4TPT | pdb_00004tpt

Crystal Structure of the Human LIMK2 Kinase Domain In Complex With a Non-ATP Competitive Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4TPT/pdb

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


• Deposited: 2014-06-09 Released: 2014-10-22 
• Deposition Author(s): Goodwin, N.C., Cianchetta, G., Hamman, B.L., Burgoon, H.A., Healy, J., Mabon, S., Strobel, E.D., Wang, S., Rawlins, D.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.274 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Literature

Discovery of a Type III Inhibitor of LIM Kinase 2 That Binds in a DFG-Out Conformation.

Goodwin, N.C., Cianchetta, G., Burgoon, H.A., Healy, J., Mabon, R., Strobel, E.D., Allen, J., Wang, S., Hamman, B.D., Rawlins, D.B.

(2015) ACS Med Chem Lett 6: 53-57

• PubMed: 25589930 
• DOI: https://doi.org/10.1021/ml500242y
• Primary Citation of Related Structures:  
  4TPT


• PubMed Abstract: 
  

  The first allosteric, type III inhibitor of LIM-kinase 2 (LIMK2) is reported. A series of molecules that feature both an N-phenylsulfonamide and tertiary amide were not only very potent at LIMK2 but also were extremely selective against a panel of other kinases. Enzymatic kinetic studies showed these molecules to be noncompetitive with ATP, suggesting allosteric inhibition. X-ray crystallography confirmed that these sulfonamides are a rare example of a type III kinase inhibitor that binds away from the highly conserved hinge region and instead resides in the hydrophobic pocket formed in the DFG-out conformation of the kinase, thus accounting for the high level of selectivity observed.

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Organizational Affiliation: 

Lexicon Pharmaceuticals , 350 Carter Road, Princeton, New Jersey 08540, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 70.04 kDa 
• Atom Count: 4,509 
• Modelled Residue Count: 556 
• Deposited Residue Count: 606 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LIM domain kinase 2	A, B	303	Homo sapiens	Mutation(s): 0  Gene Names: LIMK2 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P53671 (Homo sapiens) Explore P53671  Go to UniProtKB:  P53671
PHAROS:  P53671 GTEx:  ENSG00000182541

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
35H	C [auth A], D [auth B]	N-{4-[(1S)-1,2-dihydroxyethyl]benzyl}-N-methyl-4-(phenylsulfamoyl)benzamide C23 H24 N2 O5 S LJBXWGVECYNLLM-JOCHJYFZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
35H	BindingDB:  4TPT	IC50: 92 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.274 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.569	α = 90
b = 77.903	β = 100.84
c = 86.387	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-22 
Deposition Author(s): Goodwin, N.C., Cianchetta, G., Hamman, B.L., Burgoon, H.A., Healy, J., Mabon, S., Strobel, E.D., Wang, S., Rawlins, D.B.

Revision History  

• Version 1.0: 2014-10-22
  Type: Initial release
  
• Version 1.1: 2015-01-28
  Changes: Database references
• Version 2.0: 2023-12-27
  Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2024-10-23
  Changes: Structure summary