SMTL ID : 6xfp.1

Crystal Structure of BRAF kinase domain bound to Belvarafenib

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x V1Y: 4-amino-N-{1-[(3-chloro-2-fluorophenyl)amino]-6-methylisoquinolin-5-yl}thieno[3,2-d]pyrimidine-7-carboxamide(Non-covalent)

V1Y.1: 19 residues within 4Å: Chain A: I.28, V.36, A.46, V.47, K.48, E.66, L.70, L.79, I.92, T.94, Q.95, W.96, C.97, F.148, I.157, G.158, D.159, F.160, L.162 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:V.36, A:A.46, A:K.48, A:L.70, A:L.79, A:I.92, A:T.94, A:D.159, A:L.162 Hydrogen bonds: A:E.66, A:E.66, A:T.94, A:T.94, A:C.97, A:C.97, A:D.159 Water bridges: A:K.48 pi-Stacking: A:F.160, A:F.160 V1Y.8: 19 residues within 4Å: Chain B: I.28, V.36, A.46, V.47, K.48, E.66, L.70, L.79, I.92, T.94, Q.95, W.96, C.97, F.148, I.157, G.158, D.159, F.160, L.162 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:V.36, B:A.46, B:K.48, B:L.70, B:L.79, B:I.92, B:T.94, B:D.159, B:L.162 Hydrogen bonds: B:E.66, B:T.94, B:C.97, B:C.97, B:D.159 Water bridges: B:K.48 pi-Stacking: B:F.160, B:F.160

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain A: K.116, K.117 Ligand excluded by PLIP CL.3: 1 residues within 4Å: Chain A: H.173 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: W.15, R.74 Chain B: W.15, R.74 Ligands: CL.11 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: R.168 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: R.127, L.276, E.280 Chain B: G.43 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: L.162, R.168, W.169 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain B: K.116, K.117 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain B: H.173 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain A: W.15, R.74 Chain B: W.15, R.74 Ligands: CL.4 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain B: R.168 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain A: G.43 Chain B: R.127, L.276, E.280 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: L.162, R.168, W.169 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yen, I. et al., ARAF mutations confer resistance to the RAF inhibitor belvarafenib in melanoma. Nature (2021)

Release Date

2021-03-10

Peptides

Serine/threonine-protein kinase B-raf: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Serine/threonine-protein kinase B-raf

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