9C16 | pdb_00009c16

Human biliverdin IX beta reductase in complex with NADP and BCT002029

  • Classification: OXIDOREDUCTASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2024-05-28 Released: 2025-04-23 
  • Deposition Author(s): Kreitler, D.F.
  • Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 
    0.226 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Small molecule BLVRB redox inhibitor promotes megakaryocytopoiesis and stress thrombopoiesis in vivo.

Nesbitt, N.M.Araldi, G.L.Pennacchia, L.Marchenko, N.Assar, Z.Muzzarelli, K.M.Thekke Veedu, R.R.Medel-Lacruz, B.Lee, E.Eisenmesser, E.Z.Kreitler, D.F.Bahou, W.F.

(2025) Nat Commun 16: 3480-3480

  • DOI: https://doi.org/10.1038/s41467-025-58497-9
  • Primary Citation of Related Structures:  
    9C16, 9C17, 9C18

  • PubMed Abstract: 

    Biliverdin IXβ reductase (BLVRB) is an NADPH-dependent enzyme previously implicated in a redox-regulated mechanism of thrombopoiesis distinct from the thrombopoietin (TPO)/c-MPL axis. Here, we apply computational modeling to inform molecule design, followed by de novo syntheses and screening of unique small molecules retaining the capacity for selective BLVRB inhibition as a novel platelet-enhancing strategy. Two distinct classes of molecules are identified, and NMR spectroscopy and co-crystallization studies confirm binding modes within the BLVRB active site and ring stacking between the nicotinamide moiety of the NADP + cofactor. A diazabicyclo derivative displaying minimal off-target promiscuity and excellent bioavailability characteristics promotes megakaryocyte speciation in biphenotypic (erythro/megakaryocyte) cellular models and synergizes with TPO-dependent megakaryocyte formation in hematopoietic stem cells. Upon oral delivery into mice, this inhibitor expands platelet recovery in stress thrombopoietic models with no adverse effects. In this work, we identify and validate a cellular redox inhibitor retaining the potential to selectively promote megakaryocytopoiesis and enhance stress-associated platelet formation in vivo distinct from TPO receptor agonists.


  • Organizational Affiliation
    • Blood Cell Technologies, JLABS@NYC, New York, NY, USA. natasha@bloodcelltechnologies.com.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Flavin reductase (NADPH)210Homo sapiensMutation(s): 0 
Gene Names: BLVRBFLRSCAN
EC: 1.5.1.30 (PDB Primary Data), 1.3.1 (PDB Primary Data), 2.6.99 (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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
C [auth A]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
A1ATI (Subject of Investigation/LOI)
Query on A1ATI

Download Ideal Coordinates CCD File 
B [auth A](3M)-3-[(8R)-3-ethyl-7-oxo-2-phenyl-4,7-dihydropyrazolo[1,5-a]pyrimidin-5-yl]benzoic acid
C21 H17 N3 O3
BMSJJJWMBISUQX-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free:  0.226 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.091α = 90
b = 42.264β = 108.04
c = 66.148γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
PHASERphasing
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL150927
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL153144

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release