SMTL ID : 8qqy.1

Crystal structure of human Ephrin type-A receptor 2 (EPHA2) Kinase domain in complex with JG165

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x WT3: 6-(4-fluoranyl-3-methoxy-phenyl)-13$l^{6}-thia-2,4,8,12,19-pentazatricyclo[12.3.1.1^{3,7}]nonadeca-1(18),3,5,7(19),14,16-hexaene 13,13-dioxide(Non-covalent)

WT3.1: 16 residues within 4Å: Chain A: I.25, V.33, A.50, I.51, K.52, E.69, M.73, I.96, T.98, E.99, Y.100, M.101, G.104, A.105, L.152, S.162 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.33, A:Y.100, A:L.152 Hydrogen bonds: A:I.25, A:M.101, A:M.101, A:A.105

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

EDO.2: 7 residues within 4Å: Chain A: P.192, I.195, S.196, M.233, N.237 Ligands: EDO.7, EDO.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.196, A:M.233, A:N.237 EDO.3: 5 residues within 4Å: Chain A: A.137, N.138, K.269, F.270, A.271 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.270, A:A.271 Water bridges: A:S.202 EDO.4: 4 residues within 4Å: Chain A: R.241, M.257, W.260, Q.261 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.257 EDO.5: 3 residues within 4Å: Chain A: V.142, F.200, T.201 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.200 EDO.6: 3 residues within 4Å: Chain A: Y.197, K.199, R.264 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.197, A:K.199, A:K.199, A:R.264 EDO.7: 5 residues within 4Å: Chain A: P.192, E.193, S.196, Y.197 Ligands: EDO.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.196, A:S.196 Water bridges: A:E.193 EDO.8: 8 residues within 4Å: Chain A: I.187, R.188, T.190, I.195, W.207, M.233, I.236 Ligands: EDO.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.188, A:T.190 EDO.9: 4 residues within 4Å: Chain A: H.79, N.154, N.156, V.158 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.154, A:N.156 Water bridges: A:H.79 EDO.10: 4 residues within 4Å: Chain A: N.140, Y.141, V.142, R.144 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.140, A:V.142 Water bridges: A:Y.141, A:V.142 EDO.11: 3 residues within 4Å: Chain A: Y.224, W.225, E.226 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.224 EDO.12: 2 residues within 4Å: Chain A: E.226, S.228 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.226 EDO.13: 4 residues within 4Å: Chain A: Q.262, E.263, R.264, A.265 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.264, A:R.264, A:A.265 Water bridges: A:R.264 EDO.14: 3 residues within 4Å: Chain A: R.222, W.225, E.226 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.226, A:E.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gerninghaus, J. et al., Back-Pocket Optimization of 2-Aminopyrimidine-Based Macrocycles Leads to Potent EPHA2/GAK Kinase Inhibitors. J.Med.Chem. (2024)

Release Date

2023-11-22

Peptides

Ephrin type-A receptor 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ephrin type-A receptor 2

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