5E83 | pdb_00005e83

CRYSTAL STRUCTURE OF CARBONMONOXY HEMOGLOBIN S (LIGANDED SICKLE CELL HEMOGLOBIN) COMPLEXED WITH GBT440, CO-CRYSTALLIZATION EXPERIMENT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.207 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history

Literature

GBT440 increases haemoglobin oxygen affinity, reduces sickling and prolongs RBC half-life in a murine model of sickle cell disease.

Oksenberg, D.Dufu, K.Patel, M.P.Chuang, C.Li, Z.Xu, Q.Silva-Garcia, A.Zhou, C.Hutchaleelaha, A.Patskovska, L.Patskovsky, Y.Almo, S.C.Sinha, U.Metcalf, B.W.Archer, D.R.

(2016) Br J Haematol 175: 141-153

  • DOI: https://doi.org/10.1111/bjh.14214
  • Primary Citation Related Structures: 
    5E83

  • PubMed Abstract: 

    A major driver of the pathophysiology of sickle cell disease (SCD) is polymerization of deoxygenated haemoglobin S (HbS), which leads to sickling and destruction of red blood cells (RBCs) and end-organ damage. Pharmacologically increasing the proportion of oxygenated HbS in RBCs may inhibit polymerization, prevent sickling and provide long term disease modification. We report that GBT440, a small molecule which binds to the N-terminal α chain of Hb, increases HbS affinity for oxygen, delays in vitro HbS polymerization and prevents sickling of RBCs. Moreover, in a murine model of SCD, GBT440 extends the half-life of RBCs, reduces reticulocyte counts and prevents ex vivo RBC sickling. Importantly, oral dosing of GBT440 in animals demonstrates suitability for once daily dosing in humans and a highly selective partitioning into RBCs, which is a key therapeutic safety attribute. Thus, GBT440 has the potential for clinical use as a disease-modifying agent in sickle cell patients.


  • Organizational Affiliation
    • Global Blood Therapeutics Inc., South San Francisco, CA, USA. doksenberg@globalbloodtx.com.

Macromolecule Content 

  • Total Structure Weight: 65.3 kDa 
  • Atom Count: 5,064 
  • Modeled Residue Count: 574 
  • Deposited Residue Count: 574 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemoglobin subunit alpha
A, C
141Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens)
Explore P69905 
Go to UniProtKB:  P69905
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69905
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemoglobin subunit beta
B, D
146Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens)
Explore P68871 
Go to UniProtKB:  P68871
PHAROS:  P68871
GTEx:  ENSG00000244734 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68871
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B],
K [auth C],
N [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
5L7

Query on 5L7



Download:Ideal Coordinates CCD File
G [auth A]2-methyl-3-({2-[1-(propan-2-yl)-1H-pyrazol-5-yl]pyridin-3-yl}methoxy)phenol
C19 H21 N3 O2
PHGVAPZBZABAJF-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
H [auth A],
P [auth D],
Q [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CMO

Query on CMO



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B],
L [auth C],
O [auth D]
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
UNL

Query on UNL



Download:Ideal Coordinates CCD File
M [auth C]Unknown ligand
UGFAIRIUMAVXCW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.207 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.777α = 90
b = 59.104β = 90
c = 170.26γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Database references
  • Version 1.2: 2016-10-05
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.4: 2018-08-29
    Changes: Data collection, Database references, Structure summary
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.6: 2024-11-20
    Changes: Structure summary