7MS6

Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with (2-fluoro-4-((4-phenylpiperidin-1-yl)sulfonyl)benzoyl)glycine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Structure Activity Relationship of Allosteric Inhibitors of USP5

Mann, M.K.Zepeda-Velazquez, C.A.Alvarez, H.G.Dong, A.Kiyota, T.Aman, A.Arrowsmith, C.H.Al-Awar, R.Harding, R.J.Schapira, M.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 5A121Homo sapiensMutation(s): 0 
Gene Names: USP5ISOT
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for P45974 (Homo sapiens)
Explore P45974 
Go to UniProtKB:  P45974
PHAROS:  P45974
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZPV (Subject of Investigation/LOI)
Query on ZPV

Download Ideal Coordinates CCD File 
B [auth A]N-[2-fluoro-4-(4-phenylpiperidine-1-sulfonyl)benzoyl]glycine
C20 H21 F N2 O5 S
IOUTWRYTULEKGO-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 
  • Space Group: P 43
  • Diffraction Data DOI: 10.18430/m37ms6 Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.575α = 90
b = 53.575β = 90
c = 54.097γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-09
    Type: Initial release