2ANK

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

• PDB DOI:  https://doi.org/10.2210/pdb2ANK/pdb

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


• 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: https://doi.org/10.1016/j.bmcl.2006.01.046
• Primary Citation of Related Structures:  
  2A2X, 2ANK, 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]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 35.62 kDa 
• Atom Count: 2,608 
• Modelled Residue Count: 295 
• Deposited Residue Count: 304 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin heavy chain	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin light chain	B [auth L]	34	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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
synthetic peptide	C [auth P]	11	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
N12	D [auth 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

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALC	C [auth P]	L-PEPTIDE LINKING	C9 H17 N O2		ALA
HYP	C [auth P]	L-PEPTIDE LINKING	C5 H9 N O3		PRO
SMF	C [auth P]	L-PEPTIDE LINKING	C10 H13 N O5 S		PHE

Binding Affinity Annotations
ID	Source	Binding Affinity
N12	BindingDB:  2ANK	IC50: 47.3 (nM) from 1 assay(s)
	PDBBind:  2ANK	IC50: 47.3 (nM) from 1 assay(s)
	Binding MOAD:  2ANK	IC50: 47.3 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000480	C [auth P]	HIRUDIN ANALOGUE	Oligopeptide / Anticoagulant, Antithrombotic		Ligand Interaction

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 = 71.24	α = 90
b = 72.39	β = 101.01
c = 73.06	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  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: 2012-12-12
  Changes: Other
• Version 1.4: 2017-10-11
  Changes: Refinement description
• Version 1.5: 2018-04-04
  Changes: Data collection
• Version 1.6: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description