3KMM

Structure of human LCK kinase with a small molecule inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3KMM/pdb

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


• Deposited: 2009-11-10 Released: 2010-12-08 
• Deposition Author(s): Graves, B.J., Surgenor, A., Harris, W., Smith, I., Orchard, S., Flotow, H., Murray, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.223 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 

Starting Model: experimental

Literature

Structure of human LCK kinase with a small molecule inhibitor

Graves, B.J., Surgenor, A., Harris, W., Smith, I., Orchard, S., Flotow, H., Murray, E.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 34.13 kDa 
• Atom Count: 2,364 
• Modelled Residue Count: 271 
• Deposited Residue Count: 288 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase LCK	A	288	Homo sapiens	Mutation(s): 1  Gene Names: LCK EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P06239 (Homo sapiens) Explore P06239  Go to UniProtKB:  P06239
GTEx:  ENSG00000182866

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LHL	B [auth A]	3-(2,6-dichlorophenyl)-7-({4-[2-(diethylamino)ethoxy]phenyl}amino)-1-methyl-3,4-dihydropyrimido[4,5-d]pyrimidin-2(1H)-one C25 H28 Cl2 N6 O2 LQYPBKQMDVWUGO-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
LHL	BindingDB:  3KMM	Kd: 0.2 (nM) from 1 assay(s)
	PDBBind:  3KMM	Kd: 0.2 (nM) from 1 assay(s)
PTR	BindingDB:  3KMM	Kd: 4.00e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.223 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.579	α = 90
b = 74.16	β = 90
c = 92.85	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-08 
Deposition Author(s): Graves, B.J., Surgenor, A., Harris, W., Smith, I., Orchard, S., Flotow, H., Murray, E.

Revision History  

• Version 1.0: 2010-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-03-07
  Changes: Data collection
• Version 1.3: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description
• Version 1.5: 2023-11-22
  Changes: Data collection