9OB5 | pdb_00009ob5

CDK2/CyclinE bound to compound 20 with P-loop in the EE and CC conformations

PDB DOI: https://doi.org/10.2210/pdb9OB5/pdb

Classification: CELL CYCLE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2025-04-22 Released: 2025-04-30
Deposition Author(s): Baird, J., Holliday, M.H.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.255 (Depositor), 0.252 (DCC)
R-Value Work:
0.233 (Depositor), 0.236 (DCC)
R-Value Observed:
0.234 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Nanoscale direct-to-biology optimization of Cdk2 inhibitors

Douthwaite, J.L., Houde, D.J., Pardo, E., Moran, M.S., Baird, J., Meyer, S.R., Mahjour, B., Zhao, Q., Larrow, J.F., Juang, Y., Han, C.K., Kelley, B., Dunstan, D.R., Holliday, M.J., Billings, K.J., Mader, M.M., Taylor, A.M., Sexton, J.Z., Boezio, A.A., Cernak, T.

To be published.

Macromolecule Content

Total Structure Weight: 67.86 kDa
Atom Count: 4,757
Modeled Residue Count: 572
Deposited Residue Count: 586
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 2	A	301	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P24941
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
G1/S-specific cyclin-E1	B	285	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P24864
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1CAG (Subject of Investigation/LOI) Query on A1CAG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(1R,3R)-3-{3-[3-(pyridin-3-yl)propanamido]-1H-pyrazol-5-yl}cyclopentyl (1-methylcyclopropyl)carbamate C₂₁ H₂₇ N₅ O₃ ZPIADNJLBPEZRZ-HZPDHXFCSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.255 (Depositor), 0.252 (DCC)
R-Value Work: 0.233 (Depositor), 0.236 (DCC)
R-Value Observed: 0.234 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.57	α = 90
b = 101.57	β = 90
c = 151.48	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-04-30
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.