5NXD

LIM Domain Kinase 2 (LIMK2) In Complex With TH-300

• PDB DOI: https://doi.org/10.2210/pdb5NXD/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2017-05-10 Released: 2017-05-24 
• Deposition Author(s): Mathea, S., Salah, E., Hanke, T., Newman, J.A., Oerum, S., Wang, D., Burgess-Brown, N., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A.N., Knapp, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

LIM Domain Kinase 2 (LIMK2)In Complex With TH-300

Mathea, S., Salah, E., Hanke, T., Newman, J.A., Oerum, S., Wang, D., Burgess-Brown, N., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A.N., Knapp, S.

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.

Macromolecule Content

• Total Structure Weight: 70.61 kDa 
• Atom Count: 4,423 
• Modelled Residue Count: 542 
• Deposited Residue Count: 610 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LIM domain kinase 2	A, B	305	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9D8	C [auth A], E [auth B]	4-[(3-chlorophenyl)sulfamoyl]-~{N}-(phenylmethyl)-~{N}-propyl-benzamide C23 H23 Cl N2 O3 S VMGWOAVOASXXIH-UHFFFAOYSA-N
EDO	D [auth A], F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
9D8	BindingDB:  5NXD	IC50: min: 40, max: 50 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.275	α = 90
b = 66.605	β = 97.43
c = 82.124	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-24 
Deposition Author(s): Mathea, S., Salah, E., Hanke, T., Newman, J.A., Oerum, S., Wang, D., Burgess-Brown, N., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A.N., Knapp, S.

Revision History  

• Version 1.0: 2017-05-24
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description