6VBN

Crystal Structure of hTDO2 bound to inhibitor GNE1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.18 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report

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This is version 1.1 of the entry. See complete history


Literature

Implementation of the CYP Index for the Design of Selective Tryptophan-2,3-dioxygenase Inhibitors.

Parr, B.T.Pastor, R.Sellers, B.D.Pei, Z.Jaipuri, F.A.Castanedo, G.M.Gazzard, L.Kumar, S.Li, X.Liu, W.Mendonca, R.Pavana, R.K.Potturi, H.Shao, C.Velvadapu, V.Waldo, J.P.Wu, G.Yuen, P.W.Zhang, Z.Zhang, Y.Harris, S.F.Oh, A.J.DiPasquale, A.Dement, K.La, H.Goon, L.Gustafson, A.VanderPorten, E.C.Mautino, M.R.Liu, Y.

(2020) ACS Med Chem Lett 11: 541-549

  • DOI: https://doi.org/10.1021/acsmedchemlett.0c00004
  • Primary Citation of Related Structures:  
    6VBN

  • PubMed Abstract: 

    A class of imidazoisoindole (III) heme-binding indoleamine-2,3-dioxygenase (IDO1) inhibitors were optimized via structure-based drug design into a series of tryptophan-2,3-dioxygenase (TDO)-selective inhibitors. Kynurenine pathway modulation was demonstrated in vivo , which enabled evaluation of TDO as a potential cancer immunotherapy target. As means of mitigating the risk of drug-drug interactions arising from cytochrome P450 inhibition, a novel property-based drug design parameter, herein referred to as the CYP Index, was implemented for the design of inhibitors with appreciable selectivity for TDO over CYP3A4. We anticipate the CYP Index will be a valuable design parameter for optimizing CYP inhibition of any small molecule inhibitor containing a Lewis basic motif capable of binding heme.


  • Organizational Affiliation

    Genentech, South San Francisco, California 94080, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tryptophan 2,3-dioxygenase
A, B, C, D
385Homo sapiensMutation(s): 0 
Gene Names: TDO2TDO
EC: 1.13.11.11
UniProt & NIH Common Fund Data Resources
Find proteins for P48775 (Homo sapiens)
Explore P48775 
Go to UniProtKB:  P48775
PHAROS:  P48775
GTEx:  ENSG00000151790 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48775
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.18 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.475α = 90
b = 143.044β = 90
c = 147.236γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-06
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description