3P17

Thrombin Inhibition by Pyridin Derivatives

Structural Biology Knowledgebase: 3P17 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.176
  • R-Value Work: 0.132

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3P17

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 36126.15

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
thrombin heavy chain H 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Hirudin variant-2 I 12 Hirudo medicinalis Gene Name(s):

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
99P
Query on 99P

H D-phenylalanyl-N-(pyridin-3-ylmethyl)-L-prolinamide
C20 H24 N4 O2
KNPSDIKTQZBRCN-MSOLQXFVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

H N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

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

H SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
99P N/A in BindingDB
Ki: 33400 nM  BindingMOAD
Ki: 33400 nM  PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_001112 (DPN,PRO,0YC) H D-PHENYLALANYL-N-(PYRIDIN-3-YLMETHYL)-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: 1.43 Å
  • R-Value Free: 0.176
  • R-Value Work: 0.132
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 70.00 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: 2010-09-30
  • Released Date: 2011-11-02
  • Deposition author(s): Biela, A., Heine, A., Klebe, G.

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
  • 2012-06-20
    Type: Citation | Details: Citation update