2CF8

Complex of recombinant human thrombin with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.199
  • R-Value Work: 0.180

Literature

Macromolecules
Sequence Display for 2CF8

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 34808.29

Macromolecule Entities
Molecule Chains Length Organism Details
THROMBIN HEAVY CHAIN H 257 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: CATALYTIC, RESIDUES 364-620
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
HIRUDIN IIIA I 11 Hirudo medicinalis Fragment: C-TERMINUS, RESIDUES 55-65
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
THROMBIN LIGHT CHAIN L 28 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: LIGHT CHAIN, RESIDUES 334-361
Gene Name(s): F2 Gene View

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

H 4- [(1R,3AS,4R,8AS,8BR)- 2- (4-CHLOROBENZYL)- 1- ISOPROPYL- 3- OXODECAHYDROPYRROLO[3,4- A]PYRROLIZIN- 4- YL]BENZENECARBOXIMIDAMIDE
C26 H31 Cl N4 O
LVAIBFBNGXNDPW-NLPWIYRPSA-N
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 %)
ESH N/A in BindingDB
Ki: 8 nM  BindingMOAD
Ki: 8 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: 1.3 Å
  • R-Value Free: 0.199
  • R-Value Work: 0.180
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 71.07 α = 90.00
b = 71.51 β = 100.25
c = 72.40 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-02-17
  • Released Date: 2006-06-14
  • Deposition author(s): Schweizer, E., Hoffmann-Roeder, A., Olsen, J.A., Obst-Sander, U., Wagner, B., Kansy, M., Banner, D.W., Diederich, F.

Revision History

  • Version 1_0: 2006-06-14

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance

  • Version 1_2: 2012-12-12

    Type: Other

  • Version 1_3: 2013-08-07

    Type: Derived calculations, Other

  • Version 1_4: 2013-10-23

    Type: Other

  • Version 1_5: 2017-03-29

    Type: Structure summary