SMTL ID : 5fdp.1

Structure of DDR1 receptor tyrosine kinase in complex with D2099 inhibitor at 2.25 Angstroms resolution.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

1 x 5WR: (4~{S})-4-methyl-~{N}-[3-[(4-methylpiperazin-1-yl)methyl]-5-(trifluoromethyl)phenyl]-2-pyrimidin-5-yl-3,4-dihydro-1~{H}-isoquinoline-7-carboxamide(Non-covalent)

5WR.1: 19 residues within 4Å: Chain A: V.48, A.77, K.79, E.96, M.100, L.103, I.108, I.109, M.123, T.125, D.126, Y.127, M.128, F.186, H.188, L.197, A.207, D.208, F.209 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.48, A:A.77, A:K.79, A:E.96, A:I.109, A:I.109, A:D.208 Hydrogen bonds: A:E.96, A:E.96, A:M.128, A:D.208 Salt bridges: A:E.96, A:D.208, A:D.208

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 10 residues within 4Å: Chain A: N.134, A.192, T.193, R.194, Y.216, D.219, W.233, E.259, A.266, Q.267 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.193, A:T.193, A:R.194, A:R.194, A:A.266

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

EDO.3: 2 residues within 4Å: Chain A: M.241, G.242 No protein-ligand interaction detected (PLIP) EDO.4: 4 residues within 4Å: Chain A: H.169, A.172, H.326, A.330 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.169 EDO.5: 2 residues within 4Å: Chain A: R.33, D.58 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.33, A:D.58 EDO.6: 7 residues within 4Å: Chain A: W.251, V.255, F.269, V.292, Y.293, L.294, W.312 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.294 EDO.7: 6 residues within 4Å: Chain A: R.179, A.182, T.183, P.321, F.322, S.323 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.322

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Z. et al., Structure-Based Design of Tetrahydroisoquinoline-7-carboxamides as Selective Discoidin Domain Receptor 1 (DDR1) Inhibitors. J.Med.Chem. (2016)

Release Date

2016-06-08

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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