2ANM | pdb_00002anm

Ternary complex of an orally active thrombin inhibitor with human thrombin and a c-terminal hirudin derived exo-sit inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2ANM/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-08-11 Released: 2006-06-13 
• 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: 2.40 Å
• R-Value Free: 
  0.250 (Depositor) 
• R-Value Work: 
  0.194 (Depositor) 

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 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 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 34.15 kDa 
• Atom Count: 2,502 
• Modeled Residue Count: 284 
• Deposited Residue Count: 293 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
thrombin	A [auth H]	257	Homo sapiens	Mutation(s): 0  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 GTEx:  ENSG00000180210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
thrombin	B [auth L]	36	Homo sapiens	Mutation(s): 0  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 GTEx:  ENSG00000180210

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CDO	C [auth H]	2-((R)-1-((S)-2-(N-(6-CARBAMIMIDOYLPYRIDIN-3-YL)METHYLCARBAMOYL)-2H-PYRROL-1(5H)-YL)-3-CYCLOHEXYL-1-OXOPROPAN-2-YLAMINO)ACETIC ACID C23 H32 N6 O4 DSEQCUGXKCOSSU-MOPGFXCFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.250 (Depositor) 
• R-Value Work:  0.194 (Depositor) 

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: 2006-06-13 
Deposition Author(s): Lange, U.E.W., Baucke, D., Hornberger, W., Mack, H., Seitz, W., Hoeffken, H.W.

Revision History  

• Version 1.0: 2006-06-13
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary