1FAX

COAGULATION FACTOR XA INHIBITOR COMPLEX

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 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


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

  • 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 ...

    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.

    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
    Organizational Affiliation: 

    Max-Planck-Institut für Biochemie, Strukturforschung, D-82125 Martinsried, Federal Republic of Germany. engh@biochem.mpg.de



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FACTOR XAA254Homo sapiensMutation(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
GTEx:  ENSG00000126218
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FACTOR XAB [auth L]96Homo sapiensMutation(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
GTEx:  ENSG00000126218
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DX9
Query on DX9
Download Ideal Coordinates CCD File 
 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		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
 C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DX9Ki :  41   nM  PDBBind
DX9Ki:  22   nM  BindingDB
DX9Ki:  20   nM  BindingDB
DX9Ki:  40   nM  BindingDB
DX9IC50:  130   nM  BindingDB
DX9Ki:  41   nM  BindingDB
DX9IC50:  70   nM  BindingDB
DX9IC50:  40   nM  BindingDB
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 = 56.93α = 90
b = 73.17β = 90
c = 79.08γ = 90
Software Package:
Software NamePurpose
SAINTdata scaling
X-PLORmodel building
X-PLORrefinement
SAINTdata reduction
X-PLORphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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