2ZDA

Exploring Thrombin S1 pocket

Structural Biology Knowledgebase: 2ZDA SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.172

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2ZDA

Classification: Blood Clotting / Hydrolase Inhibitor

Total Structure Weight: 35832.90

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
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
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):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
32U
Query on 32U

H D-phenylalanyl-N-{4-[amino(iminio)methyl]benzyl}- L-prolinamide
C22 H28 N5 O2
VZFTWWJAUZOJDH-MOPGFXCFSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

H PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
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 %)
32U Ki: 1.1 - 4 nM (100) BindingDB
ΔG: -46.2 - -44 kJ/mol (100) BindingDB
-TΔS: -7.1 - 0.8 kJ/mol (100) BindingDB

N/A in BindingMoad
Ki: 4 nM  PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000600 (DPN,00S,PRO) H D-phenylalanyl-N-{4-[amino(iminio)methyl]benzyl}-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: 1.73 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.172
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 70.30 α = 90.00
b = 71.50 β = 100.50
c = 72.40 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-11-21
  • Released Date: 2008-10-28
  • 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