5OOG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.117 
  • R-Value Observed: 0.118 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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

  • 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 isome ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Flavin reductase (NADPH)A206Homo sapiensMutation(s): 0 
Gene Names: BLVRBFLR
EC: 1.5.1.30 (PDB Primary Data), 1.3.1.24 (PDB Primary Data)
Find proteins for P30043 (Homo sapiens)
Explore P30043 
Go to UniProtKB:  P30043
NIH Common Fund Data Resources
PHAROS  P30043
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A0B
Query on A0B

Download CCD File 
A
Phloxine B
C20 H3 Br4 Cl4 O5
RIVZUHBWXRGVOG-UHFFFAOYSA-M
 Ligand Interaction
NAP
Query on NAP

Download CCD File 
A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
A0BIC50:  700   nM  Binding MOAD
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
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History 

  • 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