5VLO | pdb_00005vlo

The structure of human CamKII with bound inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5VLO/pdb

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


• Deposited: 2017-04-25 Released: 2017-08-23 
• Deposition Author(s): Somoza, J.R., Villasenor, A.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Inhibitors of CamKII

Somoza, T.J., Villasenor, A.G.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 70.32 kDa 
• Atom Count: 5,137 
• Modeled Residue Count: 583 
• Deposited Residue Count: 604 
• 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	302	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9EJ	C [auth A], E [auth B]	N-[(2S)-2-(diethylamino)propyl]-2-[(2S)-2-(methylcarbamoyl)azetidin-1-yl]-6-[5-(thiophen-2-yl)pyrazolo[1,5-a]pyrimidin-3-yl]pyridine-4-carboxamide C28 H34 N8 O2 S BKSPZDICBZFRLV-MBSDFSHPSA-N
DTT	D [auth A], F [auth B]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C4 H10 O2 S2 VHJLVAABSRFDPM-IMJSIDKUSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
9EJ	BindingDB:  5VLO	IC50: 0.2 (nM) from 1 assay(s)
		EC50: 24.3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.473	α = 90
b = 67.546	β = 94.111
c = 85.45	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-23 
Deposition Author(s): Somoza, J.R., Villasenor, A.G.

Revision History  

• Version 1.0: 2017-08-23
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Data collection
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references