1JU6

Human Thymidylate Synthase Complex with dUMP and LY231514, A Pyrrolo(2,3-d)pyrimidine-based Antifolate

Structural Biology Knowledgebase: 1JU6 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.236

Literature

Macromolecules
Sequence Display for 1JU6

Classification: TRANSFERASE

Total Structure Weight: 145978.02

Macromolecule Entities
Molecule Chains Length Organism Details
THYMIDYLATE SYNTHASE A, B, C, D 313 Homo sapiens EC#: 2.1.1.45 IUBMB
Mutation: R46E
Gene Name(s): TYMS Gene View TS OK/SW-cl.29
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D 2-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3- D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-PENTANEDIOIC ACID
LY231514 (Synonym)
C20 H21 N5 O6
WBXPDJSOTKVWSJ-ZDUSSCGKSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UMP
Query on UMP

A, B, C, D 2'-DEOXYURIDINE 5'-MONOPHOSPHATE
DUMP (Synonym)
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
LYA IC50: 5700 - 110000 nM (88 - 99) BindingDB
Ki: 1.3 - 340 nM (88 - 99) BindingDB

N/A in BindingMoad
N/A in PDBbind
UMP Ki: 3000 - 6500 nM (88 - 99) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.236
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 68.14 α = 71.67
b = 69.63 β = 85.72
c = 73.96 γ = 75.11

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-08-23
  • Released Date: 2001-09-19
  • Deposition author(s): Sayre, P.H., Finer-Moore, J.S., Fritz, T.A., Biermann, D., Gates, S.B., MacKellar, W.C., Patel, V.F., Stroud, R.M.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4