1A46

THROMBIN COMPLEXED WITH HIRUGEN AND A BETA-STRAND MIMETIC INHIBITOR

Structural Biology Knowledgebase: 1A46 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Work: 0.155

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1A46

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 35986.23

Macromolecule Entities
Molecule Chains Length Organism Details
ALPHA-THROMBIN (SMALL SUBUNIT) L 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ALPHA-THROMBIN (LARGE SUBUNIT) H 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
HIRUGEN I 12 Hirudo medicinalis Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
00K
Query on 00K

H (1S,7S)-7-amino-N-[(2R,3S)-7-amino-1-(cyclohexylamino)- 2-hydroxy-1-oxoheptan-3-yl]-7-benzyl-8-oxohexahydro- 1H-pyrazolo[1,2-a]pyridazine-1-carboxamide
MOL-106 (Synonym)
C28 H44 N6 O4
FYDHYBJQXIEOSE-HXFQDRMMSA-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)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000617 (ANL,00V,00U) H MOL-106 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: 2.12 Å
  • R-Value Observed:
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 71.30 α = 90.00
b = 73.09 β = 101.12
c = 73.82 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1998-02-11
  • Released Date: 1998-05-27
  • Deposition author(s): St Charles, R., Matthews, J.H., Zhang, E., Tulinsky, A., Kahn, M.

Revision History

  • 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