1T4V

Crystal Structure Analysis of a novel Oxyguanidine bound to Thrombin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Observed: 0.210

Literature

Macromolecules
Sequence Display for 1T4V

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 34742.11

Macromolecule Entities
Molecule Chains Length Organism Details
Prothrombin L 26 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: sequence database residues 334-359
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Prothrombin H 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: sequence database residues 364-622
Gene Name(s): F2 Gene View
Hirudin IIIA I 11 Hirudo medicinalis Fragment: sequence database residues 55-65
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
14A
Query on 14A

H N-ALLYL-5-AMIDINOAMINOOXY-PROPYLOXY-3-CHLORO- N-CYCLOPENTYLBENZAMIDE
C19 H27 Cl N4 O3
XWIUMAPBZWNFNV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
14A Ki: 21 nM (100) BindingDB

IC50: 21 nM  BindingMOAD
Ki: 21 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
TYS
Query on TYS
I L-PEPTIDE LINKING C9 H11 N O6 S TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Observed: 0.210
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 70.97 α = 90.00
b = 71.75 β = 100.52
c = 72.82 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-04-30
  • Released Date: 2005-03-22
  • Deposition author(s): Spurlino, J.

Revision History

  • Version 1_0: 2005-03-22

    Type: Initial release

  • Version 1_1: 2008-04-30

    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: 2012-12-12

    Type: Other

  • Version 1_4: 2013-03-13

    Type: Other

  • Version 1_5: 2017-10-11

    Type: Advisory, Refinement description