Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 35.91 kDa 
• Atom Count: 2554 
• Modelled Residue Count: 289 
• Deposited Residue Count: 307 
• Unique protein chains: 3

1W7G

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

• PDB DOI: 10.2210/pdb1W7G/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens, Hirudo medicinalis
• Mutation(s): No 


• 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 
• R-Value Observed: 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
• Primary Citation of Related Structures:  
  1W7G


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THROMBIN	A [auth H]	259	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIRUDIN I	B [auth I]	12	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P09945 (Hirudo medicinalis) Explore P09945  Go to UniProtKB:  P09945

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
THROMBIN	C [auth L]	36	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734 GTEx:  ENSG00000180210

Small Molecules

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

Binding Affinity Annotations
ID	Source	Binding Affinity
MIU	PDBBind:  1W7G	Ki: 8000 (nM) from 1 assay(s)
	BindingDB:  1W7G	Ki: 1900 (nM) from 1 assay(s)
	Binding MOAD:  1W7G	Ki: 1.30e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

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

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.51	α = 90
b = 71.343	β = 100.59
c = 72.555	γ = 90

Software Package:

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

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
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.2: 2019-01-30
  Changes: Data collection, Experimental preparation