Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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: 39.41 kDa 
• Atom Count: 2300 
• Modelled Residue Count: 290 
• Deposited Residue Count: 350 
• Unique protein chains: 2

1FAX

COAGULATION FACTOR XA INHIBITOR COMPLEX

• PDB DOI: 10.2210/pdb1FAX/pdb

• Classification: COAGULATION FACTOR
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1996-08-23 Released: 1997-10-29 
• Deposition Author(s): Brandstetter, H., Engh, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.261 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 

Literature

X-ray structure of active site-inhibited clotting factor Xa. Implications for drug design and substrate recognition.

Brandstetter, H., Kuhne, A., Bode, W., Huber, R., von der Saal, W., Wirthensohn, K., Engh, R.A.

(1996) J Biol Chem 271: 29988-29992

• PubMed: 8939944 
• DOI: 10.1074/jbc.271.47.29988
• Primary Citation of Related Structures:  
  1FAX


• PubMed Abstract: 
  

The 3.0-A resolution x-ray structure of human des-Gla-coagulation factor Xa (fXa) has been determined in complex with the synthetic inhibitor DX-9065a. The binding geometry is characterized primarily by two interaction sites: the naphthamidine group is fixed in the S1 pocket by a typical salt bridge to Asp-189, while the pyrrolidine ring binds in the unique aryl-binding site (S4) of fXa. Unlike the large majority of inhibitor complexes with serine proteinases, Gly-216 (S3) does not contribute to hydrogen bond formation. In contrast to typical thrombin binding modes, the S2 site of fXa cannot be used by DX-9065a since it is blocked by Tyr-99, and the aryl-binding site (S4) of fXa is lined by carbonyl oxygen atoms that can accommodate positive charges. This has implications for natural substrate recognition as well as for drug design.

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Related Citations: 

• X-Ray Structure of Clotting Factor Ixa: Active Site and Module Structure Related to Xase Activity and Hemophilia B
  Brandstetter, H., Bauer, M., Huber, R., Lollar, P., Bode, W.
  (1995) Proc Natl Acad Sci U S A 92: 9796

• Structure of Human Des(1-45) Factor Xa at 2.2 A Resolution
  Padmanabhan, K., Padmanabhan, K.P., Tulinsky, A., Park, C.H., Bode, W., Huber, R., Blankenship, D.T., Cardin, A.D., Kisiel, W.
  (1993) J Mol Biol 232: 947

• A Novel Factor Xa Inhibitor: Structure-Activity Relationships and Selectivity between Factor Xa and Thrombin
  Katakura, S., Nagahara, T., Hara, T., Iwamoto, M.
  (1993) Biochem Biophys Res Commun 197: 965

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Organizational Affiliation: 

Max-Planck-Institut für Biochemie, Strukturforschung, D-82125 Martinsried, Federal Republic of Germany. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FACTOR XA	A	254	Homo sapiens	Mutation(s): 0  Gene Names: F10 EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742  Go to UniProtKB:  P00742
PHAROS:  P00742

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FACTOR XA	B [auth L]	96	Homo sapiens	Mutation(s): 0  Gene Names: F10 EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742  Go to UniProtKB:  P00742
PHAROS:  P00742

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DX9	D [auth A]	(2S)-3-(7-carbamimidoylnaphthalen-2-yl)-2-[4-({(3R)-1-[(1Z)-ethanimidoyl]pyrrolidin-3-yl}oxy)phenyl]propanoic acid C26 H28 N4 O3 AGRCGQSFFMCBRE-DGUCVARSSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DX9	BindingDB:  1FAX	Ki: min: 20, max: 41 (nM) from 4 assay(s)
		IC50: min: 40, max: 130 (nM) from 3 assay(s)
	PDBBind:  1FAX	Ki: 41 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.261 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.93	α = 90
b = 73.17	β = 90
c = 79.08	γ = 90

Software Package:

Software Name	Purpose
SAINT	data scaling
X-PLOR	model building
X-PLOR	refinement
SAINT	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1996-08-23 
• Released Date: 1997-10-29 
Deposition Author(s): Brandstetter, H., Engh, R.A.

Revision History  

• Version 1.0: 1997-10-29
  Type: Initial release
  
• Version 1.1: 2008-03-10
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance