SMTL ID : 6u2p.1

PCSK9 in complex with compound 5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: R.36, C.37, A.38, D.40, R.43 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.36, A:D.40, A:D.40, A:R.43 Water bridges: A:C.37 EDO.2: 4 residues within 4Å: Chain A: H.86, G.87, L.89, P.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.87, A:L.89 EDO.3: 2 residues within 4Å: Chain B: L.149, V.250 No protein-ligand interaction detected (PLIP) EDO.4: 6 residues within 4Å: Chain B: K.579, K.581, C.596, E.597, W.600, C.648 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.597 EDO.5: 8 residues within 4Å: Chain B: S.455, C.456, S.457, I.493, G.604, C.605, Y.618, A.619 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.455, B:S.455, B:S.457, B:C.605, B:A.619 Water bridges: B:C.456

1 x PUV: 2-fluoro-4-{[(1R)-6-methoxy-1-methyl-1-{2-oxo-2-[(1,3-thiazol-2-yl)amino]ethyl}-1,2,3,4-tetrahydroisoquinolin-7-yl]oxy}benzoic acid(Non-covalent)

PUV.6: 18 residues within 4Å: Chain B: A.298, S.299, A.300, P.301, V.303, T.305, R.327, C.328, D.330, R.382, R.428, V.430, W.431, I.444, A.445, R.446, C.447, A.448 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:P.301, B:V.430 Hydrogen bonds: B:P.301, B:T.305, B:R.327, B:R.327, B:C.328, B:R.428, B:R.428, B:R.446 Salt bridges: B:R.446 Halogen bonds: B:I.444

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Petrilli, W.L. et al., From Screening to Targeted Degradation: Strategies for the Discovery and Optimization of Small Molecule Ligands for PCSK9. Cell Chem Biol (2020)

Release Date

2019-11-06

Peptides

Proprotein convertase subtilisin/kexin type 9: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Proprotein convertase subtilisin/kexin type 9

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