5B4W

Crystal structure of Plexin inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Allosteric Inhibition of a Semaphorin 4D Receptor Plexin B1 by a High-Affinity Macrocyclic Peptide

Matsunaga, Y.Bashiruddin, N.K.Kitago, Y.Takagi, J.Suga, H.

(2016) Cell Chem Biol 23: 1341-1350

  • DOI: 10.1016/j.chembiol.2016.09.015

  • PubMed Abstract: 
  • Semaphorin axonal guidance factors are multifunctional proteins that play important roles in immune response, cancer cell proliferation, and organogenesis, making semaphorins and their signaling receptor plexins important drug targets for various dis ...

    Semaphorin axonal guidance factors are multifunctional proteins that play important roles in immune response, cancer cell proliferation, and organogenesis, making semaphorins and their signaling receptor plexins important drug targets for various diseases. However, the large and flat binding surface of the semaphorin-plexin interaction interface is difficult to target by traditional small-molecule drugs. Here, we report the discovery of a high-affinity plexin B1 (PlxnB1)-binding macrocyclic peptide, PB1m6 (KD = 3.5 nM). PB1m6 specifically inhibited the binding of physiological ligand semaphorin 4D (Sema4D) in vitro and completely suppressed Sema4D-induced cell collapse. Structural studies revealed that PB1m6 binds at a groove between the fifth and sixth blades of the sema domain in PlxnB1 distant from the Sema4D-binding site, indicating the non-competitive and allosteric nature of the inhibitory activity. The discovery of this novel allosteric site can potentially be used to target plexin family proteins for the development of drugs that modulate semaphorin and plexin signaling.


    Organizational Affiliation

    Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Plexin-B1
A, B, C, D, E, F
579Homo sapiensMutation(s): 0 
Gene Names: PLXNB1 (KIAA0407, PLXN5, SEP)
Find proteins for O43157 (Homo sapiens)
Go to Gene View: PLXNB1
Go to UniProtKB:  O43157
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Synthesized cyclic peptide
G, H, I, J, K, L
18N/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
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D, E, F
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
G, H, I, J, K, L
NON-POLYMERH2 N

--

DTR
Query on DTR
G, H, I, J, K, L
D-PEPTIDE LINKINGC11 H12 N2 O2

--

ACE
Query on ACE
G, H, I, J, K, L
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.225 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 92.426α = 90.00
b = 217.924β = 115.30
c = 106.475γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PHASERphasing
DENZOdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
AMEDJapan--

Revision History 

  • Version 1.0: 2016-12-28
    Type: Initial release