Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.86 kDa 
• Atom Count: 2493 
• Residue Count: 289 
• Unique protein chains: 3

2FEQ

orally active thrombin inhibitors

• DOI: 10.2210/pdb2FEQ/pdb

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


• Deposited: 2005-12-16 Released: 2006-08-08 
• Deposition Author(s): Mack, H., Baucke, D., Hornberger, W., Lange, U.E.W., Hoeffken, H.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 0.242 
• R-Value Work: 0.185 
• R-Value Observed: 0.185 

Literature

Orally active thrombin inhibitors. Part 1: optimization of the P1-moiety

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

(2006) Bioorg Med Chem Lett 16: 2641-2647

• PubMed: 16517159 
• DOI: 10.1016/j.bmcl.2006.02.040
• Primary Citation of Related Structures:  
  2FES, 2FEQ


• PubMed Abstract: 
  

The synthesis and SAR of novel nanomolar thrombin inhibitors with the common backbone HOOC-CH(2)-d-cyclohexylalanyl-3,4-dehydroprolyl-NH-CH(2)-aryl-C(=NH)NH(2) are described together with their ecarin clotting time (ECT) prolongation as measure for thrombin inhibition ex vivo. The aryl P1-moiety mimicking the arginine part of the d-Phe-Pro-Arg derived thrombin inhibitors turned out to be a key component for in vitro potency and in vivo activity. Optimization of this part led to compounds with improved antithrombin activity in rats and dogs after oral administration compared to the recently launched anticoagulant melagatran.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin light chain	L	36	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
Thrombin heavy chain	H	259	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
Decapeptide Hirudin Analogue	D	11	Hirudo medicinalis	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
34P	H	N-(CARBOXYMETHYL)-3-CYCLOHEXYL-D-ALANYL-N-({4-[(E)-AMINO(IMINO)METHYL]-1,3-THIAZOL-2-YL}METHYL)-L-PROLINAMIDE C21 H32 N6 O4 S MIEXIWNUQBMNML-ZBFHGGJFSA-N

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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
34P	IC50 :  1.3899999856948853   nM  PDBBind
34P	IC50:  1.399999976158142   nM  Binding MOAD

Biologically Interesting Molecules (External Reference) 2 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000612 (34P)	H	N-(carboxymethyl)-3-cyclohexyl-D-alanyl-N-({4-[(E)-amino(imino)methyl]-1,3-thiazol-2-yl}methyl)-L-prolinamide	Peptide-like /  Thrombin inhibitor		--

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000480	D	HIRUDIN ANALOGUE	Oligopeptide /  Anticoagulant, Antithrombotic		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 0.242 
• R-Value Work: 0.185 
• R-Value Observed: 0.185 
• 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
SAINT	data scaling
X-GEN	data reduction
CNX	refinement
SAINT	data reduction
X-GEN	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-12-16 
• Released Date: 2006-08-08 
Deposition Author(s): Mack, H., Baucke, D., Hornberger, W., Lange, U.E.W., Hoeffken, H.W.

Revision History 

• Version 1.0: 2006-08-08
  Type: Initial release
  
• Version 1.1: 2008-05-01
  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: 2017-10-18
  Changes: Refinement description
• Version 1.5: 2018-04-04
  Changes: Data collection