6YX1

Crystal structure of SHANK1 PDZ in complex with a peptide-small molecule hybrid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Identification of Beta-strand mediated protein-protein interaction inhibitors using ligand-directed fragment ligation

Hegedus, Z.Hobor, F.Shoemark, D.K.Celis, S.Lian, L.J.Trinh, C.H.Sessions, R.B.Edwards, T.A.Wilson, A.J.

(2021) Chem Sci 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SH3 and multiple ankyrin repeat domains protein 1 AB112Homo sapiensMutation(s): 0 
Gene Names: SHANK1
Find proteins for Q9Y566 (Homo sapiens)
Explore Q9Y566 
Go to UniProtKB:  Q9Y566
NIH Common Fund Data Resources
PHAROS:  Q9Y566
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PWT
Query on PWT

Download Ideal Coordinates CCD File 
A, B
2-[[2-(5-oxidanylidenepentanoyl)hydrazinyl]methyl]benzoic acid
C13 H16 N2 O4
WAEOIFKXEDZIQC-UHFFFAOYSA-N
 Ligand Interaction
ARG
Query on ARG

Download Ideal Coordinates CCD File 
A, B
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
LEU
Query on LEU

Download Ideal Coordinates CCD File 
A, B
LEUCINE
C6 H13 N O2
ROHFNLRQFUQHCH-YFKPBYRVSA-N
 Ligand Interaction
THR
Query on THR

Download Ideal Coordinates CCD File 
A, B
THREONINE
C4 H9 N O3
AYFVYJQAPQTCCC-GBXIJSLDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.668α = 90
b = 65.912β = 90
c = 85.637γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
PDB_EXTRACTdata extraction
STARANISOdata scaling
autoPROCdata scaling
PHASERphasing
Cootmodel building
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Engineering and Physical Sciences Research CouncilUnited KingdomEP/N035267/1
European CommissionUnited KingdomMSCA-IF-2016-749012
Royal SocietyUnited KingdomSRF/R1/191087

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release