2ZGX

Thrombin Inhibition

Structural Biology Knowledgebase: 2ZGX SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.178

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2ZGX

Classification: Hydrolase / Hydrolase Inhibitor

Total Structure Weight: 35674.83

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: UNP Residues 54-64
Gene Name(s):

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
29U
Query on 29U

H 1-[(2R)-2-aminobutanoyl]-N-(4-carbamimidoylbenzyl)- L-prolinamide
C17 H25 N5 O2
YHAMQFKGUUSJMU-KGLIPLIRSA-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 %)
29U Ki: 180 nM (100) BindingDB
ΔG: -40.1 kJ/mol (100) BindingDB
-TΔS: -1.4 kJ/mol (100) BindingDB

Ki: 180 nM  BindingMOAD
Ki: 180 nM  PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000598 (ABA,00S,PRO) H 1-[(2R)-2-aminobutanoyl]-N-(4-carbamimidoylbenzyl)-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: 1.8 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.178
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 70.42 α = 90.00
b = 71.45 β = 100.70
c = 72.46 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-01-28
  • Released Date: 2008-12-16
  • 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: 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