1SL3

crystal structue of Thrombin in complex with a potent P1 heterocycle-Aryl based inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.240
  • R-Value Work: 0.210

Literature

Macromolecules
Sequence Display for 1SL3

Classification: BLOOD CLOTTING HYDROLASE / INHIBITOR

Total Structure Weight: 35066.76

Macromolecule Entities
Molecule Chains Length Organism Details
thrombin A 287 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: alpha-thrombin
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Hirudin B 11 Hirudo medicinalis Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
170
Query on 170

A (2-[6-CHLORO-3-{[2,2-DIFLUORO-2-(1-OXIDOPYRIDIN- 2-YL)ETHYL]AMINO}-2-OXOPYRAZIN-1(2H)-YL]- N-[5-CHLORO-2-(1H-TETRAZOL-1-YL)BENZYL]ACETAMIDE
C21 H17 Cl2 F2 N9 O3
QOKFRQVFMZFNBC-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
170 Ki: 0.0014 nM (100) BindingDB

Ki: 0.0014 nM  BindingMOAD
Ki: 0.0014 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
TYS
Query on TYS
B L-PEPTIDE LINKING C9 H11 N O6 S TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.240
  • R-Value Work: 0.210
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 70.00 α = 90.00
b = 71.50 β = 100.60
c = 72.50 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-03-05
  • Released Date: 2004-08-03
  • Deposition author(s): Young, M.B., Barrow, J.C., Glass, K.L., Lundell, G.F., Newton, C.L., Pellicore, J.M., Rittle, K.E., Selnick, H.G., Stauffer, K.J., Vacca, J.P., Williams, P.D., Bohn, D., Clayton, F.C., Cook, J.J., Krueger, J.A., Kuo, L.C., Lewis, S.D., Lucas, B.J., McMasters, D.R., Miller-Stein, C., Pietrak, B.L.

Revision History

  • Version 1_0: 2004-08-03

    Type: Initial release

  • Version 1_1: 2008-04-29

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance

  • Version 1_3: 2017-10-11

    Type: Refinement description