1YPJ

Thrombin Inhibitor Complex

Structural Biology Knowledgebase: 1YPJ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.195

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1YPJ

Classification: BLOOD CLOTTING / HYDROLASE INHIBITOR

Total Structure Weight: 34594.89

Macromolecule Entities
Molecule Chains Length Organism Details
Thrombin light chain L 27 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Thrombin heavy chain H 257 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Hirudin I 10 Hirudo medicinalis Fragment: residues 1-10
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
UIB
Query on UIB

H (1R,3AS,4R,8AS,8BR)-4-{5-(PHENYL[1,3]DIOXOL- 5-YLMETHYL)-4-ETHYL-2,3,3-TRIMETHYL-6-OXO- OCTAHYDRO-PYRROLO[3,4-C]PYRROL-1-YL}-BENZAMIDINE
C26 H32 N4 O3
HQVPEQYGMUJQHM-MSYGRNIXSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
UIB N/A in BindingDB
Ki: 95 nM  BindingMOAD
Ki: 95 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: 1.78 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.195
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 70.52 α = 90.00
b = 71.81 β = 99.87
c = 71.31 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-01-31
  • Released Date: 2006-01-17
  • Deposition author(s): Fokkens, J., Obst-Sander, U., Heine, A., Diederich, F., Klebe, G.

Revision History

  • 2013-11-13
    Type: Other | Details: corrected residue number
  • 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: 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