3EQ0

Thrombin Inhibitor

Structural Biology Knowledgebase: 3EQ0 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.196

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3EQ0

Classification: Hydrolase / Hydrolase Inhibitor

Total Structure Weight: 35921.54

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-1 I 11 Hirudo medicinalis Fragment: Residues 54-64

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

H (2S)-N-[[2-(aminomethyl)-5-chloro-phenyl]methyl]- 1-[(2R)-5-carbamimidamido-2-(phenylmethylsulfonylamino)pentanoyl]pyrrolidine- 2-carboxamide
(S)-1-((R)-5-Guanidino-2-phenylmethanesulfonylamino- pentanoyl)-pyrrolidine-2-carboxylic acid 2aminomethyl- 5-chloro-benzylamide (Synonym)
C26 H36 Cl N7 O4 S
MWLLGEVAEDIFRC-PKTZIBPZSA-N
Ligand Explorer
 
JSmol
NA
Query on NA

H SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000667 H N~2~-(benzylsulfonyl)-D-arginyl-N-[2-(aminomethyl)-5-chlorobenzyl]-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: 1.53 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.196
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 70.10 α = 90.00
b = 71.40 β = 100.40
c = 72.40 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-09-30
  • Released Date: 2009-08-18
  • Deposition author(s): Baum, B., Heine, A., Klebe, G., Steinmetzer, T.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 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