8CCM

Crystal structure of Mycobacterium smegmatis thioredoxin reductase in complex with Compound 2-06


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Fragment-based design of mycobacterial thioredoxin reductase inhibitors based on computational exploration of a huge virtual space

Fuesser, F.T.Kuemmel, D.Koch, O.Otten, P.Junker, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thioredoxin reductase319Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: trxB
UniProt
Find proteins for A0R7I9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R7I9 
Go to UniProtKB:  A0R7I9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R7I9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
U9C (Subject of Investigation/LOI)
Query on U9C

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C [auth A]~{N}6-(4-aminophenyl)-1,2-benzothiazole-3,6-diamine
C13 H12 N4 S
FECJVFNLOHROBQ-UHFFFAOYSA-N
MLI
Query on MLI

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D [auth A],
E [auth A]
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
GOL
Query on GOL

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F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

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I [auth A],
J [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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G [auth A],
H [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.15α = 90
b = 68.15β = 90
c = 154.89γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentGermanyTTU 02.906

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-07
    Type: Initial release