Biological Assembly 1  

 3D View: Structure | Electron Density | 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: 32474.95 
• Atom Count: 2263 
• Residue Count: 285 
• Unique protein chains: 2

3LIW

Factor XA in complex with (R)-2-(1-ADAMANTYLCARBAMOYLAMINO)-3-(3-CARBAMIDOYL-PHENYL)-N-PHENETHYL-PROPIONIC ACID AMIDE

• DOI: 10.2210/pdb3LIW/pdb
• Entry 3LIW supersedes 1KYE

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


• Deposited: 2010-01-25 Released: 2010-04-07 
• Deposition Author(s): Mueller, M.M., Sperl, S., Sturzebecher, J., Bode, W., Moroder, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 0.266 
• R-Value Work: 0.223 

Literature

(R)-3-Amidinophenylalanine-Derived Inhibitors of Factor Xa with a Novel Active-Site Binding Mode

Mueller, M.M., Sperl, S., Sturzebecher, J., Bode, W., Moroder, L.

(2003) Biol.Chem. 383: 1185

• PubMed: 12437104 
• DOI: 10.1515/BC.2002.130
• Primary Citation of Related Structures:  
  1KYE


• PubMed Abstract: 
  

A putative non-substrate like binding mode of (R)-3-amidinophenylalanine derivatives to factor Xa, as derived from modeling experiments based on X-ray analysis of their complexes with trypsin, was used to design a new generation of inhibitors. However, the resulting inhibitory potencies were not at all consistent with the working assumption, although with an adamantyl-ureido derivative of (R)-3-amidinophenylalanine phenetyl amide a highly selective nanomolar inhibition of factor Xa was achieved. The X-ray analysis of the complex of this ligand with factor Xa revealed an unexpected new binding mode, of which the most important feature is the interaction of the C-terminal aryl moiety with a hydrophobic subregion of the S1 subsite, while the adamantyl group occupies the hydrophobic S3/S4 subsites of the enzyme.

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Organizational Affiliation: 

Max-Planck-Institut für Biochemie, Martinsried, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Activated factor Xa heavy chain	A	234	Homo sapiens	Mutation(s): 0  Gene Names: F10 EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens) Go to Gene View: F10 Go to UniProtKB:  P00742

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Factor X light chain	B	51	Homo sapiens	Mutation(s): 0  Gene Names: F10 EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens) Go to Gene View: F10 Go to UniProtKB:  P00742

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
RUP	A	(R)-2-(3-ADAMANTAN-1-YL-UREIDO)-3-(3-CARBAMIMIDOYL-PHENYL)-N-PHENETHYL-PROPIONAMIDE C29 H37 N5 O2 QYKLXCYULDLMPX-ZEFMGYOLSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
RUP	Ki: 25 nM BINDINGMOAD
RUP	Ki: 25 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 0.266 
• R-Value Work: 0.223 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 56.480	α = 90.00
b = 72.510	β = 90.00
c = 78.330	γ = 90.00

Software Package:

Software Name	Purpose
MOSFLM	data reduction
MOLREP	phasing
CCP4	data scaling
MAR345dtb	data collection
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-01-25 
• Released Date: 2010-04-07 
• Deposition Author(s): Mueller, M.M., Sperl, S., Sturzebecher, J., Bode, W., Moroder, L.
• This entry supersedes: 1KYE

Revision History 

• Version 1.0: 2010-04-07
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance