3DUX

Understanding Thrombin Inhibition

Structural Biology Knowledgebase: 3DUX SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.201

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3DUX

Classification: Hydrolase / Hydrolase Inhibitor

Total Structure Weight: 35735.35

Macromolecule Entities
Molecule Chains Length Organism Details
Thrombin Light Chain L 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Thrombin Heavy Chain H 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Hirudin variant-1 I 11 Hirudo medicinalis Fragment: Residues 54-64
Gene Name(s):

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
64U
Query on 64U

H 3-cyclohexyl-D-alanyl-N-(3-chlorobenzyl)- L-prolinamide
(2S)-1-((2R)-2-amino-3-cyclohexyl-propanoyl)- N-((3-chlorophenyl)methyl)pyrrolidine-2-carboxamide (Synonym)
C21 H30 Cl N3 O2
JGFCNVHEEMBVJG-MOPGFXCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

H SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
64U Ki: 100 nM (100) BindingDB
ΔG: -39.7 - -36.4 kJ/mol (100) BindingDB
-TΔS: -7.5 - -3.4 kJ/mol (100) BindingDB

Ki: 100 nM  BindingMOAD
Ki: 100 nM  PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000610 (ZAL,PRO,C2A) H 3-cyclohexyl-D-alanyl-N-(3-chlorobenzyl)-L-prolinamide Peptide-like /
Thrombin Inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)
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: 1.6 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.201
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 70.02 α = 90.00
b = 71.44 β = 100.50
c = 72.79 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-07-18
  • Released Date: 2009-06-23
  • Deposition author(s): Baum, B., Heine, A., Klebe, G.

Revision History

  • 2016-05-25
    Type: Source and taxonomy | Details: --
  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 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
  • 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