2VH0

Structure and property based design of factor Xa inhibitors:biaryl pyrrolidin-2-ones incorporating basic heterocyclic motifs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.188

Literature

Macromolecules
Sequence Display for 2VH0

Classification: HYDROLASE

Total Structure Weight: 44351.82

Macromolecule Entities
Molecule Chains Length Organism Details
ACTIVATED FACTOR XA HEAVY CHAIN A 254 Homo sapiens EC#: 3.4.21.6 IUBMB
Fragment: ACTIVATED DESGLA, RESIDUES 235-488
Details: DISULPHIDE LINKED TO OTHER CHAIN
Gene Name(s): F10 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ACTIVATED FACTOR XA 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
GSI
Query on GSI

A 2-(5-chlorothiophen-2-yl)-N-[(3S)-1-(4-{2- [(dimethylamino)methyl]-1H-imidazol-1-yl}- 2-fluorophenyl)-2-oxopyrrolidin-3-yl]ethanesulfonamide
C22 H25 Cl F N5 O3 S2
JENHCPNBBPPGMN-SFHVURJKSA-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 %)
GSI N/A in BindingDB
Ki: 1 nM  BindingMOAD
Ki: 3.1 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.188
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 56.54 α = 90.00
b = 72.16 β = 90.00
c = 78.66 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-11-16
  • Released Date: 2008-11-25
  • Deposition author(s): Young, R.J., Borthwick, A.D., Brown, D., Burns-Kurtis, C.L., Campbell, M., Chan, C., Charbaut, M., Convery, M.A., Diallo, H., Hortense, E., Irving, W.R., Kelly, H.A., King, N.P., Kleanthous, S., Mason, A.M., Pateman, A.J., Patikis, A., Pinto, I.L., Pollard, D.R., Senger, S., Shah, G.P., Toomey, J.R., Watson, N.S., Weston, H.E., Zhou, P.

Revision History

  • Version 1_0: 2008-11-25

    Type: Initial release

  • Version 1_1: 2011-05-08

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance