9B1Q

Crystal Structure of human Tryptophan 2,3-dioxygenase in complex with PYN1 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.202 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural Insights into Protein-Inhibitor Interactions in Human Tryptophan Dioxygenase.

Geeraerts, Z.Ishigami, I.Lewis-Ballester, A.Pham, K.N.Kozlova, A.Mathieu, C.Frederick, R.Yeh, S.R.

(2024) J Med Chem 67: 14543-14552

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01360
  • Primary Citation of Related Structures:  
    7LU7, 8VTQ, 8VUG, 8VZV, 8W1H, 8W2K, 9AT2, 9B17, 9B1Q

  • PubMed Abstract: 

    Human tryptophan dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) are two important targets in cancer immunotherapy. Extensive research has led to a large number of potent IDO inhibitors; in addition, 52 structures of IDO in complex with inhibitors with a wide array of chemical scaffolds have been documented. In contrast, progress in the development of TDO inhibitors has been limited. Only four structures of TDO in complex with competitive inhibitors that compete with the substrate L-tryptophan for binding to the active site have been reported to date. Here we systematically evaluated the structures of TDO in complex with competitive inhibitors with three types of pharmacophores, imidazo-isoindole, indole-tetrazole, and indole-benzotriazole. The comparative assessment of the protein-inhibitor interactions sheds new light into the structure-based design of enzyme-selective inhibitors.


  • Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, 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
380Homo 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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
N [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
A1AH8 (Subject of Investigation/LOI)
Query on A1AH8

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
O [auth D]
(5P)-1-[(imidazolidin-1-yl)methyl]-5-(1H-indol-3-yl)-1H-1,2,3-benzotriazole
C18 H18 N6
YHFZKNPKEVXLSM-UHFFFAOYSA-N
ZIQ
Query on ZIQ

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C],
P [auth D]
alpha-methyl-L-tryptophan
C12 H14 N2 O2
ZTTWHZHBPDYSQB-LBPRGKRZSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.959α = 90
b = 154.17β = 90
c = 88.277γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM115773
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM151419

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-21
    Type: Initial release
  • Version 1.1: 2024-09-04
    Changes: Database references
  • Version 1.2: 2024-09-11
    Changes: Database references