4H5E

Crystal structure of human FPPS in ternary complex with YS0470 and isopentenyl pyrophosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.186

Literature

Macromolecules
Sequence Display for 4H5E

Classification: TRANSFERASE / TRANSFERASE INHIBITOR

Total Structure Weight: 43868.28

Macromolecule Entities
Molecule Chains Length Organism Details
Farnesyl pyrophosphate synthase F 375 Homo sapiens EC#: 2.5.1.10 IUBMB
Fragment: UNP residues 67-419
Gene Name(s): FDPS Gene View FPS KIAA1293
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
YS4
Query on YS4

F [({4-[4-(propan-2-yloxy)phenyl]pyridin-2- yl}amino)methanediyl]bis(phosphonic acid)
C15 H20 N2 O7 P2
DTXBFSJBRGLOHO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IPR
Query on IPR

F ISOPENTYL PYROPHOSPHATE
C5 H14 O7 P2
IPFXNYPSBSIFOB-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

F MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
YS4 IC50: 28 - 1390 nM (99) BindingDB

Kd: 860 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.186
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 111.24 α = 90.00
b = 111.24 β = 90.00
c = 65.64 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-18
  • Released Date: 2012-12-26
  • Deposition author(s): Park, J., Lin, Y.-S., Tsantrizos, Y.S., Berghuis, A.M.

Revision History

  • Version 1_0: 2012-12-26

    Type: Initial release