SMTL ID : 8c7y.1

Crystal structure of BRAF V600E in complex with a hybrid compound 6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: A.102, S.103, E.104 Ligand excluded by PLIP EDO.2: 7 residues within 4Å: Chain A: Y.199, Y.215, L.233, S.234, P.235, L.256, K.258 Ligand excluded by PLIP EDO.3: 3 residues within 4Å: Chain A: L.237, K.249, R.250 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: S.95, N.139, F.142, F.154 Ligands: EDO.6, TXV.19 Ligand excluded by PLIP EDO.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: I.22, G.23, F.27, V.30, F.154 Ligands: EDO.4, TXV.19 Ligand excluded by PLIP EDO.7: 2 residues within 4Å: Chain A: R.134, L.172 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: V.18, Y.31, M.43, Q.83 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: Q.52, Q.55, A.56, N.59, K.160 Ligand excluded by PLIP EDO.10: 2 residues within 4Å: Chain A: Q.55, K.58 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: F.57, V.61, Y.78 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: K.111, D.114, I.115, Q.118, D.146, N.147, T.148 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: L.177, R.221, I.224 Ligands: EDO.15 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: Y.97, K.137, N.139, G.174, W.178 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: L.177, L.213 Ligands: EDO.13 Ligand excluded by PLIP EDO.16: 2 residues within 4Å: Chain A: G.231, S.232 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: R.185, Q.187, G.229, R.230 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: F.57, K.58, Y.78, T.80 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain B: L.251, E.254, P.264, R.268, E.272 Ligand excluded by PLIP

1 x NO3: NITRATE ION(Non-functional Binders)

NO3.18: 5 residues within 4Å: Chain A: Q.89, H.144, K.150 Chain B: T.148, K.150 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:K.150, A:Q.89, A:K.150, A:K.150 Water bridges: B:T.148, A:H.144

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: 20 residues within 4Å: Chain A: I.22, V.30, A.40, K.42, E.60, L.64, L.73, I.86, T.88, Q.89, W.90, C.91, H.133, I.151, G.152, D.153, F.154, L.156 Ligands: EDO.4, EDO.6 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.40, A:K.42, A:E.60, A:L.64, A:I.86, A:T.88, A:D.153, A:F.154, A:F.154, A:L.156 Hydrogen bonds: A:E.60, A:Q.89, A:C.91, A:D.153 Water bridges: A:K.42 TXV.22: 21 residues within 4Å: Chain B: I.22, V.30, A.40, V.41, K.42, E.60, V.63, L.64, L.73, I.86, T.88, Q.89, W.90, C.91, H.133, F.142, I.151, G.152, D.153, F.154, A.157 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:A.40, B:K.42, B:E.60, B:V.63, B:I.86, B:T.88, B:D.153, B:F.154 Hydrogen bonds: B:E.60, B:T.88, B:Q.89, B:C.91, B:D.153 Water bridges: B:K.42 pi-Stacking: B:F.154

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