5HHC

Crystal Structure of Chemically Synthesized Heterochiral {RFX037 plus VEGF-A} Protein Complex in space group P21/n


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Potent d-Protein Antagonist of VEGF-A is Nonimmunogenic, Metabolically Stable, and Longer-Circulating in Vivo.

Uppalapati, M.Lee, D.J.Mandal, K.Li, H.Miranda, L.P.Lowitz, J.Kenney, J.Adams, J.J.Ault-Riche, D.Kent, S.B.Sidhu, S.S.

(2016) Acs Chem.Biol. 11: 1058-1065

  • DOI: 10.1021/acschembio.5b01006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Polypeptides composed entirely of d-amino acids and the achiral amino acid glycine (d-proteins) inherently have in vivo properties that are proposed to be near-optimal for a large molecule therapeutic agent. Specifically, d-proteins are resistant to ...

    Polypeptides composed entirely of d-amino acids and the achiral amino acid glycine (d-proteins) inherently have in vivo properties that are proposed to be near-optimal for a large molecule therapeutic agent. Specifically, d-proteins are resistant to degradation by proteases and are anticipated to be nonimmunogenic. Furthermore, d-proteins are manufactured chemically and can be engineered to have other desirable properties, such as improved stability, affinity, and pharmacokinetics. Thus, a well-designed d-protein therapeutic would likely have significant advantages over l-protein drugs. Toward the goal of developing d-protein therapeutics, we previously generated RFX001.D, a d-protein antagonist of natural vascular endothelial growth factor A (VEGF-A) that inhibited binding to its receptor. However, RFX001.D is unstable at physiological temperatures (Tm = 33 °C). Here, we describe RFX037.D, a variant of RFX001.D with extreme thermal stability (Tm > 95 °C), high affinity for VEGF-A (Kd = 6 nM), and improved receptor blocking. Comparison of the two enantiomeric forms of RFX037 revealed that the d-protein is more stable in mouse, monkey, and human plasma and has a longer half-life in vivo in mice. Significantly, RFX037.D was nonimmunogenic in mice, whereas the l-enantiomer generated a strong immune response. These results confirm the potential utility of synthetic d-proteins as alternatives to therapeutic antibodies.


    Organizational Affiliation

    Banting and Best Department of Medical Research and Department of Molecular Genetics, the Donnelly Centre, University of Toronto , Toronto, Ontario, Canada M5S 3E1.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vascular endothelial growth factor A
A, B
102Homo sapiensMutation(s): 0 
Gene Names: VEGFA (VEGF)
Find proteins for P15692 (Homo sapiens)
Go to Gene View: VEGFA
Go to UniProtKB:  P15692
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
D- Vascular endothelial growth factor-A
C, D
69N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  14 Unique
IDChainsTypeFormula2D DiagramParent
DIL
Query on DIL
C, D
D-PEPTIDE LINKINGC6 H13 N O2

--

DLY
Query on DLY
C, D
D-PEPTIDE LINKINGC6 H14 N2 O2

--

DSN
Query on DSN
C, D
D-PEPTIDE LINKINGC3 H7 N O3

--

DVA
Query on DVA
C, D
D-PEPTIDE LINKINGC5 H11 N O2

--

DTH
Query on DTH
C, D
D-PEPTIDE LINKINGC4 H9 N O3

--

DLE
Query on DLE
C, D
D-PEPTIDE LINKINGC6 H13 N O2

--

DGL
Query on DGL
C, D
D-PEPTIDE LINKINGC5 H9 N O4

--

DAL
Query on DAL
C, D
D-PEPTIDE LINKINGC3 H7 N O2

--

DPN
Query on DPN
C, D
D-PEPTIDE LINKINGC9 H11 N O2

--

DAS
Query on DAS
C, D
D-PEPTIDE LINKINGC4 H7 N O4

--

DSG
Query on DSG
C, D
D-PEPTIDE LINKINGC4 H8 N2 O3

--

DTR
Query on DTR
C, D
D-PEPTIDE LINKINGC11 H12 N2 O2

--

DTY
Query on DTY
C, D
D-PEPTIDE LINKINGC9 H11 N O3

--

DAR
Query on DAR
C, D
D-PEPTIDE LINKINGC6 H15 N4 O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.261 
  • Space Group: P 1 21/n 1
Unit Cell:
Length (Å)Angle (°)
a = 55.290α = 90.00
b = 87.240β = 101.42
c = 81.344γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
SCALEPACKdata scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Center for Research ResourcesUnited StatesRR-15301

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-04-27
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Derived calculations