4OV6

Crystal structure of PCSK9(53-451) with Adnectin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Pharmacologic Profile of the Adnectin BMS-962476, a Small Protein Biologic Alternative to PCSK9 Antibodies for Low-Density Lipoprotein Lowering.

Mitchell, T.Chao, G.Sitkoff, D.Lo, F.Monshizadegan, H.Meyers, D.Low, S.Russo, K.DiBella, R.Denhez, F.Gao, M.Myers, J.Duke, G.Witmer, M.Miao, B.Ho, S.P.Khan, J.Parker, R.A.

(2014) J.Pharmacol.Exp.Ther. 350: 412-424

  • DOI: 10.1124/jpet.114.214221

  • PubMed Abstract: 
  • Proprotein convertase subtilisin kexin-9 (PCSK9) is an important pharmacological target for decreasing low-density lipoprotein (LDL) in cardiovascular disease, although seemingly inaccessible to small molecule approaches. Compared with therapeutic Ig ...

    Proprotein convertase subtilisin kexin-9 (PCSK9) is an important pharmacological target for decreasing low-density lipoprotein (LDL) in cardiovascular disease, although seemingly inaccessible to small molecule approaches. Compared with therapeutic IgG antibodies currently in development, targeting circulating PCSK9 with smaller molecular scaffolds could offer different profiles and reduced dose burdens. This inspired genesis of PCSK9-binding Adnectins, a protein family derived from human fibronectin-10th-type III-domain and engineered for high-affinity target binding. BMS-962476, an ∼11-kDa polypeptide conjugated to polyethylene glycol to enhance pharmacokinetics, binds with subnanomolar affinity to human. The X-ray cocrystal structure of PCSK9 with a progenitor Adnectin shows ∼910 Å(2) of PCSK9 surface covered next to the LDL receptor binding site, largely by residues of a single loop of the Adnectin. In hypercholesterolemic, overexpressing human PCSK9 transgenic mice, BMS-962476 rapidly lowered cholesterol and free PCSK9 levels. In genomic transgenic mice, BMS-962476 potently reduced free human PCSK9 (ED50 ∼0.01 mg/kg) followed by ∼2-fold increases in total PCSK9 before return to baseline. Treatment of cynomolgus monkeys with BMS-962476 rapidly suppressed free PCSK9 >99% and LDL-cholesterol ∼55% with subsequent 6-fold increase in total PCSK9, suggesting reduced clearance of circulating complex. Liver sterol response genes were consequently downregulated, following which LDL and total PCSK9 returned to baseline. These studies highlight the rapid dynamics of PCSK9 control over LDL and liver cholesterol metabolism and characterize BMS-962476 as a potent and efficacious PCSK9 inhibitor.


    Organizational Affiliation

    Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey rex_a_parker@msn.com tracy.mitchell@bms.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proprotein convertase subtilisin/kexin type 9
A, D
93Homo sapiensMutation(s): 0 
Gene Names: PCSK9 (NARC1)
EC: 3.4.21.-
Find proteins for Q8NBP7 (Homo sapiens)
Go to Gene View: PCSK9
Go to UniProtKB:  Q8NBP7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Proprotein convertase subtilisin/kexin type 9
B, E
294Homo sapiensMutation(s): 0 
Gene Names: PCSK9 (NARC1)
EC: 3.4.21.-
Find proteins for Q8NBP7 (Homo sapiens)
Go to Gene View: PCSK9
Go to UniProtKB:  Q8NBP7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Adnectin
F, G
99Homo sapiensMutation(s): 0 
Find proteins for A0A075B5G3 (Homo sapiens)
Go to UniProtKB:  A0A075B5G3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, E
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
B, D
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 75.200α = 90.00
b = 118.600β = 90.00
c = 168.700γ = 90.00
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
MAR345data collection
BUSTERrefinement
d*TREKdata scaling
PHASERphasing
d*TREKdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-02-20 
  • Released Date: 2014-07-02 
  • Deposition Author(s): Khan, J.A.

Revision History 

  • Version 1.0: 2014-07-02
    Type: Initial release
  • Version 1.1: 2014-07-16
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description