SMTL ID : 5jrq.1

BRAFV600E Kinase Domain In Complex with Chemically Linked Vemurafenib Inhibitor VEM-6-VEM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

homo-dimer

Ligands

2 x 6N9: N-{2,4-difluoro-3-[5-(4-methoxyphenyl)-1H-pyrrolo[2,3-b]pyridine-3-carbonyl]phenyl}propane-1-sulfonamide(Non-covalent)

6N9.1: 23 residues within 4Å: Chain A: I.20, V.28, A.38, V.39, K.40, L.62, L.71, L.72, 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 Ligands: DMS.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:I.20, A:A.38, A:K.40, A:L.71, A:F.73, A:I.84, A:T.86, A:T.86, A:W.88, A:F.140, A:F.152 Hydrogen bonds: A:K.40, A:T.86, A:Q.87, A:C.89, A:D.151, A:D.151, A:G.153 pi-Stacking: A:F.140, A:F.140 pi-Cation interactions: A:K.40 6N9.5: 22 residues within 4Å: Chain B: I.20, V.28, A.38, V.39, K.40, L.62, L.71, L.72, 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 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:I.20, B:A.38, B:K.40, B:L.71, B:F.73, B:I.84, B:T.86, B:T.86, B:W.88, B:F.140, B:F.140, B:F.152 Hydrogen bonds: B:K.40, B:T.86, B:Q.87, B:C.89, B:D.151, B:D.151, B:D.151, B:G.153

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

DMS.2: 8 residues within 4Å: Chain A: I.20, G.21, G.23, V.28, S.93, N.137, F.140 Ligands: 6N9.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.24 DMS.6: 3 residues within 4Å: Chain B: A.269, E.272, E.273 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.273 Salt bridges: B:E.273

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: V.68, Q.87, H.142, D.144, T.146, K.148 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.87, A:D.144, A:T.146, A:K.148, A:K.148 Water bridges: A:L.72, A:L.72

2 x TMA: TETRAMETHYLAMMONIUM ION(Non-covalent)

TMA.4: 8 residues within 4Å: Chain A: W.7, L.62, R.63, K.64, T.65, R.66, L.72, F.73 No protein-ligand interaction detected (PLIP) TMA.7: 8 residues within 4Å: Chain B: W.7, L.62, R.63, K.64, T.65, R.66, L.72, F.73 No protein-ligand interaction detected (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
A

B
B

Serine/threonine-protein kinase B-raf

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