3BYM: Proto-oncogene tyrosine-protein kinase LCK

X-ray co-crystal structure aminobenzimidazole triazine 1 bound to Lck. Determined by X-ray diffraction at 2.0 Å resolution. Released 16 Sept 2008.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,527
Mol. weight: 32.22 kDa
Ligands: AM0
Released: 16 Sept 2008

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

Secondary structure: helices and β-sheets

3BYM contains 18 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: 18 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	276	1
α-helix	282-294	13
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	487-500	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proto-oncogene tyrosine-protein kinase LCK	A	protein	272	Homo sapiens	P06239 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3BYM_1 Proto-oncogene tyrosine-protein kinase LCK (chains A)
QKPWWEDEWEVPRETLKLVERLGAGQFGEVWMGYYNGHTKVAVKSLKQGSMSPDAFLAEA
NLMKQLQHQRLVRLYAVVTQEPIYIITEYMENGSLVDFLKTPSGIKLTINKLLDMAAQIA
EGMAFIEERNYIHRDLRAANILVSDTLSCKIADFGLARLIEDNEYTAREGAKFPIKWTAP
EAINYGTFTIKSDVWSFGILLTEIVTHGRIPYPGMTNPEVIQNLERGYRMVRPDNCPEEL
YQLMRLCWKERPEDRPTFDYLRSVLEDFFTAT

Ligands and cofactors

ID	Name	Formula	Copies
AM0	N-phenyl-1-{4-[(3,4,5-trimethoxyphenyl)amino]-1,3,5-triazin-2-yl}-1H-benzimidaz…	C25 H23 N7 O3	1

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

Primary citation

Structure-based design of novel 2-amino-6-phenyl-pyrimido[5',4':5,6]pyrimido[1,2-a]benzimidazol-5(6H)-ones as potent and orally active inhibitors of lymphocyte specific kinase (Lck): synthesis, SAR, and in vivo anti-inflammatory activity. Martin, M.W., Newcomb, J., Nunes, J.J. et al. J Med Chem (2008) 51:1637-1648. DOI 10.1021/jm701095m · 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…
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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