SMTL ID : 8bio.1

Crystal structure of human Ephrin type-A receptor 2 (EPHA2) Kinase domain in complex with MRAL5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

EDO.1: 2 residues within 4Å: Chain A: E.116 Ligands: EDO.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.116 EDO.2: 1 residues within 4Å: Ligands: EDO.1 No protein-ligand interaction detected (PLIP) EDO.3: 1 residues within 4Å: Chain A: E.231 No protein-ligand interaction detected (PLIP) EDO.4: 4 residues within 4Å: Chain A: G.239, F.240, R.241, M.257 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.241 Water bridges: A:R.241, A:R.241 EDO.5: 3 residues within 4Å: Chain A: K.134, Y.135, N.138 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.138 Water bridges: A:H.78, A:Y.135 EDO.6: 3 residues within 4Å: Chain A: A.56, G.57, Y.58 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.57, A:Y.58 EDO.7: 3 residues within 4Å: Chain A: R.222, W.225, E.226 No protein-ligand interaction detected (PLIP) EDO.8: 3 residues within 4Å: Chain A: L.120, G.124, I.281 No protein-ligand interaction detected (PLIP) EDO.9: 2 residues within 4Å: Chain A: A.265, K.269 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.264, A:K.269 Water bridges: A:R.267 EDO.10: 7 residues within 4Å: Chain A: W.214, T.218, E.221, W.225, P.243, T.244, P.245 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.243 Water bridges: A:M.246 EDO.11: 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.13: 4 residues within 4Å: Chain A: A.105, D.107, K.108, R.149 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.107, A:R.111 EDO.14: 3 residues within 4Å: Chain A: E.112, K.113, E.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.113 Water bridges: A:E.116

1 x QRD: 8-(4-azanylbutyl)-6-[2-chloranyl-5-(trifluoromethyl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7-one(Non-covalent)

QRD.12: 18 residues within 4Å: Chain A: I.25, V.33, A.50, I.51, K.52, E.69, M.73, I.82, I.96, T.98, E.99, Y.100, M.101, G.104, L.152, S.162, D.163, F.164 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.50, A:I.96, A:T.98, A:L.152 Hydrogen bonds: A:M.101, A:M.101 pi-Cation interactions: A:K.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rak, M. et al., Shifting the selectivity of pyrido[2,3-d]pyrimidin-7(8H)-one inhibitors towards the salt-inducible kinase (SIK) subfamily. Eur.J.Med.Chem. (2023)

Release Date

2022-11-23

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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