SMTL ID : 5jsm.2 (1 other biounit)

BRAFV600E Kinase Domain In Complex with Chemically Linked Vemurafenib Inhibitor VEM-3-VEM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-dimer

Ligands

1 x 6NB: N,N'-{ethane-1,2-diylbis[oxyethane-2,1-diyloxy-4,1-phenylene-1H-pyrrolo[2,3-b]pyridine-5,3-diylcarbonyl(2,4-difluoro-3,1-phenylene)]}di(propane-1-sulfonamide)(Non-covalent)

6NB.1: 43 residues within 4Å: Chain A: Q.18, I.20, V.28, A.38, V.39, K.40, L.71, F.73, I.84, T.86, Q.87, W.88, C.89, S.92, S.93, H.96, F.140, G.150, D.151, F.152, G.153 Chain B: Q.18, I.20, V.28, A.38, V.39, K.40, L.71, F.73, I.84, T.86, Q.87, W.88, C.89, S.92, H.96, F.140, G.150, D.151, F.152, G.153 Ligands: DMS.2, DMS.3 41 PLIP interactions: 20 interactions with chain B, 21 interactions with chain A Hydrophobic interactions: B:I.20, B:A.38, B:K.40, B:L.71, B:F.73, B:T.86, B:T.86, B:W.88, B:F.152, B:F.152, A:I.20, A:A.38, A:K.40, A:F.73, A:I.84, A:T.86, A:W.88, A:F.140, A:F.152 Hydrogen bonds: B:T.86, B:Q.87, B:C.89, B:D.151, B:D.151, B:F.152, B:G.153, A:Q.18, A:K.40, A:T.86, A:Q.87, A:C.89, A:D.151, A:D.151, A:F.152, A:G.153 pi-Stacking: B:F.140, B:F.140, A:F.140, A:F.140 pi-Cation interactions: B:K.40, A:K.40

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 4 residues within 4Å: Chain A: I.20, G.21, H.96 Ligands: 6NB.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.96 DMS.3: 9 residues within 4Å: Chain B: I.20, G.21, S.22, G.23, V.28, N.137, N.138, F.140 Ligands: 6NB.1 No protein-ligand interaction detected (PLIP)

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

CL.4: 4 residues within 4Å: Chain B: W.7, L.72, F.73, M.74 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grasso, M. et al., Chemically Linked Vemurafenib Inhibitors Promote an Inactive BRAF(V600E) Conformation. Acs Chem.Biol. (2016)

Release Date

2016-09-14

Peptides

Serine/threonine-protein kinase B-raf: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Serine/threonine-protein kinase B-raf

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