Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 35910.88 
• Atom Count: 2367 
• Residue Count: 307 
• Unique protein chains: 3

1W7G

Alpha-thrombin complex with sulfated hirudin (residues 54-65) and L- Arginine template inhibitor CS107

• DOI: 10.2210/pdb1W7G/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Hirudo medicinalis, Homo sapiens


• Deposited: 2004-09-02 Released: 2006-05-24 
• Deposition Author(s): Remiche, J., Sauvage, E., Herman, R., Charlier, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.272 
• R-Value Work: 0.243 

Literature

Design, Synthesis and Evaluation of Graftable Thrombin Inhibitors for the Preparation of Blood-Compatible Polymer Materials.

Salvagnini, C., Michaux, C., Remiche, J., Wouters, J., Charlier, P., Marchand-Brynaert, J.

(2005) Org.Biomol.Chem. 3: 4209

• PubMed: 16294249 
• DOI: 10.1039/b510239a


• PubMed Abstract: 
  

Piperazinyl-amide derivatives of N-alpha-(3-trifluoromethyl-benzenesulfonyl)-L-arginine (1) were synthesized as graftable thrombin inhibitors. The possible disturbance of biological activity due to a variable spacer-arm fixed on the N-4 piperazinyl position was evaluated in vitro, against human alpha-thrombin, and in blood coagulation assay. Molecular modelling (in silico analysis) and X-ray diffraction studies of thrombin-inhibitor complexes were also performed. The fixation of bioactive molecules on poly(butylene terephthalate) (PBT) and poly(ethylene terephthalate) (PET) membranes was performed by wet chemistry treatment and evaluated by XPS analysis. Surface grafting of inhibitor 1d improved the membrane hemocompatibility by reducing blood clot formation on the modified surface.

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Related Citations: 

• Crystallographic Analysis at 3.0-A Resolution of the Binding to Human Thrombin of Four Active Site-Directed Inhibitors
  Banner, D.W.,Hadvary, P.
  (1991) J.Biol.Chem. 30: 20085




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Organizational Affiliation: 

Unité de Chimie Organique et Médicinale, Université catholique de Louvain, Bâtiment Lavoisier, place Louis Pasteur 1, B-1348, Louvain-la-Neuve, Belgium.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
THROMBIN	H	259	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Go to Gene View: F2 Go to UniProtKB:  P00734

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
HIRUDIN I	I	12	Hirudo medicinalis	Mutation(s): 0
Find proteins for P09945 (Hirudo medicinalis) Go to UniProtKB:  P09945

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
THROMBIN	L	36	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Go to Gene View: F2 Go to UniProtKB:  P00734

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MIU	H	N-{(1S)-1-{[4-(3-AMINOPROPYL)PIPERAZIN-1-YL]CARBONYL}-4-[(DIAMINOMETHYLENE)AMINO]BUTYL}-3-(TRIFLUOROMETHYL)BENZENESULFONAMIDE L-ARGININE TEMPLATE INHIBITOR CS107 C20 H32 F3 N7 O3 S KGJKWHCPJPBEJP-KRWDZBQOSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
MIU	Ki: ~13000 nM BINDINGMOAD
MIU	Ki: 8000 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.272 
• R-Value Work: 0.243 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 70.510	α = 90.00
b = 71.343	β = 100.59
c = 72.555	γ = 90.00

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
SCALA	data scaling
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-09-02 
• Released Date: 2006-05-24 
• Deposition Author(s): Remiche, J., Sauvage, E., Herman, R., Charlier, P.

Revision History 

• Version 1.0: 2006-05-24
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.2: 2019-01-30
  Type: Data collection, Experimental preparation