Human biliverdin IX beta reductase: NADP/Phloxine B ternary complex

Experimental Data Snapshot

  • Resolution: 1.33 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.117 
  • R-Value Observed: 0.118 

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This is version 1.4 of the entry. See complete history


In silicoand crystallographic studies identify key structural features of biliverdin IX beta reductase inhibitors having nanomolar potency.

Nesbitt, N.M.Zheng, X.Li, Z.Manso, J.A.Yen, W.Y.Malone, L.E.Ripoll-Rozada, J.Pereira, P.J.B.Mantle, T.J.Wang, J.Bahou, W.F.

(2018) J Biol Chem 293: 5431-5446

  • DOI: https://doi.org/10.1074/jbc.RA118.001803
  • Primary Citation of Related Structures:  
    5OOG, 5OOH

  • PubMed Abstract: 

    Heme cytotoxicity is minimized by a two-step catabolic reaction that generates biliverdin (BV) and bilirubin (BR) tetrapyrroles. The second step is regulated by two non-redundant biliverdin reductases (IXα (BLVRA) and IXβ (BLVRB)), which retain isomeric specificity and NAD(P)H-dependent redox coupling linked to BR's antioxidant function. Defective BLVRB enzymatic activity with antioxidant mishandling has been implicated in metabolic consequences of hematopoietic lineage fate and enhanced platelet counts in humans. We now outline an integrated platform of in silico and crystallographic studies for the identification of an initial class of compounds inhibiting BLVRB with potencies in the nanomolar range. We found that the most potent BLVRB inhibitors contain a tricyclic hydrocarbon core structure similar to the isoalloxazine ring of flavin mononucleotide and that both xanthene- and acridine-based compounds inhibit BLVRB's flavin and dichlorophenolindophenol (DCPIP) reductase functions. Crystallographic studies of ternary complexes with BLVRB-NADP + -xanthene-based compounds confirmed inhibitor binding adjacent to the cofactor nicotinamide and interactions with the Ser-111 side chain. This residue previously has been identified as critical for maintaining the enzymatic active site and cellular reductase functions in hematopoietic cells. Both acridine- and xanthene-based compounds caused selective and concentration-dependent loss of redox coupling in BLVRB-overexpressing promyelocytic HL-60 cells. These results provide promising chemical scaffolds for the development of enhanced BLVRB inhibitors and identify chemical probes to better dissect the role of biliverdins, alternative substrates, and BLVRB function in physiologically relevant cellular contexts.

  • Organizational Affiliation

    From the Departments of Medicine and natasha.nesbitt@stonybrook.edu.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Flavin reductase (NADPH)206Homo sapiensMutation(s): 0 
Gene Names: BLVRBFLR
EC: (PDB Primary Data), (PDB Primary Data)
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
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
A0B Binding MOAD:  5OOG IC50: 700 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.261α = 90
b = 49.474β = 90
c = 107.612γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
PORTUGAL 2020PortugalPOCI-01-0145-FEDER-007274
NORTE 2020PortugalNorte-01-0145-FEDER-000012

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2018-03-14
    Changes: Database references
  • Version 1.2: 2018-03-21
    Changes: Database references
  • Version 1.3: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.4: 2024-01-17
    Changes: Advisory, Data collection, Database references, Refinement description