3QTO

Thrombin Inhibition by Pyridin Derivatives

Structural Biology Knowledgebase: 3QTO SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.165
  • R-Value Work: 0.155

Literature

Macromolecules
Sequence Display for 3QTO

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 36361.41

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 variant-2 I 13 Hirudo medicinalis Fragment: residues in UNP 60-72
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
10P
Query on 10P

H D-phenylalanyl-N-[(1-methylpyridinium-3-yl)methyl]- L-prolinamide
C21 H27 N4 O2
RQARGWNLRRMMGY-MOPGFXCFSA-O
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)
PO4
Query on PO4

H PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

H GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-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 %)
10P N/A in BindingDB
Ki: 74800 nM  BindingMOAD
Ki: 74800 nM  PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_001079
Query on PRD_001079
H D-PHENYLALANYL-N-[(1-METHYLPYRIDINIUM-3-YL)METHYL]-L-PROLINAMIDE 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: 1.52 Å
  • R-Value Free: 0.165
  • R-Value Work: 0.155
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 69.80 α = 90.00
b = 71.40 β = 100.30
c = 72.50 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-02-23
  • Released Date: 2012-02-29
  • Deposition author(s): Biela, A., Heine, A., Klebe, G.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2012-06-20
    Type: Citation | Details: Citation update