1A4W

CRYSTAL STRUCTURES OF THROMBIN WITH THIAZOLE-CONTAINING INHIBITORS: PROBES OF THE S1' BINDING SITE

Structural Biology Knowledgebase: 1A4W SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.155

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1A4W

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 36072.34

Macromolecule Entities
Molecule Chains Length Organism Details
ALPHA-THROMBIN (SMALL SUBUNIT) L 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ALPHA-THROMBIN (LARGE SUBUNIT) H 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
HIRUGEN I 12 Hirudo medicinalis Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

H amino{[(4S)-4-({[5-(dimethylamino)naphthalen- 1-yl]sulfonyl}amino)-5-oxo-5-{(2R)-2-[3-oxo- 3-(1,3-thiazol-2-yl)propyl]piperidin-1-yl}pentyl]amino}methaniminium
RWJ-50215 (Synonym)
C29 H40 N7 O4 S2
KACDHMPRLCAESX-OFNKIYASSA-O
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 %)
QWE N/A in BindingDB
Ki: 1200 nM  BindingMOAD
N/A in PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000622 (ARG,5TP,ANS) H RWJ-50215 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: 1.8 Å
  • R-Value Observed:
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 71.47 α = 90.00
b = 72.00 β = 101.13
c = 73.39 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1998-02-06
  • Released Date: 1998-04-29
  • Deposition author(s): Matthews, J.H., Krishnan, R., Costanzo, M.J., Maryanoff, B.E., Tulinsky, A.

Revision History

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