1FAX

COAGULATION FACTOR XA INHIBITOR COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.261 
  • R-Value Work: 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

  • Also Cited By: 1QB9, 1QBO, 1V3X, 1WU1

  • 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 ...

    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: 
    • 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
    • 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.USA 92: 9796


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FACTOR XA
A
254Homo sapiensGene 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
MoleculeChainsSequence LengthOrganismDetails
FACTOR XA
L
96Homo sapiensGene 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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
DX9
Query on DX9

Download SDF File 
Download CCD File 
A
(2S)-3-(7-carbamimidoylnaphthalen-2-yl)-2-[4-({(3R)-1-[(1Z)-ethanimidoyl]pyrrolidin-3-yl}oxy)phenyl]propanoic acid
DX9056A
C26 H28 N4 O3
AGRCGQSFFMCBRE-DGUCVARSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DX9Ki: 20 - 41 nM (98) BINDINGDB
DX9IC50: 40 - 130 nM (98) BINDINGDB
DX9Ki: 41 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.930α = 90.00
b = 73.170β = 90.00
c = 79.080γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
SAINTdata scaling
SAINTdata reduction
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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