1NT1

thrombin in complex with selective macrocyclic inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Observed: 0.191

Literature

Macromolecules
Sequence Display for 1NT1

Classification: BLOOD CLOTTING / HYDROLASE INHIBITOR

Total Structure Weight: 34961.41

Macromolecule Entities
Molecule Chains Length Organism Details
thrombin A 287 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Hirudin H 11 Hirudo medicinalis Mutation: E362A, Q365A
Details: 10 AA HIRUDIN ANALOGUE
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
T76
Query on T76

A (6R,21AS)-17-CHLORO-6-CYCLOHEXYL-2,3,6,7,10,11,19,20- OCTAHYDRO-1H,5H-PYRROLO[1,2-K][1,4,8,11,14]BENZOXATETRAAZA- CYCLOHEPTADECINE-5,8,12,21(9H,13H,21AH)-TETRONE
C25 H33 Cl N4 O5
CNGULIMOMYJRBP-WMZHIEFXSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
T76 Ki: 0.4 - 1.3 nM (100) BindingDB

Ki: 1.3 nM  BindingMOAD
Ki: 1.3 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: 2.0 Å
  • R-Value Observed: 0.191
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 71.10 α = 90.00
b = 72.10 β = 100.90
c = 73.20 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-01-28
  • Released Date: 2003-09-02
  • Deposition author(s): Nantermet, P.G., Barrow, J.C., Newton, C.L., Pellicore, J.M., Young, M., Lewis, S.D., Lucas, B.J., Krueger, J.A., McMasters, D.R., Yan, Y., Kuo, L.C., Vacca, J.P., Selnick, H.G.

Revision History

  • 2008-04-29
    Type: Version format compliance
  • 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance