Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.95 kDa 
• Atom Count: 2663 
• Residue Count: 288 
• Unique protein chains: 3

1SB1

Novel Non-Covalent Thrombin Inhibitors Incorporating P1 4,5,6,7-Tetrahydrobenzothiazole Arginine Side Chain Mimetics

• DOI: 10.2210/pdb1SB1/pdb

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


• Deposited: 2004-02-09 Released: 2004-06-08 
• Deposition Author(s): Marinko, P., Krbavcic, A., Mlinsek, G., Solmajer, T., Trampus-Bakija, A., Stegnar, M., Stojan, J., Kikelj, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.224 
• R-Value Work: 0.200 

Literature

Novel non-covalent thrombin inhibitors incorporating P(1) 4,5,6,7-tetrahydrobenzothiazole arginine side chain mimetics

Marinko, P., Krbavcic, A., Mlinsek, G., Solmajer, T., Trampus-Bakija, A., Stegnar, M., Stojan, J., Kikelj, D.

(2004) Eur J Med Chem 39: 257-265

• PubMed: 15051174 
• DOI: 10.1016/j.ejmech.2003.12.006
• Primary Citation of Related Structures:  
  1SB1


• PubMed Abstract: 
  

The design, synthesis and biological activity of a series of novel non-covalent D-Phe-Pro-Arg motif-based thrombin inhibitors incorporating 4,5,6,7-tetrahydrobenzothiazol-2-amine as a novel arginine surrogate are described. Compound 9, the most potent in the series of thrombin inhibitors, exhibited an in vitro K(i) of 128 nM and 342-fold selectivity against trypsin. The binding mode of this novel class of thrombin inhibitors in the enzyme active site, based on the X-ray crystal structure of compound 9 co-crystallized with human alpha-thrombin, is discussed.

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Organizational Affiliation: 

Faculty of Pharmacy, University of Ljubljana, Askerceva 7, 1000 Ljubljana, Slovenia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	L	29	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	H	258	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
hirugen	I	9	N/A	Mutation(s): 0
Find proteins for P28504 (Hirudo medicinalis) Explore P28504  Go to UniProtKB:  P28504

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
165	H	N-(BENZYLSULFONYL)-3-CYCLOHEXYLALANYL-N-(2-AMINO-1,3-BENZOTHIAZOL-6-YL)PROLINAMIDE C28 H35 N5 O4 S2 HDSAIJKTEVRQHF-RPWUZVMVSA-N
NA	H	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS	I	L-PEPTIDE LINKING	C9 H11 N O6 S		TYR

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
165	Ki:  128   nM  Binding MOAD
165	Ki :  128   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.224 
• R-Value Work: 0.200 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.963	α = 90
b = 71.495	β = 100.15
c = 72.186	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-02-09 
• Released Date: 2004-06-08 
Deposition Author(s): Marinko, P., Krbavcic, A., Mlinsek, G., Solmajer, T., Trampus-Bakija, A., Stegnar, M., Stojan, J., Kikelj, D.

Revision History 

• Version 1.0: 2004-06-08
  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: 2011-11-16
  Changes: Atomic model