1DOJ

Crystal structure of human alpha-thrombin*RWJ-51438 complex at 1.7 A

Structural Biology Knowledgebase: 1DOJ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.174

Literature

Macromolecules
Sequence Display for 1DOJ

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 36211.40

Macromolecule Entities
Molecule Chains Length Organism Details
ALPHA-THROMBIN A 295 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
HIRUGEN B 11 Hirudo medicinalis Fragment: FRAGMENT OF HIRUDIN
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
1Z0
Query on 1Z0

A N-methyl-D-phenylalanyl-N-{(1S)-4-carbamimidamido- 1-[(6-carboxy-1,3-benzothiazol-2-yl)carbonyl]butyl}- L-prolinamide
RWJ-51438 (Synonym)
C29 H35 N7 O5 S
XNPQCHOSZVJBHP-BDTNDASRSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

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

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
1Z0 IC50: 45 nM (100) BindingDB
Ki: 2 nM (100) BindingDB

N/A in BindingMoad
N/A in PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000623
Query on PRD_000623
A RWJ-51438 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
B L-PEPTIDE LINKING C9 H11 N O6 S TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.174
  • Space Group: P 21 21 2

Unit Cell:

Length (Å) Angle (°)
a = 62.98 α = 90.00
b = 117.52 β = 90.00
c = 47.99 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-12-21
  • Released Date: 2000-11-03
  • Deposition author(s): Recacha, R., Costanzo, M.J., Maryanoff, B.E., Carson, M., DeLucas, L., Chattopadhyay, D.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 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
  • 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: Atom occupancy | Details: Restore author's atom occupancy
  • 2011-07-13
    Type: Linkage | Details: Linkage