4DCE

Crystal structure of human anaplastic lymphoma kinase in complex with a piperidine-carboxamide inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4DCE/pdb

• Classification: Transferase/Inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2012-01-17 Released: 2012-02-08 
• Deposition Author(s): Whittington, D.A., Epstein, L.F., Chen, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.256 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 

Starting Model: other

Literature

Rapid development of piperidine carboxamides as potent and selective anaplastic lymphoma kinase inhibitors.

Bryan, M.C., Whittington, D.A., Doherty, E.M., Falsey, J.R., Cheng, A.C., Emkey, R., Brake, R.L., Lewis, R.T.

(2012) J Med Chem 55: 1698-1705

• PubMed: 22263917 
• DOI: https://doi.org/10.1021/jm201565s
• Primary Citation of Related Structures:  
  4DCE


• PubMed Abstract: 
  

  Piperidine carboxamide 1 was identified as a novel inhibitor of anaplastic lymphoma kinase (ALK enzyme assay IC(50) = 0.174 μM) during high throughput screening, with selectivity over the related kinase insulin-like growth factor-1 (IGF1R). The X-ray cocrystal structure of 1 with the ALK kinase domain revealed an unusual DFG-shifted conformation, allowing access to an extended hydrophobic pocket. Structure-activity relationship (SAR) studies were focused on the rapid parallel optimization of both the right- and left-hand side of the molecule, culminating in molecules with improved potency and selectivity over IGF1R.

---

Organizational Affiliation: 

Medicinal Chemistry Research Technologies, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States.

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: 76.12 kDa 
• Atom Count: 4,858 
• Modelled Residue Count: 572 
• Deposited Residue Count: 666 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALK tyrosine kinase receptor	A, B	333	Homo sapiens	Mutation(s): 1  Gene Names: ALK EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UM73 (Homo sapiens) Explore Q9UM73  Go to UniProtKB:  Q9UM73
PHAROS:  Q9UM73 GTEx:  ENSG00000171094

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0JF	C [auth A], D [auth B]	(3S)-N-(4-methylbenzyl)-1-{2-[(3,4,5-trimethoxyphenyl)amino]pyrimidin-4-yl}piperidine-3-carboxamide C27 H33 N5 O4 BAQAWVMHTOQJCI-FQEVSTJZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0JF	PDBBind:  4DCE	IC50: 174 (nM) from 1 assay(s)
	BindingDB:  4DCE	IC50: min: 174, max: 384 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.256 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.612	α = 90
b = 104.819	β = 90.15
c = 57.817	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-08 
Deposition Author(s): Whittington, D.A., Epstein, L.F., Chen, H.

Revision History  

• Version 1.0: 2012-02-08
  Type: Initial release
  
• Version 1.1: 2012-05-09
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description