6NCO: Fragment-based Discovery of an apoE4 Stabilizer

Fragment-based Discovery of an apoE4 Stabilizer. Determined by X-ray diffraction at 1.71 Å resolution. Released 17 Apr 2019.

Method: X-ray diffraction
Resolution: 1.71 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,396
Mol. weight: 21.87 kDa
Ligands: KQP
Released: 17 Apr 2019

Explore 6NCO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6NCO contains 6 α-helices and 0 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	25-42	18
α-helix	45-51	7
α-helix	55-78	24
α-helix	82-84	3
α-helix	87-124	38
α-helix	131-162	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Apolipoprotein E	A	protein	185	Homo sapiens	P02649 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6NCO_1 Apolipoprotein E (chains A)
GSSHHHHHHSSGLVPRGSHMKVEQAVETEPEPELRQQTEWQSGQRWELALGRFWDYLRWV
QTLSEQVQEELLSSQVTQELRALMDETMKELKAYKSELEEQLTPVAEETRARLSKELQAA
QARLGADMEDVRGRLVQYRGEVQAMLGQSTEELRVRLASHLRKLRKRLLRDADDLQKRLA
VYQAG

Ligands and cofactors

ID	Name	Formula	Copies
KQP	1-[5-chloro-4'-(2-hydroxypropan-2-yl)[1,1'-biphenyl]-3-yl]cyclobutane-1-carboxi…	C20 H23 Cl N2 O	1

Primary citation

Fragment-Based Discovery of an Apolipoprotein E4 (apoE4) Stabilizer. Petros, A.M., Korepanova, A., Jakob, C.G. et al. J Med Chem (2019) 62:4120-4130. DOI 10.1021/acs.jmedchem.9b00178 · PubMed

Other PDB entries of the same protein (UniProt P02649 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7FCR 1.4 Å, Crystal structure of the N-terminal domain of mutants of Human Apolipoprotein-E (ApoE)
8AX9 1.55 Å, Human Apolipoprotein E4 (ApoE4) N-terminal domain (space group P212121)
8AX8 1.55 Å, Human Apolipoprotein E4 (ApoE4) N-terminal domain (space group P3121)
7FCS 1.6 Å, Crystal structure of the N-terminal domain of mutants of Human Apolipoprotein-E (ApoE)
1GS9 1.7 Å, Apolipoprotein E4, 22k domain
1OR3 1.73 Å, Apolipoprotein E3 (APOE3), trigonal truncation mutant 165
8CE0 1.75 Å, N-terminal domain of human apolipoprotein E
1NFN 1.8 Å, Apolipoprotein E3 (APOE3)
6NCN 1.82 Å, Fragment-based Discovery of an apoE4 Stabilizer
1BZ4 1.85 Å, Apolipoprotein E3 (apo-E3), truncation mutant 165
9SA6 1.89 Å, Human Apolipoprotein E4 (ApoE4) N-terminal domain (space group P212121)
1H7I 1.9 Å, Apolipoprotein E3 22kD fragment LYS146GLN mutant

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