1D4P

CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH 5-AMIDINOINDOLE-4-BENZYLPIPERIDINE INHIBITOR

Structural Biology Knowledgebase: 1D4P SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.184

Literature

Macromolecules
Sequence Display for 1D4P

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 36054.24

Macromolecule Entities
Molecule Chains Length Organism Details
ALPHA-THROMBIN A 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: LIGHT CHAIN
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ALPHA-THROMBIN B 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: HEAVY CHAIN
Gene Name(s): F2 Gene View
HIRUGEN H 12 Hirudo medicinalis Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

B (4-BENZYL-PIPERIDIN-1-YL)-(5-AMIDINOMETHYL- 3AH-INDOL-2-YL-METHANONE
C22 H25 N4 O
KVXKNKYHJPTYNK-UHFFFAOYSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

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

B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
BPP N/A in BindingDB
Ka: 2e+06 M-1  BindingMOAD
Kd: 500 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
TYS
Query on TYS
H L-PEPTIDE LINKING C9 H11 N O6 S TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.184
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 71.56 α = 90.00
b = 72.06 β = 101.20
c = 73.22 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-10-04
  • Released Date: 1999-10-20
  • Deposition author(s): Chirgadze, N.Y.

Revision History

  • 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
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature