SMTL ID : 9df4.1

EGFR Exon20 insertion mutant SVD bound with STX-721

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

monomer

Ligands

1 x 01: (2P)-3-(3-chloro-2-methoxyanilino)-2-[3-({(2R)-1-[(2E)-4-(dimethylamino)but-2-enoyl]-2-methylpyrrolidin-2-yl}ethynyl)pyridin-4-yl]-1,5,6,7-tetrahydro-4H-pyrrolo[3,2-c]pyridin-4-one

01.1: 21 residues within 4Å: Chain A: L.26, F.31, V.34, A.51, I.52, K.53, E.70, M.74, L.88, L.99, T.101, Q.102, L.103, M.104, C.108, D.111, R.152, N.153, L.155, T.165, D.166 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.26, A:F.31, A:F.31, A:V.34, A:A.51, A:K.53, A:T.101, A:L.155, A:T.165 Hydrogen bonds: A:K.53, A:M.104, A:T.165, A:D.166, A:D.166, A:D.166 Water bridges: A:N.153 Salt bridges: A:D.111

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

CL.2: 3 residues within 4Å: Chain A: M.263, I.264 Ligands: GOL.18 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: N.127, Q.131 Ligand excluded by PLIP CL.4: 6 residues within 4Å: Chain A: P.188, I.189, K.190, W.191, E.326, L.328 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: K.53, E.70, D.166, G.168 Ligand excluded by PLIP

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

EDO.6: 4 residues within 4Å: Chain A: S.268, P.270, E.274, E.278 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.278 Water bridges: A:K.260, A:K.260, A:S.268, A:S.268, A:K.271, A:E.278 EDO.7: 5 residues within 4Å: Chain A: K.22, K.36, G.37, L.38, E.316 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.22 EDO.8: 5 residues within 4Å: Chain A: E.115, H.116, D.118, N.119, L.300 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.116, A:D.118, A:N.119 EDO.9: 7 residues within 4Å: Chain A: W.216, K.224, Y.226, D.227, L.244, P.245 Ligands: GOL.22 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.226, A:D.227 Water bridges: A:S.223 EDO.10: 5 residues within 4Å: Chain A: P.230, A.231, S.232 Ligands: EDO.12, GOL.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.232, A:S.232 EDO.11: 4 residues within 4Å: Chain A: T.220, F.221, G.222, S.223 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.223 Water bridges: A:K.224 EDO.12: 8 residues within 4Å: Chain A: K.190, I.229, P.230, A.231, L.328 Ligands: EDO.10, EDO.13, GOL.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.190, A:K.190, A:A.231 EDO.13: 7 residues within 4Å: Chain A: K.190, K.224, D.227, G.228, I.229 Ligands: EDO.12, GOL.19 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.190, A:D.227, A:G.228, A:I.229 EDO.14: 3 residues within 4Å: Chain A: K.16, E.17, L.93 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.17 Water bridges: A:L.93

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 5 residues within 4Å: Chain A: T.251, I.252, D.253, R.288, Y.289 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.251, A:D.253, A:D.253, A:R.288 GOL.16: 6 residues within 4Å: Chain A: E.242, R.243, L.244, P.245, Y.255, R.259 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.243, A:R.243 Water bridges: A:G.241, A:R.259 GOL.17: 4 residues within 4Å: Chain A: M.256, K.260, M.263 Ligands: GOL.18 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.259, A:R.259 GOL.18: 5 residues within 4Å: Chain A: R.243, R.259, W.262 Ligands: CL.2, GOL.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.259 Water bridges: A:R.243 GOL.19: 4 residues within 4Å: Chain A: G.228, P.230 Ligands: EDO.12, EDO.13 No protein-ligand interaction detected (PLIP) GOL.20: 4 residues within 4Å: Chain A: Q.123, N.127, A.283, R.284 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.127, A:N.127 GOL.21: 7 residues within 4Å: Chain A: I.189, I.197, A.231, S.232, I.329, P.330 Ligands: EDO.10 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.232, A:S.232, A:S.235 GOL.22: 6 residues within 4Å: Chain A: Y.226, I.229, I.237, E.242, R.243 Ligands: EDO.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.242, A:E.242 Water bridges: A:E.242 GOL.23: 6 residues within 4Å: Chain A: G.121, S.122, Q.123, P.286, Q.287, D.295 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.122, A:S.122, A:Q.123, A:Q.287, A:D.295 Water bridges: A:Q.287, A:D.295, A:D.295 GOL.24: 4 residues within 4Å: Chain A: P.248, C.250, T.251, V.291 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pagliarini, R.A. et al., STX-721, a Covalent EGFR/HER2 Exon 20 Inhibitor, Utilizes Exon 20-Mutant Dynamic Protein States and Achieves Unique Mutant Selectivity Across Human Cancer Models. Clin.Cancer Res. (2025)

Release Date

2025-05-14

Peptides

Epidermal growth factor receptor: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Epidermal growth factor receptor

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