1BMN

HUMAN ALPHA-THROMBIN COMPLEXED WITH [S-(R*,R*)]-1-(AMINOIMINOMETHYL)-N-[[1-[N-[(2-NAPHTHALENYLSULFONYL)-L-SERYL]-PYRROLIDINYL]METHYL]-3-PIPERIDENECARBOXAMIDE (BMS-189090)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Observed: 0.162

Literature

Macromolecules
Sequence Display for 1BMN

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 35876.17

Macromolecule Entities
Molecule Chains Length Organism Details
ALPHA-THROMBIN L 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ALPHA-THROMBIN H 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
HIRUDIN I I 12 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
BM9
Query on BM9

H [S-(R*,R*)]-1-(AMINOIMINOMETHYL)-N-[[1-[N- [(2-NAPHTHALENYLSULFONYL)-L-SERYL]-3-PYRROLIDINYL]METHYL]- 3-PIPERIDENECARBOXAMIDE
BMS-189090 (Synonym)
C25 H34 N6 O5 S
JWNJPEKBZMEXIU-ONTIZHBOSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
BM9 IC50: 16 - 18 nM (100) BindingDB
Ki: 3.4 - 3.6 nM (100) BindingDB

N/A in BindingMoad
Ki: 3.6 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Observed: 0.162
  • Space Group: P 21 21 2

Unit Cell:

Length (Å) Angle (°)
a = 167.78 α = 90.00
b = 49.04 β = 90.00
c = 43.79 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1995-11-14
  • Released Date: 1996-12-07
  • Deposition author(s): Malley, M., Sack, J.

Revision History

  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description