7ER8

Crystal structure of human Biliverdin IX-beta reductase B with Sulfasalazine (SAS)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 
    0.199 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAPClick on this verticalbar to view detailsBest fitted SASClick on this verticalbar to view detailsBest fitted SO4Click on this verticalbar to view details

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
216Homo 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 
C [auth A],
G [auth B]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
SAS (Subject of Investigation/LOI)
Query on SAS

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
2-HYDROXY-(5-([4-(2-PYRIDINYLAMINO)SULFONYL]PHENYL)AZO)BENZOIC ACID
C18 H14 N4 O5 S
NCEXYHBECQHGNR-QZQOTICOSA-N
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth B],
J [auth B],
K [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
SAS BindingDB:  7ER8 Kd: min: 437, max: 440 (nM) from 2 assay(s)
-TΔS: 3.28 (kJ/mol) from 1 assay(s)
ΔH: -3.95e+1 (kJ/mol) from 1 assay(s)
ΔG: -3.63e+1 (kJ/mol) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free:  0.199 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.16α = 90
b = 117.367β = 90
c = 41.606γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PHENIXmodel building
PHASERphasing
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 NAPClick on this verticalbar to view detailsBest fitted SASClick on this verticalbar to view detailsBest fitted SO4Click on this verticalbar to view details

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