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.

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
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
PHAROS: P06239 GTEx: ENSG00000182866
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06239
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LHL Query on LHL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR Query on 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)
LHL	PDBBind: 3KMM	Kd: 0.2 (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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-12-08

Deposition Author(s):

Revision History (Full details and data files)

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
Version 1.6: 2024-11-06
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.