6FMC | pdb_00006fmc

Neuropilin1-b1 domain in complex with EG01377, 0.9 Angstrom structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.90 Å
  • R-Value Free: 
    0.132 (Depositor), 0.130 (DCC) 
  • R-Value Work: 
    0.109 (Depositor), 0.110 (DCC) 
  • R-Value Observed: 
    0.110 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted DUEClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Small Molecule Neuropilin-1 Antagonists Combine Antiangiogenic and Antitumor Activity with Immune Modulation through Reduction of Transforming Growth Factor Beta (TGF beta ) Production in Regulatory T-Cells.

Powell, J.Mota, F.Steadman, D.Soudy, C.Miyauchi, J.T.Crosby, S.Jarvis, A.Reisinger, T.Winfield, N.Evans, G.Finniear, A.Yelland, T.Chou, Y.T.Chan, A.W.E.O'Leary, A.Cheng, L.Liu, D.Fotinou, C.Milagre, C.Martin, J.F.Jia, H.Frankel, P.Djordjevic, S.Tsirka, S.E.Zachary, I.C.Selwood, D.L.

(2018) J Med Chem 61: 4135-4154

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b00210
  • Primary Citation of Related Structures:  
    6FMC, 6FMF

  • PubMed Abstract: 

    We report the design, synthesis, and biological evaluation of some potent small-molecule neuropilin-1 (NRP1) antagonists. NRP1 is implicated in the immune response to tumors, particularly in Treg cell fragility, required for PD1 checkpoint blockade. The design of these compounds was based on a previously identified compound EG00229. The design of these molecules was informed and supported by X-ray crystal structures. Compound 1 (EG01377) was identified as having properties suitable for further investigation. Compound 1 was then tested in several in vitro assays and was shown to have antiangiogenic, antimigratory, and antitumor effects. Remarkably, 1 was shown to be selective for NRP1 over the closely related protein NRP2. In purified Nrp1 + , FoxP3 + , and CD25 + populations of Tregs from mice, 1 was able to block a glioma-conditioned medium-induced increase in TGFβ production. This comprehensive characterization of a small-molecule NRP1 antagonist provides the basis for future in vivo studies.


  • Organizational Affiliation

    NCE Discovery (Domainex Ltd) , Chesterford Research Park, Little Chesterford , Saffron Walden , Essex CB10 1XL , U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neuropilin-1158Homo sapiensMutation(s): 0 
Gene Names: NRP1NRPVEGF165R
UniProt & NIH Common Fund Data Resources
Find proteins for O14786 (Homo sapiens)
Explore O14786 
Go to UniProtKB:  O14786
PHAROS:  O14786
GTEx:  ENSG00000099250 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14786
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DUE
Query on DUE

Download Ideal Coordinates CCD File 
B [auth A](2~{S})-2-[[3-[[5-[4-(aminomethyl)phenyl]-1-benzofuran-7-yl]sulfonylamino]thiophen-2-yl]carbonylamino]-5-carbamimidamido-pentanoic acid
C26 H28 N6 O6 S2
PVMUKISUHFBKET-FQEVSTJZSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.90 Å
  • R-Value Free:  0.132 (Depositor), 0.130 (DCC) 
  • R-Value Work:  0.109 (Depositor), 0.110 (DCC) 
  • R-Value Observed: 0.110 (Depositor) 
Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.44α = 90
b = 43.44β = 90
c = 91.23γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted DUEClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomISMB DTG

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary