1I00

CRYSTAL STRUCTURE OF HUMAN THYMIDYLATE SYNTHASE, TERNARY COMPLEX WITH DUMP AND TOMUDEX

Structural Biology Knowledgebase: 1I00 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.262
  • R-Value Work: 0.207

Literature

Macromolecules
Sequence Display for 1I00

Classification: TRANSFERASE

Total Structure Weight: 67911.98

Macromolecule Entities
Molecule Chains Length Organism Details
THYMIDYLATE SYNTHASE A, B 290 Homo sapiens EC#: 2.1.1.45 IUBMB
Mutation: ΔE6, ΔL7, ΔP8, ΔR9, ΔR10, ΔP11, ΔL12, ΔP13, ΔP14, ΔA15, ΔA16, ΔQ17, ΔE18, ΔR19, ΔD20, ΔA21, ΔE22, ΔP23, ΔR24, ΔP25, ΔP26, ΔH27, ΔG28
Gene Name(s): TYMS Gene View TS OK/SW-cl.29
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
D16
Query on D16

A, B TOMUDEX
ZD1694; Raltitrexed (Synonym)
C21 H22 N4 O6 S
IVTVGDXNLFLDRM-HNNXBMFYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UMP
Query on UMP

A, B 2'-DEOXYURIDINE 5'-MONOPHOSPHATE
DUMP (Synonym)
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
D16 IC50: 260 - 10000 nM (92 - 100) BindingDB
Ki: 418 nM (93) BindingDB

Kd: 460 nM  BindingMOAD
Ki: 460 nM  PDBbind
UMP Ki: 3000 - 6500 nM (93 - 100) BindingDB

N/A in BindingMoad


Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.262
  • R-Value Work: 0.207
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 89.69 α = 90.00
b = 89.69 β = 90.00
c = 142.13 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-01-27
  • Released Date: 2001-05-09
  • Deposition author(s): Almog, R.A., Waddling, C.A., Maley, F., Maley, G.F., Van Roey, P.

Revision History

  • 2012-10-10
    Type: Non-polymer description | Details: Update synonym for D16
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4