4AZ2 | pdb_00004az2

Human thrombin - inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.190 (Depositor), 0.179 (DCC) 
  • R-Value Work: 
    0.141 (Depositor) 
  • R-Value Observed: 
    0.143 (Depositor) 

Starting Model: other
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wwPDB Validation 3D Report Full Report

Validation slider image for 4AZ2

Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Design and Synthesis of Potent and Highly Selective Thrombin Inhibitors.

Hilpert, K.Ackermann, J.Banner, D.W.Gast, A.Gubernator, K.Hadvary, P.Labler, L.Muller, K.Schmid, G.Tschopp, T.B.

(1994) J Med Chem 37: 3889

  • DOI: https://doi.org/10.1021/jm00049a008
  • Primary Citation Related Structures: 
    4AX9, 4AYV, 4AYY, 4AZ2

  • PubMed Abstract: 

    Thrombin, a serine protease, plays a central role in the initiation and propagation of thrombotic events. An extensive search for new thrombin inhibitors was performed, using an unconventional approach. Screening of small basic molecules for binding in the recognition pocket of thrombin led to the discovery of (aminoiminomethyl)piperidine (amidinopiperidine) as a weak, but intrinsically selective, thrombin inhibitor. Elaboration of this molecule provided compounds which inhibit thrombin with Ki's in the range of 20-50 nM and with selectivities of 1000-4000 against trypsin. These inhibitor compounds show a new and unexpected binding mode to thrombin. Modification of the central building block and then of one of the hydrophobic substituents led to the discovery of a new family of thrombin inhibitors which has reverted to the former binding mode to thrombin. This last class of compounds shows inhibitory activities in the picomolar range, low toxicity, and a short plasma half life which favors its use for an intravenous application. From this series of thrombin inhibitors, 19f(Ro 46-6240) was selected for clinical development as an antithrombotic agent for intravenous administration.


  • Organizational Affiliation
    • Pharma Division, F. Hoffmann-La Roche Ltd., Basel, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 35.21 kDa 
  • Atom Count: 2,560 
  • Modeled Residue Count: 298 
  • Deposited Residue Count: 298 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
THROMBIN LIGHT CHAIN30Homo sapiensMutation(s): 0 
EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
PHAROS:  P00734
GTEx:  ENSG00000180210 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00734
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
THROMBIN HEAVY CHAIN257Homo sapiensMutation(s): 0 
EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
PHAROS:  P00734
GTEx:  ENSG00000180210 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00734
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P00734-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
HIRUDIN-3A'C [auth D]11Hirudo medicinalisMutation(s): 0 
UniProt
Find proteins for P28508 (Hirudo medicinalis)
Explore P28508 
Go to UniProtKB:  P28508
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28508
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9MU

Query on 9MU



Download:Ideal Coordinates CCD File
D [auth B](R)-N-((S)-1-CARBAMIMIDOYL-PIPERIDIN-3-YLMETHYL)-2-(NAPHTHALENE-2-SULFONYLAMINO)-3-PHENYL-PROPIONAMIDE
C26 H31 N5 O3 S
WWJJOLLOSVQTGQ-GBXCKJPGSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
E [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
9MU BindingDB:  4AZ2 Ki: min: 32, max: 47 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.190 (Depositor), 0.179 (DCC) 
  • R-Value Work:  0.141 (Depositor) 
  • R-Value Observed: 0.143 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.8α = 90
b = 90.8β = 90
c = 132.5γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-15
    Type: Initial release
  • Version 1.1: 2013-08-07
    Changes: Other
  • Version 1.2: 2017-06-28
    Changes: Data collection
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.4: 2024-05-01
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.5: 2024-10-16
    Changes: Structure summary