1OYT

COMPLEX OF RECOMBINANT HUMAN THROMBIN WITH A DESIGNED FLUORINATED INHIBITOR


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

A Fluorine Scan of Thrombin Inhibitors to Map the Fluorophilicity/Fluorophobicity of an Enzyme Active Site: Evidence for CF...C=O Interactions.

Olsen, J.A.Banner, D.W.Seiler, P.Obst-Sander, U.D'Arcy, A.Stihle, M.Mueller, K.Diederich, F.

(2003) Angew Chem Int Ed Engl 42: 2507-2511


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
thrombin light chain
L
36Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS  P00734
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
thrombin heavy chain
H
259Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS  P00734
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Hirudin IIB
I
11Hirudo medicinalisMutation(s): 1 
Find proteins for P28506 (Hirudo medicinalis)
Go to UniProtKB:  P28506
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FSN
Query on FSN

Download CCD File 
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 Interaction
CA
Query on CA

Download CCD File 
H
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000481
Query on PRD_000481
IN-terminal Asp des-amino Hirudin-3A'Oligopeptide /  Anticoagulant, Antithrombotic

--

External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FSNKi:  57   nM  Binding MOAD
FSNKi :  57   nM  PDBBind
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
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.693α = 90
b = 71.479β = 100.53
c = 72.802γ = 90
Software Package:
Software NamePurpose
CNXrefinement
MAR345data collection
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-24
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2016-05-25
    Changes: Source and taxonomy
  • Version 1.5: 2017-10-11
    Changes: Advisory, Refinement description