1OYT

COMPLEX OF RECOMBINANT HUMAN THROMBIN WITH A DESIGNED FLUORINATED INHIBITOR

Structural Biology Knowledgebase: 1OYT SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.205
  • R-Value Work: 0.179

Literature

Macromolecules
Sequence Display for 1OYT

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 35744.00

Macromolecule Entities
Molecule Chains Length Organism Details
thrombin light chain L 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
thrombin heavy chain H 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Hirudin IIB I 11 Hirudo medicinalis Mutation: D1X
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

H (3ASR,4RS,8ASR,8BRS)-4-(2-(4-FLUOROBENZYL)- 1,3-DIOXODEACAHYDROPYRROLO[3,4-A] PYRROLIZIN- 4-YL)BENZAMIDINE
C23 H24 F N4 O2
GJYCQHGTXMVIBG-MUGJNUQGSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

H CALCIUM ION
Ca
BHPQYMZQTOCNFJ-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 %)
FSN N/A in BindingDB
Ki: 57 nM  BindingMOAD
Ki: 57 nM  PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000481
Query on PRD_000481
I N-terminal Asp des-amino Hirudin-3A' Oligopeptide /
Anticoagulant, Antithrombotic
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.205
  • R-Value Work: 0.179
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 70.69 α = 90.00
b = 71.48 β = 100.53
c = 72.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-04-07
  • Released Date: 2003-06-24
  • Deposition author(s): Banner, D.W., Olsen, J.A.

Revision History

  • 2016-05-25
    Type: Source and taxonomy | Details: --
  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 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