Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1BC 

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

Macromolecule Content

• Total Structure Weight: 35.62 kDa 
• Atom Count: 2608 
• Residue Count: 295 
• 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
• 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: 10.1016/j.bmcl.2006.01.046
• Structures With Same Primary Citation


• 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

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 UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS  P00734 GTEx  ENSG00000180210

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

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 UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS  P00734 GTEx  ENSG00000180210

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
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		--

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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
N12	IC50:  47.29999923706055   nM  BindingDB
N12	IC50:  47.29999923706055   nM  Binding MOAD
N12	IC50 :  47.29999923706055   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 = 71.24	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

• 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
  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