SMTL ID : 6o0m.1

crystal structure of BCL-2 F104L mutation with venetoclax

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x LBM: 4-{4-[(4'-chloro-5,5-dimethyl[3,4,5,6-tetrahydro[1,1'-biphenyl]]-2-yl)methyl]piperazin-1-yl}-N-[(3-nitro-4-{[(oxan-4-yl )methyl]amino}phenyl)sulfonyl]-2-[(1H-pyrrolo[2,3-b]pyridin-5-yl)oxy]benzamide(Non-covalent)

LBM.1: 20 residues within 4Å: Chain A: A.59, D.62, L.63, R.66, Y.67, F.71, M.74, E.95, N.102, W.103, G.104, R.105, V.107, A.108, E.111, F.112, V.115, F.157, Y.161 Ligands: PEG.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.63, A:F.71, A:M.74, A:E.95, A:R.105, A:F.112 Hydrogen bonds: A:D.62, A:N.102, A:W.103, A:G.104 Salt bridges: A:D.70

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 3 residues within 4Å: Chain A: Y.67 Ligands: LBM.1, PEG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.67 PEG.3: 1 residues within 4Å: Ligands: PEG.2 No protein-ligand interaction detected (PLIP) PEG.4: 7 residues within 4Å: Chain A: R.86, F.89, A.90, W.135, E.138, Y.139, H.143 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.86, A:R.86 Water bridges: A:A.90 PEG.5: 1 residues within 4Å: Chain A: R.12 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Birkinshaw, R.W. et al., Structures of BCL-2 in complex with venetoclax reveal the molecular basis of resistance mutations. Nat Commun (2019)

Release Date

2019-05-22

Peptides

Apoptosis regulator Bcl-2,Bcl-2-like protein 1,Apoptosis regulator Bcl-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Apoptosis regulator Bcl-2,Bcl-2-like protein 1,Apoptosis regulator Bcl-2