4LOY

Crystal Structure Analysis of thrombin in complex with compound D57, 5-Chlorothiophene-2-carboxylic acid [(S)-2-[2-methyl-3-(2- oxopyrrolidin-1-yl)benzenesulfonylamino]-3-(4-methylpiperazin-1- yl)-3-oxopropyl]amide (SAR107375)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.208
  • R-Value Work: 0.177

Literature

Macromolecules
Sequence Display for 4LOY

Classification: hydrolase / hydrolase inhibitor

Total Structure Weight: 35033.81

Macromolecule Entities
Molecule Chains Length Organism Details
Thrombin heavy chain H 257 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: unp residues 364-620
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Hirudin variant-2 I 10 Hirudo medicinalis Fragment: unp residues 62-71
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Thrombin light chain L 27 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: unp residues 334-360
Gene Name(s): F2 Gene View

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
6XS
Query on 6XS

H 5-Chloro-thiophene-2-carboxylic acid [(S)- 2-[2-chloro-5-fluoro-3-(2-oxo-piperidin-1- yl)-benzenesulfonylamino]-3-(4-methyl-piperazin- 1-yl)-3-oxo-propyl]-amide
C24 H28 Cl2 F N5 O5 S2
PVTLJXXAPWJMAT-INIZCTEOSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

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

H SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
TYS
Query on TYS
I L-PEPTIDE LINKING C9 H11 N O6 S TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.208
  • R-Value Work: 0.177
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 70.52 α = 90.00
b = 71.20 β = 100.91
c = 73.14 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-07-14
  • Released Date: 2014-06-04
  • Deposition author(s): Stehlin-Gaon, C., Bocskei, Z.

Revision History

No revisions since initial release