3AC1: Pyrazin derivative

Crystal structure of pyrazin derivative bound to the kinase domain of Human LCK, (Auto-phosphorylated on TYR394). Determined by X-ray diffraction at 1.99 Å resolution. Released 30 Jun 2010.

Method: X-ray diffraction
Resolution: 1.99 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,542
Mol. weight: 33.84 kDa
Ligands: KZI
Released: 30 Jun 2010

Explore 3AC1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3AC1 contains 17 α-helices and 14 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: 17 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	239	1	1
α-helix	242-244	3
β-strand	245-254	10	1
β-strand	257-264	8	1
β-strand	268-275	8	1
α-helix	282-292	11
β-strand	300	1	2
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	2
α-helix	324-327	4
α-helix	331-334	4
α-helix	338-357	20
β-strand	360-361	2	3
α-helix	367-369	3
β-strand	370-372	3	2
β-strand	378-380	3	2
β-strand	387-388	2	3
β-strand	394-395	2	4
α-helix	409-414	6
β-strand	416-417	2	4
α-helix	419-434	16
α-helix	438-439	2
α-helix	446-455	10
α-helix	459-462	4
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
Proto-oncogene tyrosine-protein kinase LCK	A	protein	285	Homo sapiens	P06239 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3AC1_1 Proto-oncogene tyrosine-protein kinase LCK (chains A)
QTQKPQKPWWEDEWEVPRETLKLVERLGAGQFGEVWMGYYNGHTKVAVKSLKQGSMSPDA
FLAEANLMKQLQHQRLVRLYAVVTQEPIYIITEYMENGSLVDFLKTPSGIKLTINKLLDM
AAQIAEGMAFIEERNYIHRDLRAANILVSDTLSCKIADFGLARLIEDNEYTAREGAKFPI
KWTAPEAINYGTFTIKSDVWSFGILLTEIVTHGRIPYPGMTNPEVIQNLERGYRMVRPDN
CPEELYQLMRLCWKERPEDRPTFDYLRSVLEDFFTATEGQYQPQP

Ligands and cofactors

ID	Name	Formula	Copies
KZI	5-{[(1R,2S)-2-aminocyclohexyl]amino}-3-[(3,5-dimethoxyphenyl)amino]pyrazine-2-c…	C19 H26 N6 O3	1

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

Primary citation

Ab initio fragment molecular orbital study of ligand binding to leukocyte-specific protein tyrosine (LCK) kinase. Ozawa, M., Ozawa, T., Tsuji, E. et al. To be published.

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…
6PDJ 1.81 Å, Tyrosine-protein kinase LCK bound to Compound 11
1BHH 1.9 Å, Free P56LCK SH2 domain
3MPM 1.95 Å, LCK complexed with a pyrazolopyrimidine

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