SMTL ID : 6p3d.1

The co-crystal structure of BRAF(V600E) with ponatinib

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-dimer

Ligands

2 x 0LI: 3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzam ide(Non-covalent)

0LI.1: 24 residues within 4Å: Chain A: I.37, V.45, A.55, V.56, K.57, E.75, L.79, I.87, L.88, I.101, T.103, Q.104, W.105, C.106, I.146, I.147, H.148, R.149, F.157, I.166, G.167, D.168, F.169, L.171 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:K.57, A:E.75, A:L.79, A:L.88, A:I.101, A:T.103, A:W.105, A:F.157, A:F.169 Hydrogen bonds: A:E.75, A:C.106, A:D.168 Water bridges: A:K.57 pi-Cation interactions: A:H.148 Halogen bonds: A:I.166 0LI.13: 24 residues within 4Å: Chain B: I.37, V.45, A.55, V.56, K.57, E.75, L.79, I.87, L.88, I.101, T.103, Q.104, W.105, C.106, I.146, I.147, H.148, R.149, F.157, I.166, G.167, D.168, F.169, L.171 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:K.57, B:E.75, B:L.79, B:L.88, B:I.101, B:T.103, B:W.105, B:F.157, B:F.169 Hydrogen bonds: B:E.75, B:E.75, B:C.106, B:D.168 Water bridges: B:K.57 pi-Cation interactions: B:H.148 Halogen bonds: B:I.166

16 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: R.278, P.279, S.280, R.283 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: P.260, K.261, R.262 Ligand excluded by PLIP SO4.4: 2 residues within 4Å: Chain A: K.272, K.273 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: R.36, G.38, S.39 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain A: R.36, S.39, T.44, Y.46, N.60 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: E.123, M.124, R.256, N.258 Ligand excluded by PLIP SO4.8: 8 residues within 4Å: Chain A: V.85, T.163, K.165 Chain B: Q.104, H.159, T.163, K.165 Ligands: SO4.20 Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Chain A: W.24, R.80 Chain B: W.24, R.80 Ligands: SO4.21 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain B: R.278, P.279, S.280, R.283 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain B: P.260, K.261, R.262 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain B: K.272, K.273 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain B: R.36, G.38, S.39 Ligand excluded by PLIP SO4.18: 5 residues within 4Å: Chain B: R.36, S.39, T.44, Y.46, N.60 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain B: E.123, M.124, R.256, N.258 Ligand excluded by PLIP SO4.20: 8 residues within 4Å: Chain A: Q.104, H.159, T.163, K.165 Chain B: V.85, T.163, K.165 Ligands: SO4.8 Ligand excluded by PLIP SO4.21: 5 residues within 4Å: Chain A: W.24, R.80 Chain B: W.24, R.80 Ligands: SO4.9 Ligand excluded by PLIP

2 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.10: 5 residues within 4Å: Chain A: G.108, S.109, H.114, L.158, D.161 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.109, A:S.109, A:D.161 NH4.22: 5 residues within 4Å: Chain B: G.108, S.109, H.114, L.158, D.161 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.109, B:L.158, B:D.161, B:D.161

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 5 residues within 4Å: Chain A: L.115, H.116, G.226, Q.227, L.228 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.115, A:L.228 EDO.12: 5 residues within 4Å: Chain A: D.139, P.282, L.285, A.286 Chain B: H.51 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.51, A:A.286 EDO.23: 5 residues within 4Å: Chain B: L.115, H.116, G.226, Q.227, L.228 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.115, B:H.116, B:L.228 EDO.24: 5 residues within 4Å: Chain A: H.51 Chain B: D.139, P.282, L.285, A.286 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.139, B:A.286, A:H.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cotto-Rios, X.M. et al., Inhibitors of BRAF dimers using an allosteric site. Nat Commun (2020)

Release Date

2020-09-23

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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