7ERE

Crystal structure of human Biliverdin IX-beta reductase B with Pyrantel Pamoate (PPA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Repositioning Food and Drug Administration-Approved Drugs for Inhibiting Biliverdin IX beta Reductase B as a Novel Thrombocytopenia Therapeutic Target.

Kim, M.Ha, J.H.Choi, J.Kim, B.R.Gapsys, V.Lee, K.O.Jee, J.G.Chakrabarti, K.S.de Groot, B.L.Griesinger, C.Ryu, K.S.Lee, D.

(2022) J Med Chem 65: 2548-2557

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01664
  • Primary Citation of Related Structures:  
    7ER6, 7ER7, 7ER8, 7ER9, 7ERA, 7ERB, 7ERC, 7ERD, 7ERE

  • PubMed Abstract: 

    Biliverdin IXβ reductase B (BLVRB) has recently been proposed as a novel therapeutic target for thrombocytopenia through its reactive oxygen species (ROS)-associated mechanism. Thus, we aim at repurposing drugs as new inhibitors of BLVRB. Based on IC 50 (<5 μM), we have identified 20 compounds out of 1496 compounds from the Food and Drug Administration (FDA)-approved library and have clearly mapped their binding sites to the active site. Furthermore, we show the detailed BLVRB-binding modes and thermodynamic properties (Δ H , Δ S , and K D ) with nuclear magnetic resonance (NMR) and isothermal titration calorimetry together with complex structures of eight water-soluble compounds. We anticipate that the results will serve as a novel platform for further in-depth studies on BLVRB effects for related functions such as ROS accumulation and megakaryocyte differentiation, and ultimately treatments of platelet disorders.


  • Organizational Affiliation

    Protein Structure Research Team, Korea Basic Science Institute, 162 Yeongudanji-Ro, Ochang-Eup, Cheongju-Si, Chungcheongbuk-Do 28119, South Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Flavin reductase (NADPH)
A, B, C, D
207Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
L [auth C],
O [auth D]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
JBR (Subject of Investigation/LOI)
Query on JBR

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
M [auth C],
P [auth D]
4-[(3-carboxy-2-oxidanyl-naphthalen-1-yl)methyl]-3-oxidanyl-naphthalene-2-carboxylic acid
C23 H16 O6
WLJNZVDCPSBLRP-UHFFFAOYSA-N
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
K [auth B]
N [auth C]
Q [auth D]
H [auth A],
J [auth B],
K [auth B],
N [auth C],
Q [auth D],
R [auth D],
S [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
JBR BindingDB:  7ERE Kd: 1800 (nM) from 1 assay(s)
-TΔS: -4.53e+0 (kJ/mol) from 1 assay(s)
ΔH: -2.83e+1 (kJ/mol) from 1 assay(s)
ΔG: -3.28e+1 (kJ/mol) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.982α = 90
b = 117.381β = 90
c = 81.97γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHENIXmodel building
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-19
    Type: Initial release
  • Version 1.1: 2022-02-23
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description