4MW5

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3-chloro-5-methoxybenzyl)amino]propyl}-3-phenylurea (Chem 1415)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.189

Literature

Macromolecules
Sequence Display for 4MW5

Classification: LIGASE / LIGASE INHIBITOR

Total Structure Weight: 124511.81

Macromolecule Entities
Molecule Chains Length Organism Details
Methionyl-tRNA synthetase A, B 542 Trypanosoma brucei EC#: 6.1.1.10 IUBMB
Fragment: UNP residues 237-773
Mutation: A309T, K452A, K453R, E454A, A499V, S503N
Gene Name(s): Tb10.70.6470
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
415
Query on 415

B 1-{3-[(3-chloro-5-methoxybenzyl)amino]propyl}- 3-phenylurea
C18 H22 Cl N3 O2
UCQXABGZXQUVHG-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MET
Query on MET

A METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMS
Query on DMS

A, B DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CAS
Query on CAS
A, B L-PEPTIDE LINKING C5 H12 As N O2 S CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.189
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 87.45 α = 90.00
b = 105.73 β = 90.00
c = 206.59 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-09-24
  • Released Date: 2014-04-30
  • Deposition author(s): Koh, C.Y., Kim, J.E., Wetzel, A.B., de van der Schueren, W.J., Shibata, S., Liu, J., Zhang, Z., Fan, E., Verlinde, C.L.M.J., Hol, W.G.J.
  • Previous versions: 3U1G

Revision History

No revisions since initial release