SMTL ID : 6mob.1

Crystal structure of KIT1 in complex with DP2976 via co-crystallization

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

14 x NO3: NITRATE ION(Non-functional Binders)

NO3.1: 4 residues within 4Å: Chain A: R.21, F.26, P.100, L.102 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.21 NO3.2: 4 residues within 4Å: Chain A: T.29, A.32, K.37, K.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.61, A:K.61 NO3.3: 6 residues within 4Å: Chain A: G.33, A.34, F.35, G.36, L.190, R.192 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.33, A:A.34, A:F.35, A:G.36, A:L.190, A:R.192 Water bridges: A:R.192 NO3.4: 4 residues within 4Å: Chain A: L.60, R.69, P.100, T.101 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.101, A:T.101 Water bridges: A:L.60, A:R.69, A:T.101 NO3.5: 5 residues within 4Å: Chain A: T.9, E.70, M.73, S.74, K.77 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.77 Water bridges: A:K.77 NO3.6: 7 residues within 4Å: Chain A: K.16, W.17, E.18, F.19, L.46, L.92, G.93 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.18 NO3.7: 6 residues within 4Å: Chain A: K.211, S.245, Y.247, P.248, G.249, M.250 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.245, A:G.249, A:M.250 Water bridges: A:S.245 NO3.8: 6 residues within 4Å: Chain A: Y.110, F.116, R.119, K.120, L.139, R.181 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.119, A:R.119, A:K.120, A:K.120, A:R.181 NO3.9: 4 residues within 4Å: Chain A: R.118, R.121, G.243, S.244 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.121, A:R.121 Water bridges: A:S.245, A:S.245 NO3.10: 4 residues within 4Å: Chain A: W.237, P.248, M.266, L.267 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.267 Water bridges: A:L.267 NO3.11: 7 residues within 4Å: Chain A: Y.247, M.250, M.259, I.260, F.264, R.265, M.266 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.265 NO3.12: 3 residues within 4Å: Chain A: G.263, F.264, R.265 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.265 Water bridges: A:R.265 NO3.13: 5 residues within 4Å: Chain A: K.48, A.51, A.52, M.53 Ligands: NO3.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.48, A:A.52 Water bridges: A:I.47, A:K.48 NO3.14: 3 residues within 4Å: Chain A: A.51, A.52 Ligands: NO3.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.52

1 x JWY: N-{4-chloro-5-[1-ethyl-7-(methylamino)-2-oxo-1,2-dihydro-1,6-naphthyridin-3-yl]-2-fluorophenyl}-N'-phenylurea(Non-covalent)

JWY.15: 22 residues within 4Å: Chain A: V.38, A.56, V.57, K.58, E.75, L.79, L.82, V.89, V.103, T.105, E.106, Y.107, C.108, G.111, L.160, H.167, L.176, I.185, C.186, D.187, F.188, A.191 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:V.38, A:A.56, A:K.58, A:L.82, A:V.103, A:T.105, A:L.160, A:I.185, A:F.188, A:A.191 Hydrogen bonds: A:K.58, A:E.75, A:C.108, A:C.108, A:D.187 Water bridges: A:E.75 pi-Cation interactions: A:K.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Smith, B.D. et al., Ripretinib (DCC-2618) Is a Switch Control Kinase Inhibitor of a Broad Spectrum of Oncogenic and Drug-Resistant KIT and PDGFRA Variants. Cancer Cell (2019)

Release Date

2019-07-31

Peptides

Mast/stem cell growth factor receptor Kit: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Mast/stem cell growth factor receptor Kit