3KL6

Discovery of Tetrahydropyrimidin-2(1H)-one derivative TAK-442: A potent, selective and orally active factor Xa inhibitor

Structural Biology Knowledgebase: 3KL6 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.194

Literature

Macromolecules
Sequence Display for 3KL6

Classification: HYDROLASE

Total Structure Weight: 34238.70

Macromolecule Entities
Molecule Chains Length Organism Details
Coagulation Factor X heavy chain A 241 Homo sapiens EC#: 3.4.21.6 IUBMB
Fragment: Factor X heavy chain residues 235-475
Gene Name(s): F10 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Coagulation Factor X light chain B 57 Homo sapiens EC#: 3.4.21.6 IUBMB
Fragment: Factor X light chain residues 126-179
Gene Name(s): F10 Gene View

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
443
Query on 443

A 1-(1-{(2S)-3-[(6-chloronaphthalen-2-yl)sulfonyl]- 2-hydroxypropanoyl}piperidin-4-yl)tetrahydropyrimidin- 2(1H)-one
C22 H26 Cl N3 O5 S
GEHAEMCVKDPMKO-HXUWFJFHSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
443 IC50: 2.2 - 3.5 nM (98) BindingDB
Ki: 1.8 nM (98) BindingDB

IC50: 10 nM  BindingMOAD
IC50: 3.5 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.194
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 49.00 α = 90.00
b = 70.35 β = 90.00
c = 78.55 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-11-06
  • Released Date: 2009-12-01
  • Deposition author(s): Aertgeerts, K.

Revision History

  • 2013-04-24
    Type: Other | Details: --
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4