6G5N

Crystal structure of human SP100 in complex with bromodomain-focused fragment XS039818e 1-(3-Phenyl-1,2,4-oxadiazol-5-yl)methanamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

Starting Model: other
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Identifying small molecule binding sites for epigenetic proteins at domain-domain interfaces

Talon, R.P.H.Bowkett, D.Tallant, C.Schofield, C.von Delft, F.Knapp, S.Bruton, G.Brennan, P.E.

(2018) bioRxiv 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear autoantigen Sp-100
A, B
180Homo sapiensMutation(s): 0 
Gene Names: SP100
UniProt & NIH Common Fund Data Resources
Find proteins for P23497 (Homo sapiens)
Explore P23497 
Go to UniProtKB:  P23497
PHAROS:  P23497
GTEx:  ENSG00000067066 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23497
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
E [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
ENK (Subject of Investigation/LOI)
Query on ENK

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H [auth A](3-phenyl-1,2,4-oxadiazol-5-yl)methanamine
C9 H9 N3 O
QFBMJBDECSEYCZ-UHFFFAOYSA-N
ZN
Query on ZN

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C [auth A],
D [auth A],
I [auth B],
J [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
K [auth B],
L [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
M [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.879α = 90
b = 45.426β = 102.14
c = 83.477γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary