SMTL ID : 5jsm.1 (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

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

DMS.1: 4 residues within 4Å: Chain A: H.125, A.126, S.128, F.192 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.192 DMS.2: 9 residues within 4Å: Chain A: I.20, G.21, S.22, G.23, V.28, S.93, N.137, F.140 Ligands: 6NB.6 No protein-ligand interaction detected (PLIP) DMS.3: 4 residues within 4Å: Chain A: S.232, P.233, D.234, L.235 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.235, A:S.236 DMS.7: 8 residues within 4Å: Chain B: I.20, G.21, S.22, G.23, V.28, N.137, F.140 Ligands: 6NB.6 No protein-ligand interaction detected (PLIP)

2 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.4: 5 residues within 4Å: Chain A: W.7, R.66, L.72, F.73, M.74 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.7, A:W.7, A:L.72 Hydrogen bonds: A:M.74 BEN.12: 9 residues within 4Å: Chain B: D.6, W.7, E.8, I.9, P.10, W.33, M.74, G.75 Ligands: CL.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.74 pi-Stacking: B:W.33

3 x EOH: ETHANOL(Non-functional Binders)

EOH.5: 2 residues within 4Å: Chain A: D.144, T.146 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.144 EOH.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EOH.10: 7 residues within 4Å: Chain B: F.25, L.42, V.44, Q.51, F.55, L.154, E.157 No protein-ligand interaction detected (PLIP)

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.6: 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.7 41 PLIP interactions: 21 interactions with chain A, 20 interactions with chain B Hydrophobic interactions: A:I.20, A:A.38, A:K.40, A:F.73, A:T.86, A:W.88, A:F.140, A:F.152, B:I.20, B:A.38, B:K.40, B:F.73, B:I.84, B:W.88, B:W.88, B:F.140, B:F.152 Hydrogen bonds: A:Q.18, A:K.40, A:T.86, A:Q.87, A:C.89, A:D.151, A:D.151, A:D.151, A:F.152, A:G.153, B:K.40, B:Q.87, B:C.89, B:D.151, B:D.151, B:D.151, B:F.152, B:G.153 pi-Stacking: A:F.140, A:F.140, B:F.140, B:F.140 pi-Cation interactions: A:K.40 Water bridges: B:K.158

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

CL.8: 5 residues within 4Å: Chain B: F.4, K.56, V.59, G.60, R.63 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain B: W.7, L.72, F.73, M.74 Ligands: BEN.12 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 4 residues within 4Å: Chain B: K.64, R.66, Y.123, K.127 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.123, B:K.127

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
A

B
B

Serine/threonine-protein kinase B-raf

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