8IM2

Crystal structure of human HPPD complexed with NTBC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure-based discovery of pyrazole-benzothiadiazole hybrid as human HPPD inhibitors.

Dong, J.Xiao, H.Chen, J.N.Zheng, B.F.Xu, Y.L.Chen, M.X.Yang, W.C.Lin, H.Y.Yang, G.F.

(2023) Structure 31: 1604

  • DOI: https://doi.org/10.1016/j.str.2023.09.005
  • Primary Citation of Related Structures:  
    8IM2, 8IM3

  • PubMed Abstract: 

    4-Hydroxyphenylpyruvate dioxygenase (HPPD) has attracted increasing attention as a target for treating type I tyrosinemia and other diseases with defects in tyrosine catabolism. Only one commercial drug, 2-(2-nitro-4-trifluoromethylbenzoyl)-1, 3-cyclohexanedione (NTBC), clinically treat type I tyrosinemia, but show some severe side effects in clinical application. Here, we determined the structure of human HPPD-NTBC complex, and developed new pyrazole-benzothiadiazole 2,2-dioxide hybrids from the binding of NTBC. These compounds showed improved inhibition against human HPPD, among which compound a10 was the most active candidate. The Absorption Distribution Metabolism Excretion Toxicity (ADMET) predicted properties suggested that a10 had good druggability, and was with lower toxicity than NTBC. The structure comparison between inhibitor-bound and ligand-free form human HPPD showed a large conformational change of the C-terminal helix. Furthermore, the loop 1 and α7 helix were found adopting different conformations to assist the gating of the cavity, which explains the gating mechanism of human HPPD.


  • Organizational Affiliation

    National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, P.R.China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-hydroxyphenylpyruvate dioxygenase
A, B, C, D, E
A, B, C, D, E, F
393Homo sapiensMutation(s): 0 
Gene Names: HPDPPD
EC: 1.13.11.27
UniProt & NIH Common Fund Data Resources
Find proteins for P32754 (Homo sapiens)
Explore P32754 
Go to UniProtKB:  P32754
PHAROS:  P32754
GTEx:  ENSG00000158104 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32754
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NTD
Query on NTD

Download Ideal Coordinates CCD File 
H [auth A]
K [auth B]
N [auth C]
R [auth D]
T [auth E]
H [auth A],
K [auth B],
N [auth C],
R [auth D],
T [auth E],
W [auth F]
2-{HYDROXY[2-NITRO-4-(TRIFLUOROMETHYL)PHENYL]METHYLENE}CYCLOHEXANE-1,3-DIONE
C14 H10 F3 N O5
PMHVFNYNPNKNRO-UHFFFAOYSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
I [auth A]
L [auth B]
O [auth C]
P [auth D]
U [auth E]
I [auth A],
L [auth B],
O [auth C],
P [auth D],
U [auth E],
X [auth F]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
CO
Query on CO

Download Ideal Coordinates CCD File 
G [auth A]
J [auth B]
M [auth C]
Q [auth D]
S [auth E]
G [auth A],
J [auth B],
M [auth C],
Q [auth D],
S [auth E],
V [auth F]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.55α = 90
b = 147.442β = 97.12
c = 133.93γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-18
    Type: Initial release
  • Version 1.1: 2023-12-27
    Changes: Database references