Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.62 kDa 
• Atom Count: 2560 
• Residue Count: 287 
• Unique protein chains: 4

1BHX

X-RAY STRUCTURE OF THE COMPLEX OF HUMAN ALPHA THROMBIN WITH THE INHIBITOR SDZ 229-357

• DOI: 10.2210/pdb1BHX/pdb

• Classification: SERINE PROTEASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1998-06-10 Released: 1998-11-04 
• Deposition Author(s): Kallen, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.232 
• R-Value Work: 0.187 
• R-Value Observed: 0.187 

Literature

Rational design, synthesis, and X-ray structure of selective noncovalent thrombin inhibitors.

Wagner, J., Kallen, J., Ehrhardt, C., Evenou, J.P., Wagner, D.

(1998) J Med Chem 41: 3664-3674

• PubMed: 9733491 
• DOI: 10.1021/jm981013e
• Primary Citation of Related Structures:  
  1BHX


• PubMed Abstract: 
  

We have designed, synthesized, and tested in vitro a novel class of noncovalent thrombin inhibitors. The main feature of these inhibitors is a 6,5-fused bicyclic core structure that fills the S2 pocket of the active site of thrombin. The bicycle introduces conformational constraint into the ligand and locks the Xaa-Pro amide bond into the desired trans configuration. Among the known ring systems, we selected by molecular modeling the 7-thiaindolizidinones (BTD) as our basic template. The influence of several structural features was analyzed: the length of the argininal side chain, the stereochemistry at C6, and the importance of making optimal use of the S3 pocket. Finally, an X-ray crystal structure of inhibitor 15 bound to thrombin was obtained at a resolution of 2.3 A. These designed thrombin inhibitors, which were prepared by an efficient synthesis, showed high selectivity over trypsin and other serine proteases. Further derivation based on the information obtained by X-ray crystallography should certainly allow to improve the potency.

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Organizational Affiliation: 

Novartis Pharma AG, CH-4002 Basel, Switzerland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA THROMBIN	A	30	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
ALPHA THROMBIN	B	147	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
ALPHA THROMBIN	F	105	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA THROMBIN	E	5	Homo sapiens	Mutation(s): 0  EC: 3.4.21.5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R56	F	5-OXO-6-PHENYLMETHANESULFONYLAMINO-HEXAHYDRO-THIAZOLO[3,2-A]PYRIDINE-3-CARBOXYLIC ACID (3-GUANIDINO-PROPYL)-AMIDE C19 H28 N6 O4 S2 SOIIHESTBYNJRH-PMPSAXMXSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
R56	Ki:  145   nM  Binding MOAD
R56	Ki :  145   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.232 
• R-Value Work: 0.187 
• R-Value Observed: 0.187 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71	α = 90
b = 72.2	β = 100.7
c = 73.1	γ = 90

Software Package:

Software Name	Purpose
MADNES	data collection
PROCOR	data reduction
Agrovata	data reduction
X-PLOR	model building
X-PLOR	refinement
MADNES	data reduction
PROCOR	data scaling
Agrovata	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-06-10 
• Released Date: 1998-11-04 
Deposition Author(s): Kallen, J.

Revision History 

• Version 1.0: 1998-11-04
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2018-04-18
  Changes: Data collection, Other, Refinement description