SMTL ID : 4bkj.1 (1 other biounit)

Crystal structure of the human DDR1 kinase domain in complex with imatinib

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x STI: 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE(Non-covalent)

STI.1: 20 residues within 4Å: Chain A: V.26, A.55, V.56, K.57, E.74, I.77, M.78, L.81, I.87, M.101, T.103, Y.105, M.106, V.165, H.166, R.167, L.175, A.185, D.186, F.187 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:A.55, A:K.57, A:L.81, A:M.101, A:T.103, A:Y.105, A:L.175, A:D.186, A:F.187 Hydrogen bonds: A:E.74, A:E.74, A:T.103, A:T.103, A:M.106, A:D.186 Salt bridges: A:D.186 pi-Cation interactions: A:H.166

10 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:F.180 Water bridges: A:N.179 EDO.3: 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.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.255, A:N.258 EDO.4: 5 residues within 4Å: Chain A: W.214, E.215, R.292, E.293, S.294 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.294 EDO.5: 7 residues within 4Å: Chain A: R.157, A.160, T.224, P.299, F.300, S.301 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.300, A:S.301 Water bridges: A:S.301 EDO.6: 5 residues within 4Å: Chain A: N.85, A.150, Q.151, S.154, H.304 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.154 Water bridges: A:N.85, A:N.85, A:N.85, A:H.147, A:S.154 EDO.7: 8 residues within 4Å: Chain A: T.224, A.225, V.228, S.294, R.297, P.298, P.299 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.297 EDO.8: 6 residues within 4Å: Chain A: W.229, F.247, Y.271, L.272, W.290 Ligands: EDO.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.229, A:L.272 EDO.9: 2 residues within 4Å: Chain A: D.36, V.38 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.38 EDO.10: 5 residues within 4Å: Chain A: H.147, Q.151, N.179, F.180, T.181 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.151, A:N.179 Water bridges: A:N.85, A:Q.151 EDO.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Canning, P. et al., Structural Mechanisms Determining Inhibition of the Collagen Receptor Ddr1 by Selective and Multi-Targeted Type II Kinase Inhibitors. J.Mol.Biol. (2014)

Release Date

2013-05-22

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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