1GHV

A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE

Structural Biology Knowledgebase: 1GHV SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.188

Literature

Macromolecules
Sequence Display for 1GHV

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 35459.63

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 257 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
120
Query on 120

H 2-(2-OXO-1,2-DIHYDRO-PYRIDIN-3-YL)-1H-BENZOIMIDAZOLE- 5-CARBOXAMIDINE
C13 H12 N5 O
PUOKYJMONGPAIM-UHFFFAOYSA-O
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 %)
120 Ki: 45000 nM (100) BindingDB

Ki: 45000 nM  BindingMOAD
Ki: 45000 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: 1.85 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.188
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 71.62 α = 90.00
b = 72.07 β = 101.14
c = 73.20 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-01-22
  • Released Date: 2002-01-22
  • Deposition author(s): Katz, B.A., Elrod, K., Luong, C., Rice, M., Mackman, R.L., Sprengeler, P.A., Spencer, J., Hatayte, J., Janc, J., Link, J., Litvak, J., Rai, R., Rice, K., Sideris, S., Verner, E., Young, W.

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
  • 2011-11-16
    Type: Atom occupancy | Details: Atom occupancy
  • 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
  • 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