SMTL ID : 9by4.1

Co-crystal structure of the kinase domain of EGFR with non-covalent osimertinib

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

monomer

Ligands

3 x PDO: 1,3-PROPANDIOL(Non-covalent)

PDO.1: 8 residues within 4Å: Chain A: R.152, W.196, M.197, A.198, S.201, Y.207, S.211, S.215 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.198, A:S.201, A:S.201, A:S.215 Water bridges: A:L.154 PDO.4: 4 residues within 4Å: Chain A: R.157, N.158, D.171 Ligands: Q6K.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.171 Water bridges: A:N.158 PDO.5: 9 residues within 4Å: Chain A: K.61, E.78, M.82, C.91, L.104, T.106, L.160, T.170 Ligands: Q6K.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.106 Hydrogen bonds: A:K.61, A:K.61, A:T.170, A:T.170

1 x Q6K: ~{N}-[2-[2-(dimethylamino)ethyl-methyl-amino]-4-methoxy-5-[[4-(1-methylindol-3-yl)pyrimidin-2-yl]amino]phenyl]propanamide(Non-covalent)

Q6K.2: 14 residues within 4Å: Chain A: L.34, F.39, V.42, A.59, Q.107, L.108, M.109, P.110, G.112, C.113, D.116, L.160 Ligands: PDO.4, PDO.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.34, A:F.39, A:V.42, A:V.42, A:A.59, A:L.160 Hydrogen bonds: A:M.109, A:M.109, A:C.113 Salt bridges: A:D.116

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 2 residues within 4Å: Chain A: P.49, D.324 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.324, A:D.324

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsutsui, Y. et al., Comprehensive characterization of EGFR-tyrosine kinase inhibitor interactions probed by hydrogen-deuterium exchange and mass spectrometry (HDX-MS). To Be Published

Release Date

2025-05-28

Peptides

Epidermal growth factor receptor: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Epidermal growth factor receptor

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