6CD6 | pdb_00006cd6

Crystal Structure of the Human CAMKK1A in complex with GSK650394

• PDB DOI: https://doi.org/10.2210/pdb6CD6/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-02-08 Released: 2018-03-07 
• Deposition Author(s): Santiago, A.S., Counago, R.M., Righetto, G.L., Ramos, P.Z., Silva, P.N.B., Drewry, D., Elkins, J.M., Massirer, K.B., Arruda, P., Edwards, A.M., Structural Genomics Consortium (SGC)
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.285 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Human CAMKK1A in complex with GSK650394

Santiago, A.S., Counago, R.M., Righetto, G.L., Ramos, P.Z., Silva, P.N.B., Drewry, D., Elkins, J.M., Massirer, K.B., Arruda, P., Edwards, A.M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 132.48 kDa 
• Atom Count: 8,439 
• Modeled Residue Count: 1,062 
• Deposited Residue Count: 1,160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium/calmodulin-dependent protein kinase kinase 1	A, B, C, D	290	Homo sapiens	Mutation(s): 0  Gene Names: CAMKK1, CAMKKA EC: 2.7.11.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N5S9 (Homo sapiens) Explore Q8N5S9  Go to UniProtKB:  Q8N5S9
PHAROS:  Q8N5S9 GTEx:  ENSG00000004660

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DXV	E [auth A], G [auth B], I [auth C], K [auth D]	2-cyclopentyl-4-(5-phenyl-1H-pyrrolo[2,3-b]pyridin-3-yl)benzoic acid C25 H22 N2 O2 WVSBGSNVCDAMCF-UHFFFAOYSA-N
CL	F [auth A], H [auth B], J [auth C], L [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
DXV	BindingDB:  6CD6	IC50: min: 3.1, max: 33 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.285 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.378	α = 90
b = 96.042	β = 90.03
c = 141.26	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-03-07 
Deposition Author(s): Santiago, A.S., Counago, R.M., Righetto, G.L., Ramos, P.Z., Silva, P.N.B., Drewry, D., Elkins, J.M., Massirer, K.B., Arruda, P., Edwards, A.M., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	13/50724-5

Revision History  

• Version 1.0: 2018-03-07
  Type: Initial release
  
• Version 1.1: 2019-04-17
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description