2CF9

Complex of recombinant human thrombin with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.6 of the entry. See complete history

Literature

Multipolar Interactions in the D Pocket of Thrombin: Large Differences between Tricyclic Imide and Lactam Inhibitors.

Schweizer, E.Hoffmann-Roeder, A.Olsen, J.A.Seiler, P.Obst-Sander, U.Wagner, B.Kansy, M.Banner, D.W.Diederich, F.

(2006) Org.Biomol.Chem. 4: 2364

  • DOI: 10.1039/b602585d
  • Primary Citation of Related Structures:  2CF8

  • PubMed Abstract: 
  • Two series of tricyclic inhibitors of the serine protease thrombin, imides (+/-)-1-(+/-)-8 and lactams (+/-)-9-(+/-)-13, were analysed to evaluate contributions of orthogonal multipolar interactions with the backbone C=O moiety of Asn98 to the free e ...

    Two series of tricyclic inhibitors of the serine protease thrombin, imides (+/-)-1-(+/-)-8 and lactams (+/-)-9-(+/-)-13, were analysed to evaluate contributions of orthogonal multipolar interactions with the backbone C=O moiety of Asn98 to the free enthalpy of protein-ligand complexation. The lactam derivatives are much more potent and more selective inhibitors (K(i) values between 0.065 and 0.005 microM, selectivity for thrombin over trypsin between 361- and 1609-fold) than the imide compounds (Ki values between 0.057 and 23.7 microM, selectivity for thrombin over trypsin between 3- and 67-fold). The increase in potency and selectivity is explained by the favorable occupancy of the P-pocket of thrombin by the additional isopropyl substituent in the lactam derivatives. The nature of the substituent on the benzyl ring filling the D pocket strongly influences binding potency in the imide series, with Ki values increasing in the sequence: F < OCH2O < Cl < H < OMe < OH < N(pyr)< Br. This sequence can be explained by both steric fit and the occurrence of orthogonal multipolar interactions with the backbone C[double bond, length as m-dash]O moiety of Asn98. In contrast, the substituent on the benzyl ring hardly affects the ligand potency in the lactam series. This discrepancy was clarified by the comparison of X-ray structures solved for co-crystals of thrombin with imide and lactam ligands. Whereas the benzyl substituents in the imide inhibitors are sufficiently close (< or =3.5 Angstroms) to the C=O group of Asn98 to allow for attractive orthogonal multipolar interactions, the distances in the lactam series are too large (> or =4 Angstroms) for attractive dipolar contacts to be effective.


    Organizational Affiliation

    Laboratorium für Organische Chemie, ETH-Zürich, Hönggerberg HCI, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THROMBIN HEAVY CHAIN
H
257Homo sapiensGene 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
HIRUDIN IIIA
I
11Hirudo medicinalisN/A
Find proteins for P28508 (Hirudo medicinalis)
Go to UniProtKB:  P28508
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
THROMBIN LIGHT CHAIN
L
28Homo sapiensGene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
348
Query on 348

Download SDF File 
Download CCD File 
H
4-[(1R,3AS,4R,8AS,8BR)-1-ISOPROPYL-2-(4-METHOXYBENZYL)-3-OXODECAHYDROPYRROLO[3,4-A]PYRROLIZIN-4-YL]BENZENECARBOXIMIDAMIDE
C27 H34 N4 O2
XETNTDPUFDNJKX-BDUWWWMKSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
H
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000481
Query on PRD_000481
IN-terminal Asp des-amino Hirudin-3A'Oligopeptide / Anticoagulant, Antithrombotic

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
348Ki: 15 nM BINDINGMOAD
348Ki: 15 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.160 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 71.290α = 90.00
b = 71.840β = 100.56
c = 73.060γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-06-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2012-11-30
    Type: Other
  • Version 1.3: 2013-08-07
    Type: Derived calculations, Other
  • Version 1.4: 2013-10-23
    Type: Other
  • Version 1.5: 2017-03-29
    Type: Structure summary
  • Version 1.6: 2017-07-05
    Type: Data collection