8U8X: Receptor tyrosine-protein kinase erbB-2

crystal structure of the receptor tyrosine kinase Human HER2 (ERBB2) YVMA mutant kinase domain in complex with inhibitor compound 27. Determined by X-ray diffraction at 1.69 Å resolution. Released 12 Jun 2024.

Method: X-ray diffraction
Resolution: 1.69 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,801
Mol. weight: 40.2 kDa
Ligands: W9N
Released: 12 Jun 2024

Explore 8U8X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8U8X contains 25 α-helices and 12 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: 25 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	713-714	2	1
α-helix	715-716	2
α-helix	717-719	3
β-strand	720-729	10	1
β-strand	732-739	8	1
β-strand	748-755	8	1
α-helix	756-757	2
α-helix	770-777	8
β-strand	786	1	2
β-strand	789-794	6	1
β-strand	798-803	6	1
α-helix	804-805	2
β-strand	809	1	2
α-helix	810-817	8
α-helix	818-820	3
α-helix	823-842	20
α-helix	852-854	3
β-strand	855-859	5	2
β-strand	862-865	4	2
α-helix	870-874	5
α-helix	878-880	3
α-helix	882-884	3
α-helix	890-892	3
α-helix	895-900	6
α-helix	905-920	16
α-helix	924-925	2
α-helix	932-934	3
α-helix	935-940	6
α-helix	945-948	4
β-strand	951	1	3
α-helix	953-962	10
α-helix	967-969	3
α-helix	971-972	2
α-helix	973-984	12
α-helix	987-989	3
β-strand	991	1	3
α-helix	1024-1026	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Receptor tyrosine-protein kinase erbB-2	A	protein	348	Homo sapiens	P04626 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8U8X_1 Receptor tyrosine-protein kinase erbB-2 (chains A)
MGTELVEPLTPSGAMPNQAQMRILKETELRKVKVLGSGAFGTVYKGIWIPDGENVKIPVA
IKVLRENTSPKANKEILDEAYVMAYVMAGVGSPYVSRLLGICLTSTVQLVTQLMPYGCLL
DHVRENRGRLGSQDLLNWCMQIAKGMSYLEDVRLVHRDLAARNVLVKSPNHVKITDFGLA
RLLDIDETEYHADGGKVPIKWMALESILRRRFTHQSDVWSYGVTVWELMTFGAKPYDGIP
AREIPDLLEKGERLPQPPICTIDVYMIMVKCWMIDSECRPRFRELVSEFSRMARDPQRFV
VIQNEDLGPASPLDSTFYRSLLEDDDMGDLVDAEEYLVPQQGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
W9N	1-{(1R,3r,5S)-3-[(3M)-4-methyl-3-{3-methyl-4-[(1-methyl-1H-benzimidazol-5-yl)ox…	C31 H33 N7 O2	1

Water and common crystallization additives (CL, PEG) are not listed.

Primary citation

Discovery of Potent and Selective Covalent Inhibitors of HER2 WT and HER2 YVMA . Hicken, E.J., Brown, K., Dwulet, N.C. et al. J Med Chem (2024) 67:9759-9771. DOI 10.1021/acs.jmedchem.4c00978 · PubMed

Other PDB entries of the same protein (UniProt P04626 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1MFG 1.25 Å, The Structure of ERBIN PDZ domain bound to the Carboxy-terminal tail of the ErbB2 Receptor
8VB5 1.48 Å, Crystal structure of kinase domain of HER2 Exon 20 insertion mutant in complex with…
8JYR 1.69 Å, Crystal structure of anti-HER2 antibody H2Mab-119 in complex with HER2 domain I
8JYQ 1.75 Å, Crystal structure of cancer-specific anti-HER2 antibody H2Mab-214 in complex with…
7PCD 1.77 Å, HER2 in complex with a covalent inhibitor
5TQS 1.88 Å, Phospholipase C gamma-1 C-terminal SH2 domain bound to a phosphopeptide derived from the…
1MFL 1.88 Å, The Structure of ERBIN PDZ domain bound to the Carboxy-terminal tail of the ErbB2 Receptor
4GFU 2.0 Å, PTPN18 in complex with HER2-pY1248 phosphor-peptides
6LBX 2.03 Å, Crystal structure of HER2 Domain IV and Rb-H2
9IUT 2.09 Å, Crystal structure of cancer-specific anti-HER2 antibody H2Mab-250 in complex with…
5MY6 2.25 Å, Crystal structure of a HER2-Nb complex
3PP0 2.25 Å, Crystal Structure of the Kinase domain of Human HER2 (erbB2).

Browse structure collections

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