6GKO

Mouse thymidylate synthase cocrystallized with dUMP and soaked in phenolphthalein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

Starting Model: experimental
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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

Thymidylate synthase fragment screening

Maj, P.Wilk, P.Jarmula, A.Weiss, M.S.Rode, W.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thymidylate synthase
A, B
307Mus musculusMutation(s): 0 
Gene Names: Tyms
EC: 2.1.1.45
UniProt
Find proteins for P07607 (Mus musculus)
Explore P07607 
Go to UniProtKB:  P07607
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07607
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FGT
Query on FGT

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
3,3-bis(4-hydroxyphenyl)-2-benzofuran-1-one
C20 H14 O4
KJFMBFZCATUALV-UHFFFAOYSA-N
UMP
Query on UMP

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
FGT BindingDB:  6GKO Ki: 1200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.701α = 90
b = 87.441β = 96.02
c = 68.515γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description