9BJC | pdb_00009bjc

Crystal structure of CDK2/Cyclin E1 in complex with XC208

• PDB DOI: https://doi.org/10.2210/pdb9BJC/pdb

• Classification: CELL CYCLE,TRANSFERASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2024-04-25 Released: 2025-08-27 
• Deposition Author(s): Hosford, C.J., Yano, J., Thevakumaran, N., Davison, J., Romeril, S., Choi, Y., Hadjithomas, M., Verdine, G.L.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 
  0.213 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Nature-guided discovery of a tunable kinase inhibitor scaffold

Verdine, G.L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 67.49 kDa 
• Atom Count: 4,860 
• Modeled Residue Count: 574 
• Deposited Residue Count: 583 
• Unique protein chains: 2

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, 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
G1/S-specific cyclin-E1	B	284	Homo sapiens	Mutation(s): 0  Gene Names: CCNE1, CCNE
UniProt & NIH Common Fund Data Resources
Find proteins for P24864 (Homo sapiens) Explore P24864  Go to UniProtKB:  P24864
PHAROS:  P24864 GTEx:  ENSG00000105173

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AQZ (Subject of Investigation/LOI)	C [auth A]	(5aS,6S,7S)-3,7-dihydroxy-6-methoxy-1,4,6,9-tetramethyl-6,7-dihydrodibenzo[b,f][1,4]oxazepine-8,11(5aH,10H)-dione C18 H21 N O6 RSOUMUSKPLQSCG-RYRKJORJSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free:  0.213 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.332	α = 90
b = 76.332	β = 90
c = 258.708	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-27 
Deposition Author(s): Hosford, C.J., Yano, J., Thevakumaran, N., Davison, J., Romeril, S., Choi, Y., Hadjithomas, M., Verdine, G.L.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-08-27
  Type: Initial release