1NO9

Design of weakly basic thrombin inhibitors incorporating novel P1 binding functions: molecular and X-ray crystallographic studies.

Structural Biology Knowledgebase: 1NO9 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.204
  • R-Value Work: 0.183

Literature

Macromolecules
Sequence Display for 1NO9

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 35859.05

Macromolecule Entities
Molecule Chains Length Organism Details
Alpha Thrombin L 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: Light Chain
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Alpha Thrombin H 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: Heavy Chain
Gene Name(s): F2 Gene View
hirugen I 11 Hirudo medicinalis Fragment: Chain I
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
4ND
Query on 4ND

H N4-(N,N-DIPHENYLCARBAMOYL)-AMINOGUANIDINE
C14 H15 N5 O
QLXOHIUDKNRVBZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

H N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
4ND N/A in BindingDB
N/A in BindingMoad
Ki: 24 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: 1.9 Å
  • R-Value Free: 0.204
  • R-Value Work: 0.183
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 71.41 α = 90.00
b = 72.19 β = 100.57
c = 72.71 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-01-16
  • Released Date: 2003-08-26
  • Deposition author(s): De Simone, G., Menchise, V., Omaggio, S., Pedone, C., Scozzafava, A., Supuran, C.T.

Revision History

  • 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