SMTL ID : 4ckr.1

Crystal structure of the human DDR1 kinase domain in complex with DDR1-IN-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x DI1: 4-[(4-ethylpiperazin-1-yl)methyl]-n-{4-methyl-3-[(2-oxo-2,3-dihydro-1h-indol-5-yl)oxy]phenyl}-3-(trifluoromethyl)benzamide(Non-covalent)

DI1.1: 22 residues within 4Å: Chain A: V.26, A.55, K.57, E.74, M.78, L.81, I.86, I.87, M.101, T.103, D.104, Y.105, M.106, L.159, V.165, H.166, R.167, L.175, I.184, A.185, D.186, F.187 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:V.26, A:A.55, A:K.57, A:K.57, A:E.74, A:M.101, A:T.103, A:R.167, A:L.175, A:D.186, A:F.187 Hydrogen bonds: A:K.57, A:E.74, A:E.74, A:M.106, A:D.186 Salt bridges: A:D.186 pi-Cation interactions: A:H.166 Halogen bonds: A:I.184

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

EDO.2: 7 residues within 4Å: Chain A: N.108, F.114, V.176, G.177, E.178, N.179, F.180 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.177, A:N.179, A:F.180 EDO.3: 7 residues within 4Å: Chain A: R.157, A.160, T.224, P.299, F.300, S.301 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.300, A:S.301 EDO.4: 6 residues within 4Å: Chain A: N.112, E.237, C.242, A.244, Q.245, P.246 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.112, A:E.237 Water bridges: A:T.171, A:C.242 EDO.5: 7 residues within 4Å: Chain A: T.224, A.225, S.294, R.297, P.298, P.299 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.297 EDO.6: 5 residues within 4Å: Chain A: N.85, A.150, Q.151, S.154, H.304 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.154, A:S.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, H. et al., Discovery of a Potent and Selective Ddr1 Receptor Tyrosine Kinase Inhibitor. Acs Chem.Biol. (2013)

Release Date

2014-01-15

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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