Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 65836.34 
• Atom Count: 4646 
• Residue Count: 574 
• Unique protein chains: 2

1K0Y

X-ray Crystallographic Analyses of Symmetrical Allosteric Effectors of Hemoglobin. Compounds Designed to Link Primary and Secondary Binding Sites

• DOI: 10.2210/pdb1K0Y/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Homo sapiens


• Deposited: 2001-09-21 Released: 2001-10-03 
• Deposition Author(s): Safo, M.K., Boyiri, T., Burnett, J.C., Danso-Danquah, R., Moure, C.M., Joshi, G.S., Abraham, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.189 
• R-Value Work: 0.163 

Literature

X-ray crystallographic analyses of symmetrical allosteric effectors of hemoglobin: compounds designed to link primary and secondary binding sites.

Safo, M.K., Boyiri, T., Burnett, J.C., Danso-Danquah, R., Moure, C.M., Joshi, G.S., Abraham, D.J.

(2002) Acta Crystallogr.,Sect.D 58: 634-644

• PubMed: 11914488 


• PubMed Abstract: 
  

The rational design and X-ray crystallographic analyses of two symmetrical allosteric effectors of hemoglobin (Hb) are reported. Compound design was directed by the previously solved co-crystal structure of one of the most potent allosteric effectors of Hb, 2-[4-[(3,5-dichlorophenylcarbamoyl)-methyl]-phenoxy]-2-methylpropionic acid (RSR4), which revealed two distinct binding sites for this compound in the Hb central water cavity. The primary binding site has been observed for all compounds of this structural class, which stabilize deoxy Hb by engaging in inter-dimer contacts with three of the four protein subunits. Interactions at the secondary binding site of RSR4 occur primarily between the beta(1) and beta(2) subunits and serve to further constrain the deoxy state. Based on these observations, it was hypothesized that compounds with the ability to simultaneously span and link both of these sites would possess increased potency, but at a lower molar concentration than RSR4. Two symmetrical compounds were designed and synthesized based on this hypothesis. The symmetrical effector approach was taken to minimize the number of compound orientations needed to successfully bind at either of the distinct allosteric sites. X-ray crystallographic analyses of these two effectors in complex with Hb revealed that they successfully spanned the RSR4 primary and secondary binding sites. However, the designed compounds interacted with the secondary binding site in such a way that intra-dimer, as opposed to inter-dimer, interactions were generated. In agreement with these observations, in vitro evaluation of the symmetrical effectors in Hb solution indicated that neither compound possessed the potency of RSR4. A detailed analysis of symmetrical effector-Hb contacts and comparisons with the binding contacts of RSR4 are discussed.

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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 23298-0540, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
hemoglobin alpha chain	A, C	141	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
hemoglobin beta chain	B, D	146	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	B, D	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
HEM	A, B, C, D	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
CNO	D	2-{4-[(3{2-[4-(1-CARBOXY-1-METHYL-ETHOXY)-PHENYL]-ACETYLAMINO}-PHENYLCARBAMOYL)-METHYL]-PHENOXY}-2-METHYL-PROPIONIC ACID C30 H32 N2 O8 QRJRPWUABHMWAG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.189 
• R-Value Work: 0.163 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 63.280	α = 90.00
b = 83.790	β = 99.33
c = 53.800	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	refinement
X-PLOR	model building
X-PLOR	phasing
CCP4	data scaling
BIOTEX	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-09-21 
• Released Date: 2001-10-03 
• Deposition Author(s): Safo, M.K., Boyiri, T., Burnett, J.C., Danso-Danquah, R., Moure, C.M., Joshi, G.S., Abraham, D.J.

Revision History 

• Version 1.0: 2001-10-03
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance