1FPC

ACTIVE SITE MIMETIC INHIBITION OF THROMBIN

Structural Biology Knowledgebase: 1FPC SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Observed: 0.147

Literature

Macromolecules
Sequence Display for 1FPC

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 35915.24

Macromolecule Entities
Molecule Chains Length Organism Details
thrombin L 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
thrombin H 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Hirudin I 12 Hirudo medicinalis Mutation: D53N
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0ZI
Query on 0ZI

amino{[(4S)-4-({[5-(dimethylamino)naphthalen- 1-yl]sulfonyl}amino)-5-(4-ethylpiperidin- 1-yl)-5-oxopentyl]amino}methaniminium
DAPA (Synonym)
C25 H39 N6 O3 S
IIYZWOIELWZHJV-NRFANRHFSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
0ZI N/A in BindingDB
Ki: 100 nM  BindingMOAD
N/A in PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000376
Query on PRD_000376
H dansylarginine-N-(3-ethyl-1,5-pentanediyl)amide Peptide-like /
Inhibitor
Ligand Explorer
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
TYS
Query on TYS
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: 0.147
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 72.10 α = 90.00
b = 72.60 β = 101.00
c = 73.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1994-10-16
  • Released Date: 1995-02-27
  • Deposition author(s): Tulinsky, A., Mathews, I.I.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 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
  • 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