8K4K

Crystal structure of human Biliverdin IX-beta reductase B with Olsalazine carbon derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.192 (Depositor), 0.191 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 
    0.163 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

An Innovative Inhibitor with a New Chemical Moiety Aimed at Biliverdin IX beta Reductase for Thrombocytopenia and Resilient against Cellular Degradation.

Jung, H.M.Ha, J.H.Dela Cerna, M.V.C.Burlison, J.A.Choi, J.Kim, B.R.Bang, J.K.Ryu, K.S.Lee, D.

(2024) Pharmaceutics 16

  • DOI: https://doi.org/10.3390/pharmaceutics16091148
  • Primary Citation of Related Structures:  
    8K4K

  • PubMed Abstract: 

    Biliverdin IXβ reductase (BLVRB) has emerged as a promising therapeutic target for thrombocytopenia due to its involvement in reactive oxygen species (ROS) mechanisms. During the pursuit of inhibitors targeting BLVRB, olsalazine (OSA) became apparent as one of the most potent candidates. However, the direct application of OSA as a BLVRB inhibitor faces challenges, as it is prone to degradation into 5-aminosalicylic acid through cleavage of the diazenyl bond by abundant azoreductase (AzoR) enzymes in gut microbiota and eukaryotic cells. To overcome this obstacle, we devised olsalkene (OSK), an inhibitor where the diazenyl bond in OSA has been substituted with an alkene bond. OSK not only matches the efficacy of OSA but also demonstrates improved stability against degradation by AzoR, presenting a promising solution to this limitation. Furthermore, we have found that both OSK and OSA inhibit BLVRB, regardless of the presence of nicotinamide adenine dinucleotide phosphate, unlike other known inhibitors. This discovery opens new avenues for investigating the roles of BLVRB in blood disorders, including thrombocytopenia.


  • Organizational Affiliation

    Korea Basic Science Institute, 162 Yeongudanji-Ro, Ochang-Eup, Cheongju-Si 28119, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Flavin reductase (NADPH)
A, B
206Homo sapiensMutation(s): 0 
Gene Names: BLVRBFLR
EC: 1.5.1.30 (PDB Primary Data), 1.3.1.24 (PDB Primary Data), 2.6.99 (UniProt), 1.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P30043 (Homo sapiens)
Explore P30043 
Go to UniProtKB:  P30043
PHAROS:  P30043
GTEx:  ENSG00000090013 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30043
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
VE2 (Subject of Investigation/LOI)
Query on VE2

Download Ideal Coordinates CCD File 
H [auth A],
K [auth B]
5-[(E)-2-(3-carboxy-4-oxidanyl-phenyl)ethenyl]-2-oxidanyl-benzoic acid
C16 H12 O6
SEOGGUVUVSSDJX-OWOJBTEDSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
I [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.192 (Depositor), 0.191 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 0.163 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.143α = 90
b = 117.304β = 90
c = 41.559γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted VE2Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentKorea, Republic OfC320000
National Research Foundation (NRF, Korea)Korea, Republic Of2023R1A2C1006973
National Research Foundation (NRF, Korea)Korea, Republic Of2022H1D3A2A02093655

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release
  • Version 1.1: 2025-01-29
    Changes: Database references