1DWD

CRYSTALLOGRAPHIC ANALYSIS AT 3.0-ANGSTROMS RESOLUTION OF THE BINDING TO HUMAN THROMBIN OF FOUR ACTIVE SITE-DIRECTED INHIBITORS

Structural Biology Knowledgebase: 1DWD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Observed: 0.156

Literature

Macromolecules
Sequence Display for 1DWD

Classification: HYDROLASE / HYROLASE INHIBITOR

Total Structure Weight: 35810.11

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
HIRUDIN IIIA I 11 Hirudo medicinalis Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

H 1-[N-(naphthalen-2-ylsulfonyl)glycyl-4-carbamimidoyl- D-phenylalanyl]piperidine
NAPAP (Synonym)
C27 H31 N5 O4 S
XXTWZTPVNIYSJZ-XMMPIXPASA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
MID EC50: 750 nM (100) BindingDB
IC50: 200 - 690 nM (100) BindingDB
Ki: 4 - 6000 nM (87 - 100) BindingDB

N/A in BindingMoad
Ki: 6.6 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Observed: 0.156
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 90.80 α = 90.00
b = 90.80 β = 90.00
c = 132.50 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1992-08-19
  • Released Date: 1994-01-31
  • Deposition author(s): Banner, D.W., Hadvary, P.

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