3F68

Thrombin Inhibition

Structural Biology Knowledgebase: 3F68 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.196

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3F68

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 35777.39

Macromolecule Entities
Molecule Chains Length Organism Details
Prothrombin L 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: UNP residues 328-363, Thrombin light chain
Gene Name(s): F2 Gene View
Prothrombin H 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: UNP residues 364-622, Thrombin heavy chain
Gene Name(s): F2 Gene View
Hirudin variant-2 I 11 Hirudo medicinalis Fragment: UNP residues 61-71

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
91U
Query on 91U

H N-acetyl-3-cyclohexyl-D-alanyl-N-(3-chlorobenzyl)- L-prolinamide
C23 H32 Cl N3 O3
NEBILTDHZWSWJN-RTWAWAEBSA-N
Ligand Explorer
 
JSmol
NA
Query on NA

H SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
91U N/A in BindingDB
Ki: 8700 nM  BindingMOAD
Ki: 8700 nM  PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000611 H N-acetyl-3-cyclohexyl-D-alanyl-N-(3-chlorobenzyl)-L-prolinamide Peptide-like /
Thrombin Inhibitor
Ligand Explorer
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
TYS
Query on TYS
I L-PEPTIDE LINKING C9 H11 N O6 S TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.196
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 70.28 α = 90.00
b = 71.95 β = 100.05
c = 72.50 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-11-05
  • Released Date: 2009-10-20
  • Deposition author(s): Baum, B., Heine, A., Klebe, G.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 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
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence