1C5N

STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING, SUB-MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR

Structural Biology Knowledgebase: 1C5N SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.220

Literature

Macromolecules
Sequence Display for 1C5N

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 35606.61

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 I 10 Hirudo medicinalis Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

H 4-IODOBENZO[B]THIOPHENE-2-CARBOXAMIDINE
C9 H8 I N2 S
YERQOXAYAFWFEJ-UHFFFAOYSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

H CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

H SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ESI Ki: 20000 nM (100) BindingDB

Ki: 20000 nM  BindingMOAD
Ki: 20000 nM  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: 1.5 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.220
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 72.14 α = 90.00
b = 72.26 β = 101.23
c = 73.09 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-12-22
  • Released Date: 2000-12-22
  • Deposition author(s): Katz, B.A., Mackman, R., Luong, C., Radika, K., Martelli, A., Sprengeler, P.A., Wang, J., Chan, H., Wong, L.

Revision History

  • 2016-06-01
    Type: Source and taxonomy | Details: --
  • 2013-03-13
    Type: Other | Details: Remove PRD info on PRD molecule with WAIT status
  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-08-17
    Type: Sequence database correspondence | Details: --
  • 2011-08-03
    Type: Atom nomenclature | Details: --
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Linkage | Details: Linkage