9BLH | pdb_00009blh

Crystal structure of calcium/calmodulin-dependent protein kinase type II subunit delta complexed with ribociclib

• PDB DOI: https://doi.org/10.2210/pdb9BLH/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-04-30 Released: 2025-05-07 
• Deposition Author(s): Tomchick, D.R., Majumdar, A., Tagliabracci, V.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Robert A. Welch Foundation, Howard Hughes Medical Institute (HHMI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.251 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Bacterial ubiquitin ligase engineered for small molecule and protein target identification

Ye, J.S., Majumdar, A., Park, B.C., Black, M.H., Hsieh, T.-S., Osinski, A., Servage, K.A., Kulkarni, K., Naidoo, J., Alto, N.M., Stratton, M.M., Ready, J.M., Pawlowski, K., Tomchick, D.R., Tagliabracci, V.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 69.23 kDa 
• Atom Count: 4,788 
• Modeled Residue Count: 579 
• Deposited Residue Count: 600 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium/calmodulin-dependent protein kinase type II subunit delta	A, B	300	Homo sapiens	Mutation(s): 0  Gene Names: CAMK2D, CAMKD EC: 2.7.11.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q13557 (Homo sapiens) Explore Q13557  Go to UniProtKB:  Q13557
PHAROS:  Q13557 GTEx:  ENSG00000145349

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6ZZ (Subject of Investigation/LOI)	C [auth A], D [auth B]	7-cyclopentyl-N,N-dimethyl-2-{[5-(piperazin-1-yl)pyridin-2-yl]amino}-7H-pyrrolo[2,3-d]pyrimidine-6-carboxamide C23 H30 N8 O RHXHGRAEPCAFML-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.251 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.322	α = 90
b = 82.817	β = 90
c = 172.914	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-07 
Deposition Author(s): Tomchick, D.R., Majumdar, A., Tagliabracci, V.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	DP2GM137419
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	K99GM147532
Robert A. Welch Foundation	United States	I-1911
Robert A. Welch Foundation	United States	I-1704
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2025-05-07
  Type: Initial release