1PPC

GEOMETRY OF BINDING OF THE BENZAMIDINE-AND ARGININE-BASED INHIBITORS N-ALPHA-(2-NAPHTHYL-SULPHONYL-GLYCYL)-DL-P-AMIDINOPHENYLALANYL-PIPERIDINE (NAPAP) AND (2R,4R)-4-METHYL-1-[N-ALPHA-(3-METHYL-1,2,3,4-TETRAHYDRO-8-QUINOLINESULPHONYL)-L-ARGINYL]-2-PIPERIDINE CARBOXYLIC ACID (MQPA) TO HUMAN ALPHA-THROMBIN: X-RAY CRYSTALLOGRAPHIC DETERMINATION OF THE NAPAP-TRYPSIN COMPLEX AND MODELING OF NAPAP-THROMBIN AND MQPA-THROMBIN

Structural Biology Knowledgebase: 1PPC SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Observed: 0.181

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1PPC

Classification: HYDROLASE / hydrolase inhibitor

Total Structure Weight: 23886.11

Macromolecule Entities
Molecule Chains Length Organism Details
TRYPSIN E 223 Bos taurus EC#: 3.4.21.4 IUBMB
Gene Name(s):

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

E 1-[N-(naphthalen-2-ylsulfonyl)glycyl-4-carbamimidoyl- D-phenylalanyl]piperidine
NAPAP (Synonym)
C27 H31 N5 O4 S
XXTWZTPVNIYSJZ-XMMPIXPASA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

E CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
MID Ki: 325 - 690 nM (100) BindingDB

Ki: 690 nM  BindingMOAD
N/A in PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000451 (APH,PIP,NAS,GLY) E N(alpha)-(2-naphthylsulfonylglycyl)-4-amidinophenylalanine piperidide Peptide-like /
Inhibitor
Ligand Explorer

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Observed: 0.181
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 63.51 α = 90.00
b = 69.19 β = 90.00
c = 63.81 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1991-10-24
  • Released Date: 1994-01-31
  • Deposition author(s): Bode, W., Turk, D.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 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
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description