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
Mutation(s): No

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free: 0.189
R-Value Work: 0.163
R-Value Observed: 0.164

wwPDB Validation3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 D Biol Crystallogr 58: 634-644

PubMed: 11914488 Search on PubMed
DOI: 10.1107/s0907444902002627
Primary Citation of Related Structures:
1K0Y

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.

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. msafo@hsc.vcu.edu

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

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
Protein Feature View Expand
( Mouse scroll to zoom / Hold left click to move ) Reference Sequence

Find similar proteins by:

(by identity cutoff) | Structure

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
Protein Feature View Expand
( Mouse scroll to zoom / Hold left click to move ) Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download CCD File	A, B, C, D	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Ligand Interaction
CNO Query on CNO Download CCD File	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		Ligand Interaction
SO4 Query on SO4 Download CCD File	B, D	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction