4E28

Structure of human thymidylate synthase in inactive conformation with a novel non-peptidic inhibitor

Structural Biology Knowledgebase: 4E28 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.188

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4E28

Classification: TRANSFERASE / TRANSFERASE INHIBITOR

Total Structure Weight: 38385.93

Macromolecule Entities
Molecule Chains Length Organism Details
Thymidylate synthase A 325 Homo sapiens EC#: 2.1.1.45 IUBMB
Fragment: UNP residues 26-311
Gene Name(s): TYMS Gene View TS OK/SW-cl.29

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0MZ
Query on 0MZ

A 2-{(2Z,5S)-4-hydroxy-2-[(2E)-(2-hydroxybenzylidene)hydrazinylidene]- 2,5-dihydro-1,3-thiazol-5-yl}-N-[3-(trifluoromethyl)phenyl]acetamide
C19 H15 F3 N4 O3 S
OBVIGUGYWMTZGZ-MQEPLNOPSA-N
Ligand Explorer
 
JSmol
9MZ
Query on 9MZ

A 2-{(5S)-2-[(2E)-2-(2-hydroxybenzylidene)hydrazinyl]- 4-oxo-4,5-dihydro-1,3-thiazol-5-yl}-N-[3- (trifluoromethyl)phenyl]acetamide
C19 H15 F3 N4 O3 S
OBVIGUGYWMTZGZ-MQEPLNOPSA-N
Ligand Explorer
 
JSmol
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
0MZ N/A in BindingDB
Ki: 1300 nM  BindingMOAD
Ki: 1300 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CME
Query on CME
A L-PEPTIDE LINKING C5 H11 N O3 S2 CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.188
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 95.75 α = 90.00
b = 95.75 β = 90.00
c = 82.41 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-03-07
  • Released Date: 2012-11-14
  • Deposition author(s): Tochowicz, A., Finer-Moore, J., Stroud, R.M., Costi, M.P.

Revision History

  • 2012-12-12
    Type: Citation | Details: Citation update