6PDJ: Tyrosine-protein kinase LCK

Tyrosine-protein kinase LCK bound to Compound 11. Determined by X-ray diffraction at 1.81 Å resolution. Released 9 Oct 2019.

Method: X-ray diffraction
Resolution: 1.81 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,536
Mol. weight: 34.32 kDa
Ligands: ODJ, CXS, NI
Released: 9 Oct 2019

Explore 6PDJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6PDJ contains 19 α-helices and 16 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	239	1	1
α-helix	242-244	3
β-strand	245-253	9	1
β-strand	257-264	8	1
β-strand	268-275	8	1
α-helix	276	1
β-strand	277	1	2
β-strand	280	1	2
α-helix	282-285	4
α-helix	291-294	4
β-strand	300	1	3
α-helix	301-302	2
β-strand	303-307	5	1
α-helix	312	1
β-strand	313-317	5	1
β-strand	323	1	3
α-helix	324-327	4
α-helix	331-334	4
α-helix	338-357	20
β-strand	360-361	2	4
α-helix	367-369	3
β-strand	370-372	3	3
β-strand	378-380	3	3
β-strand	387-388	2	4
β-strand	394-395	2	5
α-helix	404-406	3
α-helix	409-414	6
β-strand	416-417	2	5
α-helix	419-434	16
α-helix	438-439	2
α-helix	446-455	10
α-helix	467-476	10
α-helix	481-483	3
α-helix	485-486	2
α-helix	487-499	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tyrosine-protein kinase Lck	A	protein	288	Homo sapiens	P06239 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6PDJ_1 Tyrosine-protein kinase Lck (chains A)
GHMQTQKPQKPWWEDEWEVPRETLKLVERLGAGQFGEVWMGYYNGHTKVAVKSLKQGSMS
PDAFLAEANLMKQLQHQRLVRLYAVVTQEPIYIITEYMENGSLVDFLKTPSGIKLTINKL
LDMAAQIAEGMAFIEERNYIHRDLRAANILVSDTLSCKIADFGLARLIEDNEYTAREGAK
FPIKWTAPEAINYGTFTIKSDVWSFGILLTEIVTHGRIPYPGMTNPEVIQNLERGYRMVR
PDNCPEELYQLMRLCWKERPEDRPTFDYLRSVLEDFFTATEGQYQPQP

Ligands and cofactors

ID	Name	Formula	Copies
ODJ	N-{4-[(6-methoxypyrazolo[1,5-a]pyridine-3-carbonyl)amino]-3-methylphenyl}-1-met…	C25 H22 N6 O3	1
CXS	3-cyclohexyl-1-propylsulfonic acid	C9 H19 N O3 S	1
NI	Nickel (II) ion	Ni	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Discovery of Pyridazinone and Pyrazolo[1,5-a]pyridine Inhibitors of C-Terminal Src Kinase. O'Malley, D.P., Ahuja, V., Fink, B. et al. ACS Med Chem Lett (2019) 10:1486-1491. DOI 10.1021/acsmedchemlett.9b00354 · PubMed

Other PDB entries of the same protein (UniProt P06239 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1LKK 1.0 Å, Human P56-lck tyrosine kinase SH2 domain in complex with the phosphotyrosyl peptide…
2IIM 1.0 Å, SH3 Domain of Human Lck
8X2P 1.4 Å, The Crystal Structure of LCK from Biortus.
1QPC 1.6 Å, Structural analysis of the lymphocyte-specific kinase lck in complex with non-selective…
3LCK 1.7 Å, The kinase domain of human lymphocyte kinase (LCK), activated form (auto-phosphorylated…
4C3F 1.72 Å, Structure of Lck in complex with a compound discovered by Virtual Fragment Linking
1BHF 1.8 Å, P56LCK SH2 domain inhibitor complex
1LCJ 1.8 Å, SH2 (src homology-2) domain of human P56-lck tyrosine kinase complexed with the 11…
1LKL 1.8 Å, Human P56-lck tyrosine kinase SH2 domain in complex with the phosphotyrosyl peptide…
1BHH 1.9 Å, Free P56LCK SH2 domain
3MPM 1.95 Å, LCK complexed with a pyrazolopyrimidine
3AC1 1.99 Å, Crystal structure of pyrazin derivative bound to the kinase domain of Human LCK,…

Browse structure collections

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