Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Pseudo Symmetry: Dihedral - D2  (3D View)
Pseudo Stoichiometry: Homo 4-mer - A4 Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 8-mer - A4B4 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 8-mer - A8 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 8-mer - A4B4 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 8-mer - A8 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 65.60 kDa 
• Atom Count: 5152 
• Residue Count: 574 
• Unique protein chains: 2

1QXE

Structural Basis for the Potent Antisickling Effect of a Novel Class of 5-Membered Heterocyclic Aldehydic Compounds

• DOI: 10.2210/pdb1QXE/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2003-09-05 Released: 2003-09-16 
• Deposition Author(s): Safo, M.K., Abdulmalik, O., Danso-Danquah, R., Nokuri, S., Joshi, G.S., Musayev, F.N., Asakura, T., Abraham, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.223 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 

Literature

Structural basis for the potent antisickling effect of a novel class of five-membered heterocyclic aldehydic compounds

Safo, M.K., Abdulmalik, O., Danso-Danquah, R., Burnett, J.C., Nokuri, S., Joshi, G.S., Musayev, F.N., Asakura, T., Abraham, D.J.

(2004) J Med Chem 47: 4665-4676

• PubMed: 15341482 
• DOI: 10.1021/jm0498001
• Primary Citation of Related Structures:  
  1QXE, 1QXD


• PubMed Abstract: 
  

Naturally occurring five-membered heterocyclic aldehydes, including 5-hydroxymethyl-2-furfural, increase the oxygen affinity of hemoglobin (Hb) and strongly inhibit the sickling of homozygous sickle red blood (SS) cells. X-ray studies of Hb complexed with these compounds indicate that they form Schiff base adducts in a symmetrical fashion with the N-terminal alphaVal1 nitrogens of Hb. Interestingly, two cocrystal types were isolated during crystallization experiments with deoxygenated Hb (deoxyHb): one crystal type was composed of the low-affinity or tense (T) state Hb quaternary structure; the other crystal type was composed of high-affinity or relaxed state Hb (with a R2 quaternary structure). The R2 crystal appears to be formed as a result of the aldehydes binding to fully or partially ligated Hb in the deoxyHb solution. Repeated attempts to crystallize the compounds with liganded Hb failed, except on rare occasions when very few R state crystals were obtained. Oxygen equilibrium, high performance liquid chromatography (HPLC), antisickling, and X-ray studies suggest that the examined heterocyclic aldehydes may be acting to prevent polymerization of sickle hemoglobin (HbS) by binding to and stabilizing liganded Hb in the form of R2 and/or various relaxed state Hbs, as well as binding to and destabilizing unliganded T state Hb. The proposed mechanism may provide a general model for the antisickling effects of aldehyde containing small molecules that bind to N-terminal alphaVal1 nitrogens of Hb. The examined compounds also represent a new class of potentially therapeutic agents for treating sickle cell disease (SCD).

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Organizational Affiliation: 

Department of Medicinal Chemistry, School of Pharmacy and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia 23298, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin alpha chain	A, C	141	Homo sapiens	Mutation(s): 0  Gene Names: HBA1, HBA2
Find proteins for P69905 (Homo sapiens) Explore P69905  Go to UniProtKB:  P69905
NIH Common Fund Data Resources
PHAROS  P69905 GTEx  ENSG00000188536GTEx  ENSG00000206172

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin beta chain	B, D	146	Homo sapiens	Mutation(s): 0  Gene Names: HBB
Find proteins for P68871 (Homo sapiens) Explore P68871  Go to UniProtKB:  P68871
NIH Common Fund Data Resources
PHAROS  P68871 GTEx  ENSG00000244734

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	A, B, C, D	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
FUX	A, C	5-HYDROXYMETHYL-FURFURAL C6 H6 O3 NOEGNKMFWQHSLB-UHFFFAOYSA-N
SO4	A, B, C, D	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
OXY	A, B, C, D	OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.223 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.857	α = 90
b = 91.857	β = 90
c = 143.53	γ = 120

Software Package:

Software Name	Purpose
bioteX	data collection
bioteX	data reduction
CNS	refinement
bioteX	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-09-05 
• Released Date: 2003-09-16 
Deposition Author(s): Safo, M.K., Abdulmalik, O., Danso-Danquah, R., Nokuri, S., Joshi, G.S., Musayev, F.N., Asakura, T., Abraham, D.J.

Revision History 

• Version 1.0: 2003-09-16
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description