1NM6

thrombin in complex with selective macrocyclic inhibitor at 1.8A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.216

Literature

Macromolecules
Sequence Display for 1NM6

Classification: BLOOD CLOTTING / HYDROLASE INHIBITOR

Total Structure Weight: 35023.48

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 B 11 Hirudo medicinalis Mutation: 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
L86
Query on L86

A (11S)-11-BENZYL-6-CHLORO-1,2,10,11,12,13,14,15,16,17,18,19- DODECAHYDRO-5,9-METHANO-2,5,8,10,13,17-BENZOHEXAAZACYCLOHENICOSINE- 3,24-DIONE
COMPOUND 31 (Synonym)
C27 H33 Cl N6 O2
LYVSCNRRXJZCRV-QHCPKHFHSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
L86 Ki: 0.09 nM (100) BindingDB

Ki: 0.09 nM  BindingMOAD
Ki: 0.09 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
TYS
Query on TYS
B L-PEPTIDE LINKING C9 H11 N O6 S TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.216
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 69.70 α = 90.00
b = 71.40 β = 100.50
c = 72.30 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-01-09
  • 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

  • Version 1_0: 2003-09-02

    Type: Initial release

  • Version 1_1: 2008-04-29

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance

  • Version 1_3: 2017-10-11

    Type: Refinement description