1YPJ

Thrombin Inhibitor Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.6 of the entry. See complete history

Literature

A simple protocol to estimate differences in protein binding affinity for enantiomers without prior resolution of racemates

Fokkens, J.Klebe, G.

(2006) Angew.Chem.Int.Ed.Engl. 45: 985-989


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thrombin light chain
L
27Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Thrombin heavy chain
H
257Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Hirudin
I
10Hirudo medicinalisMutation(s): 0 
Find proteins for P28504 (Hirudo medicinalis)
Go to UniProtKB:  P28504
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UIB
Query on UIB

Download SDF File 
Download CCD File 
H
(1R,3AS,4R,8AS,8BR)-4-{5-(PHENYL[1,3]DIOXOL-5-YLMETHYL)-4-ETHYL-2,3,3-TRIMETHYL-6-OXO-OCTAHYDRO-PYRROLO[3,4-C]PYRROL-1-YL}-BENZAMIDINE
C26 H32 N4 O3
HQVPEQYGMUJQHM-MSYGRNIXSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
I
L-PEPTIDE LINKINGC9 H11 N O6 STYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UIBKi: 95 nM BINDINGMOAD
UIBKi: 95 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 70.521α = 90.00
b = 71.809β = 99.87
c = 71.308γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SHELXmodel building
SHELXL-97refinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-17
    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: 2013-11-13
    Type: Other
  • Version 1.6: 2017-10-11
    Type: Refinement description