Biological Assembly 1  

 3D View: Structure | 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 PISA (software)

Macromolecule Content

• Total Structure Weight: 35615.66 
• Atom Count: 2434 
• Residue Count: 304 
• Unique protein chains: 3

2ANK

orally active thrombin inhibitors in complex with thrombin and an exosite decapeptide

• DOI: 10.2210/pdb2ANK/pdb

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


• Deposited: 2005-08-11 Released: 2006-11-14 
• Deposition Author(s): Lange, U.E.W., Baucke, D., Hornberger, W., Mack, H., Seitz, W., Hoeffken, H.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 0.211 
• R-Value Work: 0.172 

Literature

Orally active thrombin inhibitors. Part 2: optimization of the P2-moiety

Lange, U.E.W., Baucke, D., Hornberger, W., Mack, H., Seitz, W., Hoeffken, H.W.

(2006) BIOORG.MED.CHEM.LETT. 16: 2648-2653

• PubMed: 16460939 
• DOI: 10.1016/j.bmcl.2006.01.046
• Primary Citation of Related Structures:  
  2A2X, 2ANM


• PubMed Abstract: 
  

Synthesis and SAR of orally active thrombin inhibitors of the d-Phe-Pro-Arg type with focus on the P2-moiety are described. The unexpected increase in in vitro potency, oral bioavailability, and in vivo activity of inhibitors with dehydroproline as P2-isostere is discussed. Over a period of 24h the antithrombin activity of the most active inhibitors with IC(50)s in the nanomolar range was determined in dogs demonstrating high thrombin inhibitory activity in plasma and an appropriate duration of action after oral administration.

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Organizational Affiliation: 

Abbott GmbH & Co. KG, D-67061 Ludwigshafen, Germany. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Thrombin heavy chain	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
Thrombin light chain	L	34	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: 3
Molecule	Chains	Sequence Length	Organism	Details
synthetic peptide	P	11	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
N12	H	N-[(1R)-2-[(1-{[({6-[AMINO(IMINO)METHYL]PYRIDIN-3-YL}METHYL)AMINO]CARBONYL}CYCLOPENTYL)AMINO]-1-(CYCLOHEXYLMETHYL)-2-OXOETHYL]GLYCINE C24 H36 N6 O4 OYDOPLZDDBTLCK-LJQANCHMSA-N

Biologically Interesting Molecules 1 Unique
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000480	P	HIRUDIN ANALOGUE	Oligopeptide / Anticoagulant, Antithrombotic		--

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
N12	IC50: 47.3 nM BINDINGMOAD
N12	IC50: 47.3 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 0.211 
• R-Value Work: 0.172 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 71.240	α = 90.00
b = 72.390	β = 101.01
c = 73.060	γ = 90.00

Software Package:

Software Name	Purpose
X-GEN	data scaling
CNX	phasing
X-GEN	data reduction
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-08-11 
• Released Date: 2006-11-14 
• Deposition Author(s): Lange, U.E.W., Baucke, D., Hornberger, W., Mack, H., Seitz, W., Hoeffken, H.W.

Revision History 

• Version 1.0: 2006-11-14
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2012-12-12
  Type: Other
• Version 1.4: 2017-10-11
  Type: Refinement description
• Version 1.5: 2018-04-04
  Type: Data collection