1TOM

ALPHA-THROMBIN COMPLEXED WITH HIRUGEN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Synthesis, evaluation, and crystallographic analysis of L-371,912: A potent and selective active-site thrombin inhibitor.

Lyle, T.A.Chen, Z.G.Appleby, S.D.Freidinger, R.M.Gardell, S.J.Lewis, S.D.Li, Y.Lyle, E.A.Lynch, J.J.Mulichak, A.M.Ng, A.S.NaylorOlsen, A.M.Sanders, W.M.

(1997) Bioorg.Med.Chem.Lett. 7: 67-72


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALPHA-THROMBIN
L
36Homo 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
ALPHA-THROMBIN
H
259Homo 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
HIRUGEN
I
12Hirudo medicinalisMutation(s): 0 
Find proteins for P28507 (Hirudo medicinalis)
Go to UniProtKB:  P28507
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MIN
Query on MIN

Download SDF File 
Download CCD File 
H
METHYL-PHE-PRO-AMINO-CYCLOHEXYLGLYCINE
C22 H34 N4 O2
MDSVGJAUFNXYRR-WTGUMLROSA-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 %)
MINKi: 0.09 nM BINDINGMOAD
MINKi: 5 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 71.250α = 90.00
b = 72.190β = 101.85
c = 73.110γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1996-12-06 
  • Released Date: 1997-03-12 
  • Deposition Author(s): Chen, Z.

Revision History 

  • Version 1.0: 1997-03-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    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