1FQ4

CRYSTAL STRUCTURE OF A COMPLEX BETWEEN HYDROXYETHYLENE INHIBITOR CP-108,420 AND YEAST ASPARTIC PROTEINASE A

Structural Biology Knowledgebase: 1FQ4 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Observed: 0.170

Literature

Macromolecules
Sequence Display for 1FQ4

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 37547.80

Macromolecule Entities
Molecule Chains Length Organism Details
SACCHAROPEPSIN A 329 Saccharomyces cerevisiae EC#: 3.4.23.25 IUBMB
Mutation: L315I
Gene Name(s): PEP4 PHO9 PRA1 YPL154C P2585
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
2Y2
Query on 2Y2

A N-[(2R)-1-{[(2S,3R,5R)-1-cyclohexyl-3-hydroxy- 5-{[2-(morpholin-4-yl)ethyl]carbamoyl}oct- 7-yn-2-yl]amino}-3-(methylsulfanyl)-1-oxopropan- 2-yl]-1H-benzimidazole-2-carboxamide
420, (Synonym)
C33 H48 N6 O5 S
MDCNERSXJOKFTF-ZLPBPMGLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NDG
Query on NDG

A 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BGC
Query on BGC

A BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000563
Query on PRD_000563
A CP-108,420 Peptide-like /
Enzyme Inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Observed: 0.170
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 86.91 α = 90.00
b = 86.91 β = 90.00
c = 110.22 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-09-03
  • Released Date: 2000-09-20
  • Deposition author(s): Cronin, N.B., Badasso, M.O., Tickle, I.J., Dreyer, T., Hoover, D.J., Rosati, R.L., Humblet, C.C., Lunney, E.A., Cooper, J.B.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4