SMTL ID : 7be6.1

Structure of DDR1 receptor tyrosine kinase in complex with inhibitor SR159

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

monomer

Ligands

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

EDO.1: 10 residues within 4Å: Chain A: M.212, A.213, W.214, I.217, W.229, F.247, V.255, N.258, A.259 Ligands: EDO.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.213, A:V.255, A:N.258 EDO.2: 6 residues within 4Å: Chain A: W.229, F.247, Y.271, L.272, W.290 Ligands: EDO.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.272 Water bridges: A:W.229 EDO.3: 5 residues within 4Å: Chain A: T.224, S.294, R.297, P.298, P.299 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.297 Water bridges: A:F.300 EDO.4: 7 residues within 4Å: Chain A: D.168, G.188, M.189, Y.198, V.206, P.208 Ligands: TJW.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.206 Water bridges: A:M.189 EDO.5: 3 residues within 4Å: Chain A: D.70, E.74 Ligands: TJW.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.74 EDO.8: 6 residues within 4Å: Chain A: W.214, E.215, R.292, E.293, S.294, E.295 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.293, A:E.293, A:S.294 EDO.10: 4 residues within 4Å: Chain A: K.57, E.74, D.186 Ligands: TJW.9 No protein-ligand interaction detected (PLIP)

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 1 residues within 4Å: Chain A: R.305 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.305

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 1 residues within 4Å: Chain A: K.73 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.73

1 x TJW: 5-amino-N-(4-(((2S)-4-cyclohexyl-1-((1-(methylsulfonyl)piperidin-3-yl)amino)-1-oxobutan-2-yl)carbamoyl)benzyl)-1-phenyl-1H-pyrazole-4-carboxamide(Non-covalent)

TJW.9: 23 residues within 4Å: Chain A: V.26, A.55, E.74, I.77, M.78, I.87, M.101, T.103, D.104, Y.105, M.106, E.107, G.109, F.164, H.166, I.184, A.185, D.186, F.187, G.188 Ligands: EDO.4, EDO.5, EDO.10 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:A.55, A:I.77, A:I.87, A:T.103, A:Y.105, A:F.164 Hydrogen bonds: A:E.74, A:E.74, A:T.103, A:T.103, A:M.106, A:D.186, A:D.186 Salt bridges: A:D.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rohm, S. et al., Development of a Selective Dual Discoidin Domain Receptor (DDR)/p38 Kinase Chemical Probe. J.Med.Chem. (2021)

Release Date

2021-03-03

Peptides

Epithelial discoidin domain-containing receptor 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Epithelial discoidin domain-containing receptor 1

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