8R5M | pdb_00008r5m

E-selectin complexed with glycomimetic ligand DS0567


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 
    0.239 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.210 (Depositor) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8R5M

Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history

Literature

Analogues of the pan-selectin antagonist rivipansel (GMI-1070).

Wagner, B.Smiesko, M.Jakob, R.P.Muhlethaler, T.Cramer, J.Maier, T.Rabbani, S.Schwardt, O.Ernst, B.

(2024) Eur J Med Chem 272: 116455-116455

  • DOI: https://doi.org/10.1016/j.ejmech.2024.116455
  • Primary Citation Related Structures: 
    8R5L, 8R5M

  • PubMed Abstract: 

    The selectin family consisting of E-, P- and L-selectin plays dominant roles in atherosclerosis, ischemia-reperfusion injury, inflammatory diseases, and metastatic spreading of some cancers. An early goal in selectin-targeted drug discovery campaigns was to identify ligands binding to all three selectins, so-called pan-selectin antagonists. The physiological epitope, tetrasaccharide sialyl Lewis x (sLe x , 1) binds to all selectins, albeit with very different affinities. Whereas P- and L-selectin require additional interactions contributed by sulfate groups for high binding affinity, E-selectin can functionally bind sLe x -modified glycolipids and glycoproteins. Rivipansel (3) marked the first pan-selectin antagonist, which simultaneously interacted with both the sLe x and the sulfate binding site. The aim of this contribution was to improve the pan-selectin affinity of rivipansel (3) by leveraging a new class of sLe x mimetics in combination with an optimized linker length to the sulfate bearing group. As a result, the pan-selectin antagonist 11b exhibits an approximatively 5-fold improved affinity for E-, as well as P-selectin.


  • Organizational Affiliation
    • University of Basel, Department of Pharmaceutical Sciences, Group Molecular Pharmacy, Klingelbergstrasse 50, 4056, Basel, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 33.65 kDa 
  • Atom Count: 2,394 
  • Modeled Residue Count: 280 
  • Deposited Residue Count: 280 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
E-selectin280Homo sapiensMutation(s): 0 
Gene Names: SELEELAM1
UniProt & NIH Common Fund Data Resources
Find proteins for P16581 (Homo sapiens)
Explore P16581 
Go to UniProtKB:  P16581
PHAROS:  P16581
GTEx:  ENSG00000007908 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16581
Glycosylation
Glycosylation Sites: 7Go to GlyGen: P16581-1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y6O
(Subject of Investigation/LOI)

Query on Y6O



Download:Ideal Coordinates CCD File
I [auth A](2~{S})-3-cyclohexyl-2-[(2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(1~{R},2~{R},3~{S})-3-ethyl-2-[(2~{S},3~{S},4~{R},5~{S},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-cyclohexyl]oxy-6-(hydroxymethyl)-5-oxidanyl-3-(phenylcarbonyloxy)oxan-4-yl]oxy-propanoic acid
C36 H54 O14
OLOMFBSAQARLKG-UFBMZIPWSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
J [auth A],
K [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free:  0.239 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.210 (Depositor) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.45α = 90
b = 73.22β = 94.38
c = 52.24γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-23
    Type: Initial release