SMTL ID : 9qxn.1

Crystal Structure of wild-type EGFR in complex with the reversible inhibitor Sevabertinib (BAY 2927088)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

monomer

Ligands

2 x SIN: SUCCINIC ACID(Non-covalent)

SIN.1: 5 residues within 4Å: Chain A: D.266, M.269, I.270, K.273 Ligands: DMS.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:M.269 Water bridges: A:D.266 Salt bridges: A:K.273, A:K.273 SIN.2: 6 residues within 4Å: Chain A: E.33, F.36, I.39, Y.51, E.70, Q.111 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.111, A:Q.111

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: R.127, K.237 Ligand excluded by PLIP

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 6 residues within 4Å: Chain A: K.273, P.283, E.287, L.288, E.291 Ligands: SIN.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.273 Salt bridges: A:E.291 DMS.6: 4 residues within 4Å: Chain A: H.97, Q.144, Q.173, H.174 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:H.174

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 4 residues within 4Å: Chain A: Q.136, Y.137, N.140, Q.173 No protein-ligand interaction detected (PLIP)

1 x 01: 3-[(3-chloranyl-2-methoxy-phenyl)amino]-2-[3-[[(2~{S})-1,4-dioxan-2-yl]methoxy]pyridin-4-yl]-1,5,6,7-tetrahydropyrrolo[3,2-c]pyridin-4-one

01.7: 19 residues within 4Å: Chain A: L.42, G.43, F.47, V.50, A.67, I.68, K.69, E.86, M.90, L.101, L.112, T.114, Q.115, L.116, M.117, N.166, L.168, T.178, D.179 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.47, A:A.67, A:K.69, A:L.112, A:T.114, A:L.168, A:T.178 Hydrogen bonds: A:K.69, A:M.117, A:T.178, A:T.178, A:D.179, A:D.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Siegel, F. et al., Sevabertinib, a Reversible HER2 Inhibitor with Activity in Lung Cancer. Cancer Discov (2025)

Release Date

2025-10-15

Peptides

Epidermal growth factor receptor: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Epidermal growth factor receptor