3QX5

Thrombin Inhibition by Pyridin Derivatives

Structural Biology Knowledgebase: 3QX5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.156
  • R-Value Work: 0.132

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3QX5

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 36395.83

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 13 Hirudo medicinalis Fragment: residues in UNP 60-72

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
02P
Query on 02P

H D-phenylalanyl-N-[(4-chloro-1-methylpyridinium- 2-yl)methyl]-L-prolinamide
C21 H26 Cl N4 O2
BNDOLKJAONQVEV-MOPGFXCFSA-O
Ligand Explorer
 
JSmol
GOL
Query on GOL

H GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
NA
Query on NA

H SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
NAG
Query on NAG

H N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
JSmol
PO4
Query on PO4

H PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
02P N/A in BindingDB
Ki: 63500 nM  BindingMOAD
Ki: 63500 nM  PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_001085 H D-PHENYLALANYL-N-[(4-CHLORO-1-METHYLPYRIDINIUM-2-YL)METHYL]-L-PROLINAMIDE Peptide-like /
Thrombin inhibitor
Ligand Explorer
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: 1.35 Å
  • R-Value Free: 0.156
  • R-Value Work: 0.132
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 70.20 α = 90.00
b = 71.10 β = 100.60
c = 72.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-03-01
  • Released Date: 2012-03-07
  • 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