5KDQ | pdb_00005kdq

Deoxyhemoglobin in Complex with an Aryloxyalkanoic acid

• PDB DOI: https://doi.org/10.2210/pdb5KDQ/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2016-06-08 Released: 2016-06-22 
• Deposition Author(s): Ahmed, M.H., Omar, A.M., Safo, M.K.
• Funding Organization(s): MAARIFAH, National Institutes of Health/National Institute on Minority Health and Health Disparities (NIH/NIMHD), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.257 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Aryloxyalkanoic Acids as Non-Covalent Modifiers of the Allosteric Properties of Hemoglobin.

Omar, A.M., Mahran, M.A., Ghatge, M.S., Bamane, F.H., Ahmed, M.H., El-Araby, M.E., Abdulmalik, O., Safo, M.K.

(2016) Molecules 21

• PubMed: 27529207 
• DOI: https://doi.org/10.3390/molecules21081057
• Primary Citation Related Structures: 
  5KDQ


• PubMed Abstract: 
  

  Hemoglobin (Hb) modifiers that stereospecifically inhibit sickle hemoglobin polymer formation and/or allosterically increase Hb affinity for oxygen have been shown to prevent the primary pathophysiology of sickle cell disease (SCD), specifically, Hb polymerization and red blood cell sickling. Several such compounds are currently being clinically studied for the treatment of SCD. Based on the previously reported non-covalent Hb binding characteristics of substituted aryloxyalkanoic acids that exhibited antisickling properties, we designed, synthesized and evaluated 18 new compounds (KAUS II series) for enhanced antisickling activities. Surprisingly, select test compounds showed no antisickling effects or promoted erythrocyte sickling. Additionally, the compounds showed no significant effect on Hb oxygen affinity (or in some cases, even decreased the affinity for oxygen). The X-ray structure of deoxygenated Hb in complex with a prototype compound, KAUS-23, revealed that the effector bound in the central water cavity of the protein, providing atomic level explanations for the observed functional and biological activities. Although the structural modification did not lead to the anticipated biological effects, the findings provide important direction for designing candidate antisickling agents, as well as a framework for novel Hb allosteric effectors that conversely, decrease the protein affinity for oxygen for potential therapeutic use for hypoxic- and/or ischemic-related diseases.

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Organizational Affiliation: 
• Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia. [e-mail].
Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Cairo 11884, Egypt. [e-mail].
Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt. [e-mail].
Department of Medicinal Chemistry, and The Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA. [e-mail].
Department of Biochemistry, Faculty of Medicine, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia. [e-mail].
Department of Medicinal Chemistry, and The Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA. [e-mail].
Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia. [e-mail].
Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Helwan University, Cairo 11790, Egypt. [e-mail].
Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA. [e-mail].
Department of Medicinal Chemistry, and The Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA. [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 65 kDa 
• Atom Count: 4,954 
• Modeled Residue Count: 574 
• Deposited Residue Count: 574 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha	A, C	141	Homo sapiens	Mutation(s): 0  Gene Names: HBA1, HBA2
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens) Explore P69905  Go to UniProtKB:  P69905
PHAROS:  P69905 GTEx:  ENSG00000188536 ENSG00000206172

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], H [auth B], I [auth C], K [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
KOH	J [auth C]	3-[2-chloranyl-4-(1~{H}-imidazol-2-yl)phenoxy]propanoic acid C12 H11 Cl N2 O3 JDFUCVHWLSVLIA-UHFFFAOYSA-N
PO4	F [auth A], G [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.257 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.222	α = 90
b = 80.83	β = 80.77
c = 53.397	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-06-22 
Deposition Author(s): Ahmed, M.H., Omar, A.M., Safo, M.K.

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Funding Organization	Location	Grant Number
MAARIFAH	Saudi Arabia	BIO1253-03-10
National Institutes of Health/National Institute on Minority Health and Health Disparities (NIH/NIMHD)	United States	MD009124
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	K01HL103186
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA16059

Revision History  

• Version 1.0: 2016-06-22
  Type: Initial release
  
• Version 1.1: 2016-08-31
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description