3UTU

High affinity inhibitor of human thrombin

Structural Biology Knowledgebase: 3UTU SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.271
  • R-Value Work: 0.217

Literature

Macromolecules
Sequence Display for 3UTU

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 36023.61

Macromolecule Entities
Molecule Chains Length Organism Details
Thrombin light chain L 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Thrombin heavy chain H 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Hirudin variant-1 I 11 Hirudo medicinalis Fragment: UNP RESIDUES 54-64
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

H (2S)-N-[(4-carbamimidoylphenyl)methyl]-1- [(2S)-2-[(3-chloro-4-methoxybenzene)sulfonamido]- 3-{[(4-cyanophenyl)methyl]carbamoyl}propanoyl]pyrrolidine- 2-carboxamide
C32 H34 Cl N7 O6 S
YNEVNNWCKYNFGX-SVBPBHIXSA-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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
1TS N/A in BindingDB
Ki: 0.012 nM  BindingMOAD
Ki: 0.012 nM  PDBbind
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: 1.55 Å
  • R-Value Free: 0.271
  • R-Value Work: 0.217
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 70.77 α = 90.00
b = 71.35 β = 100.65
c = 72.39 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-11-26
  • Released Date: 2012-08-29
  • Deposition author(s): Baum, B., Steinmetzer, T., Heine, A., Klebe, G.

Revision History

  • 2014-03-12
    Type: Citation | Details: Citation update
  • 2013-03-13
    Type: Other | Details: Remove PRD info on PRD molecule with WAIT status
  • 2012-12-12
    Type: Other | Details: Add PRD info