1D9I

STRUCTURE OF THROMBIN COMPLEXED WITH SELECTIVE NON-ELECTOPHILIC INHIBITORS HAVING CYCLOHEXYL MOIETIES AT P1

Structural Biology Knowledgebase: 1D9I SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.153

Literature

Macromolecules
Sequence Display for 1D9I

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 35036.23

Macromolecule Entities
Molecule Chains Length Organism Details
THROMBIN A 288 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
HIRUGEN I 10 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
00P
Query on 00P

A (5S)-N-[(trans-4-aminocyclohexyl)methyl]- 1,3-dioxo-2-[2-(phenylsulfonyl)ethyl]-2,3,5,8- tetrahydro-1H-[1,2,4]triazolo[1,2-a]pyridazine- 5-carboxamide
C22 H29 N5 O5 S
PTMIAKQUJFKTNB-LNLFQRSKSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
00P N/A in BindingDB
Ki: 0.78 nM  BindingMOAD
N/A in PDBbind
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: 2.3 Å
  • R-Value Observed:
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 71.46 α = 90.00
b = 72.19 β = 100.70
c = 73.12 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-10-27
  • Released Date: 2000-10-30
  • Deposition author(s): Krishnan, R., Mochalkin, I., Arni, R., Tulinsky, A.

Revision History

  • 2013-03-13
    Type: Other | Details: Remove PRD info on PRD molecule with WAIT status
  • 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