SMTL ID : 8bin.1

Crystal structure of human Ephrin type-A receptor 2 (EPHA2) Kinase domain in complex with MR21

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

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

EDO.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.2: 6 residues within 4Å: Chain A: P.192, I.195, S.196, M.233, N.237 Ligands: EDO.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.237 EDO.3: 5 residues within 4Å: Chain A: M.73, F.76, S.77, R.83, L.84 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.73, A:S.77, A:L.84 EDO.4: 5 residues within 4Å: Chain A: A.137, N.138, K.269, F.270, A.271 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.270, A:A.271 EDO.6: 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.7: 3 residues within 4Å: Chain A: E.112, K.113, E.116 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.113 EDO.8: 2 residues within 4Å: Chain A: S.228, H.230 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.228 Water bridges: A:N.229

1 x QRR: 8-(4-azanylbutyl)-6-(2-chlorophenyl)-2-(methylamino)pyrido[2,3-d]pyrimidin-7-one(Non-covalent)

QRR.5: 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, R.149, L.152, D.163 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.50, A:K.52, A:I.96, A:T.98, A:L.152, A:L.152 Hydrogen bonds: A:M.101, A:M.101, A:R.149 pi-Cation interactions: A:K.52

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

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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