6T6F

Crystal structure of human calmodulin-dependent protein kinase 1D (CAMK1D) bound to compound 8 (CS275)

• PDB DOI: https://doi.org/10.2210/pdb6T6F/pdb

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


• Deposited: 2019-10-18 Released: 2020-01-15 
• Deposition Author(s): Sorrell, F., Kraemer, A., Butterworth, S., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.238 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 

Literature

CAMK1D bound to CS275

Sorrell, F., Kraemer, A., Butterworth, S., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: equilibrium centrifugation

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 74.16 kDa 
• Atom Count: 4,753 
• Modelled Residue Count: 575 
• Deposited Residue Count: 644 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium/calmodulin-dependent protein kinase type 1D	A, B	322	Homo sapiens	Mutation(s): 0  Gene Names: CAMK1D, CAMKID EC: 2.7.11.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IU85 (Homo sapiens) Explore Q8IU85  Go to UniProtKB:  Q8IU85
PHAROS:  Q8IU85 GTEx:  ENSG00000183049

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MMW (Subject of Investigation/LOI)	C [auth A], D [auth B]	2-[(3~{S})-3-azanylpiperidin-1-yl]-4-[[3-(trifluoromethyl)phenyl]amino]pyrimidine-5-carboxamide C17 H19 F3 N6 O ASMLDRAEBPYENO-NSHDSACASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.238 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.95	α = 90
b = 115.73	β = 90
c = 53.96	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
xia2	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-01-15 
Deposition Author(s): Sorrell, F., Kraemer, A., Butterworth, S., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	202708

Revision History  

• Version 1.0: 2020-01-15
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description