author(s): Kang, Y.N., Stuckey, J.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the cdk2 in complex with oxindole inhibitor

Kang, Y.N., Stuckey, J.A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 34.45 kDa 
• Atom Count: 2,570 
• Modeled Residue Count: 284 
• 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): 1  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 GTEx:  ENSG00000123374

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
42K	B [auth A]	4-[(2Z)-2-(7-oxidanylidene-3,6-dihydropyrrolo[3,2-e]benzotriazol-8-ylidene)hydrazinyl]benzenesulfonamide C14 H11 N7 O3 S AQAPFJBZSZVEGI-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
42K	BindingDB:  4FKQ	Kd: min: 191, max: 528 (nM) from 2 assay(s)
		-TΔS: min: -8.34e+0, max: -7.78e+0 (kJ/mol) from 2 assay(s)
		ΔH: min: -3.03e+1, max: -2.75e+1 (kJ/mol) from 2 assay(s)
		ΔG: min: -3.82e+1, max: -3.58e+1 (kJ/mol) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.361	α = 90
b = 72.112	β = 90
c = 72.402	γ = 90

Software Package:

Software Name	Purpose
MD2	data collection
PHASER	phasing
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-08 
Deposition Author(s): Kang, Y.N., Stuckey, J.A.

Revision History  

• Version 1.0: 2013-05-08
  Type: Initial release
  
• Version 1.1: 2013-05-22
  Changes: Other
• Version 1.2: 2016-11-30
  Changes: Non-polymer description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-27
  Changes: Structure summary