6BWU

Crystal structure of carboxyhemoglobin in complex with beta Cys93 modifying agent, TD3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Triazole Disulfide Compound Increases the Affinity of Hemoglobin for Oxygen and Reduces the Sickling of Human Sickle Cells.

Nakagawa, A.Ferrari, M.Schleifer, G.Cooper, M.K.Liu, C.Yu, B.Berra, L.Klings, E.S.Safo, R.S.Chen, Q.Musayev, F.N.Safo, M.K.Abdulmalik, O.Bloch, D.B.Zapol, W.M.

(2018) Mol. Pharm. 15: 1954-1963

  • DOI: 10.1021/acs.molpharmaceut.8b00108
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Sickle cell disease is an inherited disorder of hemoglobin (Hb). During a sickle cell crisis, deoxygenated sickle hemoglobin (deoxyHbS) polymerizes to form fibers in red blood cells (RBCs), causing the cells to adopt "sickled" shapes. Using small mol ...

    Sickle cell disease is an inherited disorder of hemoglobin (Hb). During a sickle cell crisis, deoxygenated sickle hemoglobin (deoxyHbS) polymerizes to form fibers in red blood cells (RBCs), causing the cells to adopt "sickled" shapes. Using small molecules to increase the affinity of Hb for oxygen is a potential approach to treating sickle cell disease, because oxygenated Hb interferes with the polymerization of deoxyHbS. We have identified a triazole disulfide compound (4,4'-di(1,2,3-triazolyl)disulfide, designated TD-3), which increases the affinity of Hb for oxygen. The crystal structures of carboxy- and deoxy-forms of human adult Hb (HbA), each complexed with TD-3, revealed that one molecule of the monomeric thiol form of TD-3 (5-mercapto-1H-1,2,3-triazole, designated MT-3) forms a disulfide bond with β-Cys93, which inhibits the salt-bridge formation between β-Asp94 and β-His146. This inhibition of salt bridge formation stabilizes the R-state and destabilizes the T-state of Hb, resulting in reduced magnitude of the Bohr effect and increased affinity of Hb for oxygen. Intravenous administration of TD-3 (100 mg/kg) to C57BL/6 mice increased the affinity of murine Hb for oxygen, and the mice did not appear to be adversely affected by the drug. TD-3 reduced in vitro hypoxia-induced sickling of human sickle RBCs. The percentage of sickled RBCs and the P 50 of human SS RBCs by TD-3 were inversely correlated with the fraction of Hb modified by TD-3. Our study shows that TD-3, and possibly other triazole disulfide compounds that bind to Hb β-Cys93, may provide new treatment options for patients with sickle cell disease.


    Organizational Affiliation

    Division of Rheumatology, Allergy and Immunology, Department of Medicine , Massachusetts General Hospital and Harvard Medical School , Boston , Massachusetts 02114 , United States.,Division of Hematology , The Children's Hospital of Philadelphia , Philadelphia , Pennsylvania 19104 , United States.,Anesthesia Center for Critical Care Research, Department of Anesthesia, Critical Care, and Pain Medicine , Massachusetts General Hospital and Harvard Medical School , Boston , Massachusetts 02114 , United States.,Department of Medicinal Chemistry, The Institute for Structural Biology, Drug Discovery, and Development, School of Pharmacy , Virginia Commonwealth University , Richmond , Virginia 23298 , United States.,The Pulmonary Center , Boston University School of Medicine , Boston , Massachusetts 02118 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit alpha
A
141Homo sapiensMutation(s): 0 
Gene Names: HBA1, HBA2
Find proteins for P69905 (Homo sapiens)
Go to Gene View: HBA1 HBA2
Go to UniProtKB:  P69905
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit beta
B
146Homo sapiensMutation(s): 0 
Gene Names: HBB
Find proteins for P68871 (Homo sapiens)
Go to Gene View: HBB
Go to UniProtKB:  P68871
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EBJ
Query on EBJ

Download SDF File 
Download CCD File 
B
1H-1,2,3-triazole-5-thiol
C2 H3 N3 S
LLCOQBODWBFTDD-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CMO
Query on CMO

Download SDF File 
Download CCD File 
A, B
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.198 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 53.300α = 90.00
b = 53.300β = 90.00
c = 191.966γ = 90.00
Software Package:
Software NamePurpose
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2018-01-03
    Type: Initial release
  • Version 1.1: 2018-01-17
    Type: Author supporting evidence
  • Version 1.2: 2019-01-16
    Type: Data collection, Database references