2Y80

Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with aminoindane and phenylpyrrolidine P4 motifs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.189

Literature

Macromolecules
Sequence Display for 2Y80

Classification: BLOOD CLOTTING

Total Structure Weight: 44309.78

Macromolecule Entities
Molecule Chains Length Organism Details
ACTIVATED FACTOR XA HEAVY CHAIN A 254 Homo sapiens EC#: 3.4.21.6 IUBMB
Details: DISULPHIDE LINKED TO OTHER CHAIN
Gene Name(s): F10 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
FACTOR X LIGHT CHAIN B 134 Homo sapiens EC#: 3.4.21.6 IUBMB
Fragment: ACTIVATED DESGLA, RESIDUES 46-179
Details: DISULPHIDE LINKED TO OTHER CHAIN
Gene Name(s): F10 Gene View

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
439
Query on 439

A 6-CHLORO-N-{(3S)-1-[(1S)-1-(DIMETHYLAMINO)- 2,3-DIHYDRO-1H-INDEN-5-YL]-2-OXO-3-PYRROLIDINYL}- 2-NAPHTHALENESULFONAMIDE
C25 H26 Cl N3 O3 S
DBFTVRMJVISJEX-BJKOFHAPSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
439 Ki: 3 - 9 nM (100) BindingDB

Ki: 9 nM  BindingMOAD
Ki: 9 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.189
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 56.73 α = 90.00
b = 72.01 β = 90.00
c = 78.69 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-02-02
  • Released Date: 2011-03-16
  • Deposition author(s): Young, R.J., Adams, C., Blows, M., Brown, D., Burns-Kurtis, C.L., Chaudry, L., Chan, C., Convery, M.A., Davies, D.E., Exall, A.M., Foster, G., Harling, J.D., Hortense, E., Irving, W.R., Irvine, S., Jackson, S., Kleanthous, S., Pateman, A.J., Patikis, A.N., Roethka, T.J., Senger, S., Stelman, G.J., Toomey, J.R., West, R.I., Whittaker, C., Zhou, P., Watson, N.S.

Revision History

  • Version 1_0: 2011-03-16

    Type: Initial release

  • Version 1_1: 2011-05-08

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance