SMTL ID : 8c7x.1

Crystal structure of BRAF in complex with a hybrid compound 6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: Y.201, Y.217, L.235, S.236, P.237, L.258, K.260 Ligand excluded by PLIP EDO.2: 3 residues within 4Å: Chain A: A.104, S.105, E.106 Ligand excluded by PLIP EDO.3: 3 residues within 4Å: Chain A: L.239, K.251, R.252 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: G.25, F.29, V.32, F.156 Ligands: EDO.5, TXV.19 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: S.97, N.141, F.144, F.156 Ligands: EDO.4, TXV.19 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: V.20, Y.33, Q.85 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: L.253, E.256, P.266, R.270, E.274 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: K.139, N.141, G.176, W.180 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: I.134, R.136, N.192, Y.194 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: F.59, K.60, V.63, Y.80 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: Q.54, Q.57, A.58, N.61, K.162 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: R.136, D.137, L.174 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain A: Q.57, K.60 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: M.111, N.245, P.247 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: S.96, H.100, H.101, S.105 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain B: N.61, E.62, V.65 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: V.72, L.76, K.152 Chain B: V.72, L.76, K.152 Ligand excluded by PLIP

3 x BR: BROMIDE ION(Non-covalent)

BR.16: 1 residues within 4Å: Chain A: R.223 Ligand excluded by PLIP BR.17: 2 residues within 4Å: Chain A: N.222, R.223 Ligand excluded by PLIP BR.18: 4 residues within 4Å: Chain A: W.11, R.70 Chain B: W.11, R.70 Ligand excluded by PLIP

2 x TXV: ~{N}-[3-[(5-chloranyl-1~{H}-pyrrolo[2,3-b]pyridin-3-yl)carbonyl]-2,4-bis(fluoranyl)phenyl]-3-(2-cyanopropan-2-yl)benzamide(Non-covalent)

TXV.19: 21 residues within 4Å: Chain A: I.24, V.32, A.42, K.44, E.62, V.65, L.66, L.75, I.88, T.90, Q.91, W.92, C.93, H.135, I.153, G.154, D.155, F.156, L.158 Ligands: EDO.4, EDO.5 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:A.42, A:K.44, A:E.62, A:V.65, A:I.88, A:T.90, A:D.155, A:F.156, A:L.158 Hydrogen bonds: A:E.62, A:Q.91, A:C.93, A:D.155 Water bridges: A:K.44 TXV.22: 20 residues within 4Å: Chain B: I.24, V.32, A.42, K.44, E.62, V.65, L.66, L.75, I.88, T.90, Q.91, W.92, C.93, H.135, F.144, I.153, G.154, D.155, F.156, A.159 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:A.42, B:K.44, B:E.62, B:V.65, B:T.90, B:D.155, B:F.156 Hydrogen bonds: B:E.62, B:T.90, B:Q.91, B:C.93, B:D.155 Water bridges: B:K.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arora, R. et al., Design, synthesis and characterisation of a novel type II B-RAF paradox breaker inhibitor. Eur.J.Med.Chem. (2023)

Release Date

2023-02-22

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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