SMTL ID : 6ig8.1

Crystal structure of CSF-1R kinase domain with a small molecular inhibitor, JTE-952

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 1 residues within 4Å: Chain A: D.59 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.59, H2O.4, H2O.7 MG.2: 1 residues within 4Å: Chain A: E.58 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: K.25, W.26, G.56, L.101 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.25, A:K.25 Water bridges: A:L.101

1 x A7O: (3-{4-[(4-cyclopropylphenyl)methoxy]-3-methoxyphenyl}azetidin-1-yl)(4-{[(2S)-2,3-dihydroxypropoxy]methyl}pyridin-2-yl)methanone(Non-covalent)

A7O.4: 23 residues within 4Å: Chain A: W.1, L.39, V.47, A.65, K.67, E.84, M.88, L.91, V.98, T.114, E.115, Y.116, C.117, C.118, Y.119, G.120, C.179, H.181, N.188, L.190, G.200, D.201, F.202 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.1, A:W.1, A:V.47, A:L.91, A:V.98, A:T.114, A:Y.116, A:L.190, A:D.201 Hydrogen bonds: A:C.117, A:D.201 Water bridges: A:D.121 pi-Cation interactions: A:K.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ikegashira, K. et al., Discovery of a novel azetidine scaffold for colony stimulating factor-1 receptor (CSF-1R) Type II inhibitors by the use of docking models. Bioorg.Med.Chem.Lett. (2019)

Release Date

2019-08-07

Peptides

Macrophage colony-stimulating factor 1 receptor: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Macrophage colony-stimulating factor 1 receptor

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