1ETS

REFINED 2.3 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF BOVINE THROMBIN COMPLEXES FORMED WITH THE BENZAMIDINE AND ARGININE-BASED THROMBIN INHIBITORS NAPAP, 4-TAPAP AND MQPA: A STARTING POINT FOR IMPROVING ANTITHROMBOTICS

Structural Biology Knowledgebase: 1ETS SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Observed: 0.178

Literature

Macromolecules
Sequence Display for 1ETS

Classification: HYDROLASE / HYDROLASE inhibitor

Total Structure Weight: 36029.57

Macromolecule Entities
Molecule Chains Length Organism Details
EPSILON-THROMBIN L 49 Bos taurus EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
EPSILON-THROMBIN H 259 Bos taurus EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View

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

H 1-[N-(naphthalen-2-ylsulfonyl)glycyl-4-carbamimidoyl- D-phenylalanyl]piperidine
NAPAP (Synonym)
C27 H31 N5 O4 S
XXTWZTPVNIYSJZ-XMMPIXPASA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
MID EC50: 750 nM (87) BindingDB
IC50: 200 - 690 nM (87) BindingDB
Ki: 4 - 6000 nM (86 - 100) BindingDB

Ki: 6 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Observed: 0.178
  • Space Group: P 42 21 2

Unit Cell:

Length (Å) Angle (°)
a = 88.73 α = 90.00
b = 88.73 β = 90.00
c = 102.90 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1992-07-06
  • Released Date: 1994-01-31
  • Deposition author(s): Bode, W., Brandstetter, H.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4