SMTL ID : 5gnk.1

Crystal structure of EGFR 696-988 T790M in complex with LXX-6-34

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x 80U: 1-[(3R)-3-[4-azanyl-3-[3-chloranyl-4-[(1-methylimidazol-2-yl)methoxy]phenyl]pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl]prop-2-en-1-one(Covalent)

80U.1: 20 residues within 4Å: Chain A: L.27, G.28, V.35, A.52, K.54, M.75, C.84, L.86, L.97, M.99, Q.100, M.102, C.106, R.150, L.153, T.163, D.164, F.165 Ligands: EDO.26, EDO.27 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.27, A:V.35, A:V.35, A:A.52, A:R.150, A:L.153 Hydrogen bonds: A:Q.100, A:M.102, A:D.164 Halogen bonds: A:L.97

11 x NO3: NITRATE ION(Non-functional Binders)

NO3.2: 4 residues within 4Å: Chain A: K.22, L.39, I.41, K.48 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.22, A:K.48 NO3.3: 5 residues within 4Å: Chain A: E.113, H.114, K.115, D.116, N.117 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.115, A:D.116, A:N.117 Water bridges: A:E.113, A:E.113, A:E.113, A:N.117 NO3.4: 5 residues within 4Å: Chain A: N.125, V.128, Q.129, K.132 Ligands: EDO.23 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.82, A:Q.129 Water bridges: A:K.132, A:K.132 NO3.5: 9 residues within 4Å: Chain A: G.30, A.31, F.32, G.33, K.54, R.150, N.151, D.164 Ligands: EDO.26 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.31, A:F.32, A:G.33, A:K.54, A:K.54, A:R.150, A:R.150 NO3.6: 6 residues within 4Å: Chain A: W.214, T.218, S.221, P.243, P.246 Ligands: NO3.31 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.221 NO3.7: 5 residues within 4Å: Chain A: P.103, F.104, Y.110, E.113, H.114 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.114 Water bridges: A:P.103, A:F.104, A:E.113 NO3.8: 3 residues within 4Å: Chain A: K.23, I.24, Y.36 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.24 Water bridges: A:V.26 NO3.9: 5 residues within 4Å: Chain A: P.186, I.187, K.188, W.189, A.229 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.186, A:I.187, A:K.188 NO3.10: 5 residues within 4Å: Chain A: E.193, I.262, D.263, A.264 Ligands: EDO.17 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.263, A:A.264 Water bridges: A:E.193, A:R.267 NO3.29: 6 residues within 4Å: Chain A: Y.110, H.114, N.117, I.118, Y.122, P.157 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.110, A:Y.110, A:N.117 Water bridges: A:G.119 NO3.31: 8 residues within 4Å: Chain A: W.214, K.222, P.223, Y.224, D.225, L.242, P.243 Ligands: NO3.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.224, A:D.225

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

EDO.11: 4 residues within 4Å: Chain A: R.14, W.40, R.85, L.87 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: E.18, F.21, K.23, Q.96 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: G.33, T.34, E.55, R.57 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: N.80, P.81, H.82, K.132 Ligands: EDO.15 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: K.132, I.274 Ligands: EDO.14 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: L.192, E.193, H.197 Ligands: NO3.10 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain A: T.201, H.202, Q.203 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: K.115, F.219, I.290, Q.291 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: Q.203, D.265, R.267, K.269, E.272 Ligand excluded by PLIP EDO.21: 2 residues within 4Å: Chain A: K.279, Y.287 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain A: E.67, D.70, E.71, L.142 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain A: N.125, Q.129, Q.158 Ligands: NO3.4 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain A: R.112, G.220 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain A: L.236, E.237, I.262 Ligand excluded by PLIP EDO.26: 7 residues within 4Å: Chain A: S.29, G.30, V.35, R.150 Ligands: 80U.1, NO3.5, EDO.27 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain A: S.29 Ligands: 80U.1, EDO.26 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain A: D.146, A.148, R.150, P.186, W.189 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain A: K.25, L.27, K.37 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain A: R.241, V.257, W.260, M.261 Ligand excluded by PLIP

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

CL.16: 6 residues within 4Å: Chain A: C.84, R.85, M.99, Q.100, M.102, K.161 Ligand excluded by PLIP CL.28: 4 residues within 4Å: Chain A: P.81, K.155, H.159, K.161 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, A. et al., Discovery of (R)-1-(3-(4-Amino-3-(3-chloro-4-(pyridin-2-ylmethoxy)phenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl)piperidin-1-yl)prop-2-en-1-one (CHMFL-EGFR-202) as a Novel Irreversible EGFR Mutant Kinase Inhibitor with a Distinct Binding Mode. J. Med. Chem. (2017)

Release Date

2017-04-05

Peptides

Epidermal growth factor receptor: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Epidermal growth factor receptor