1GJ5

SELECTIVITY AT S1, H2O DISPLACEMENT, UPA, TPA, SER190/ALA190 PROTEASE, STRUCTURE-BASED DRUG DESIGN

Structural Biology Knowledgebase: 1GJ5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.193

Literature

Macromolecules
Sequence Display for 1GJ5

Classification: BLOOD CLOTTING HYDROLASE / INHIBITOR

Total Structure Weight: 35590.78

Macromolecule Entities
Molecule Chains Length Organism Details
THROMBIN L 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: LIGHT CHAIN, RESIDUES 328-363
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
THROMBIN H 258 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: HEAVY CHAIN, RESIDUES 364-620
Gene Name(s): F2 Gene View
ACETYL HIRUDIN I 11 Hirudo medicinalis Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
130
Query on 130

H 2-(2-HYDROXY-BIPHENYL)-1H-BENZOIMIDAZOLE- 5-CARBOXAMIDINE
C20 H16 N4 O
LMGQGPVCSYOMNS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

H SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
130 N/A in BindingDB
N/A in BindingMoad
Ki: 11000 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
TYS
Query on TYS
I L-PEPTIDE LINKING C9 H11 N O6 S TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.193
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 71.33 α = 90.00
b = 71.96 β = 101.05
c = 72.96 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-04-27
  • Released Date: 2002-04-27
  • Deposition author(s): Katz, B.A., Sprengeler, P.A., Luong, C., Verner, E., Spencer, J.R., Breitenbucher, J.G., Hui, H., McGee, D., Allen, D., Martelli, A., Mackman, R.L.

Revision History

  • 2013-03-13
    Type: Other | Details: Remove PRD info on PRD molecule with WAIT status
  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-13
    Type: Atom occupancy | Details: Restore author's atom occupancy
  • 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
  • 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