1O0D

Human Thrombin complexed with a d-Phe-Pro-Arg-type Inhibitor and a C-terminal Hirudin derived exo-site inhibitor

Structural Biology Knowledgebase: 1O0D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.199

Literature

Macromolecules
Sequence Display for 1O0D

Classification: BLOOD CLOTTING / HYDROLASE INHIBITOR

Total Structure Weight: 35848.15

Macromolecule Entities
Molecule Chains Length Organism Details
Thrombin light chain L 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: light chain
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Thrombin heavy chain H 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: heavy chain
Gene Name(s): F2 Gene View
Decapeptide Hirudin Analogue D 11 Hirudo medicinalis

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
163
Query on 163

H (2-{2-[(5-CARBAMIMIDOYL-1-METHYL-1H-PYRROL- 2-YLMETHYL)-CARBAMOYL]-PYRROL-1-YL}- 1-CYCLOHEXYLMETHYL- 2-OXO-ETHYLAMINO)-ACETIC ACID
C23 H32 N6 O4
AXMHAIYMRMPDQD-QGZVFWFLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
163 N/A in BindingDB
IC50: 6.2 nM  BindingMOAD
IC50: 6.2 nM  PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000480
Query on PRD_000480
D HIRUDIN ANALOGUE Oligopeptide /
Anticoagulant, Antithrombotic
Ligand Explorer

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.199
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 70.88 α = 90.00
b = 71.96 β = 101.06
c = 73.52 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-02-21
  • Released Date: 2003-10-14
  • Deposition author(s): Lange, U.E., Bauke, D., Hornberger, W., Mack, H., Seitz, W., Hoeffken, H.W.

Revision History

  • 2016-05-25
    Type: Source and taxonomy | Details: --
  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords