1HVY

Human thymidylate synthase complexed with dUMP and Raltitrexed, an antifolate drug, is in the closed conformation

Structural Biology Knowledgebase: 1HVY SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.201

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1HVY

Classification: TRANSFERASE

Total Structure Weight: 135828.00

Macromolecule Entities
Molecule Chains Length Organism Details
THYMIDYLATE SYNTHASE A, B, C, D 288 Homo sapiens EC#: 2.1.1.45 IUBMB
Fragment: RESIDUES 26-313
Mutation: C43X
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
BME
Query on BME

A, B, C, D BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
D16
Query on D16

A, B, C, D TOMUDEX
ZD1694; Raltitrexed (Synonym)
C21 H22 N4 O6 S
IVTVGDXNLFLDRM-HNNXBMFYSA-N
Ligand Explorer
 
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
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
D16 IC50: 260 - 10000 nM (92 - 100) BindingDB
Ki: 418 nM (93) BindingDB

N/A in BindingMoad
IC50: 290 nM  PDBbind
UMP Ki: 3000 - 6500 nM (93 - 100) BindingDB

N/A in BindingMoad

Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CME
Query on CME
A, B, C, D L-PEPTIDE LINKING C5 H11 N O3 S2 CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.201
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 68.85 α = 70.23
b = 70.50 β = 83.29
c = 74.53 γ = 73.28

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-01-08
  • Released Date: 2001-01-31
  • Deposition author(s): Phan, J., Koli, S., Minor, W., Dunlap, R.B., Berger, S.H., Lebioda, L.

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