3KMM | pdb_00003kmm

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 (Depositor), 0.214 (DCC)
R-Value Work:
0.165 (Depositor), 0.165 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 271
Deposited Residue Count: 288
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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
PTR	BindingDB: 3KMM	Kd: 4.00e+5 (nM) from 1 assay(s)
LHL	BindingDB: 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 (Depositor), 0.214 (DCC)
R-Value Work: 0.165 (Depositor), 0.165 (DCC)
R-Value Observed: 0.167 (Depositor)

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

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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.