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Amide Rings are small motifs in proteins and polypeptides. They consist of 9-atom or 11-atom rings formed by two CO...HN hydrogen bonds between a side chain amide group and the main chain atoms of a short polypeptide.[1] They are observed with glutamine or asparagine side chains within proteins and polypeptides. Structurally similar rings occur in the binding of purine, pyrimidine and nicotinamide bases to the main chain atoms of proteins. About 4% of asparagines and glutamines form amide rings; in databases of protein domain structures, one is present, on average, every other protein.
In such rings the polypeptide has the conformation of beta sheet or of type II polyproline helix (PPII). A number of glutamines and asparagines help bind short peptides (with the PPII conformation) in the groove of class II MHC (Major Histocompatibility Complex) proteins[2] by forming these motifs. An 11-atom amide ring, involving a glutamine residue, occurs at the interior of the light chain variable domains of some Immunoglobulin G antibodies and assists in linking the two beta-sheets.
An amide ring is employed in the specificity of the adaptor protein GRB2 for a particular asparagine within proteins it binds. GRB2 binds strongly to the pentapeptide EYINQ (when the tyrosine is phosphorylated); in such structures a 9-atom amide ring occurs between the amide side chain of the pentapeptide's asparagine and the main chain atoms of residue 109 of GRB2.[3]
^Le Questel, JY; Morris DG (1993). "Common ring motifs in proteins involving asparagine or glutamine groups hydrogen-bonded to main-chain atoms". Journal of Molecular Biology. 231 (3): 888–896. doi:10.1006/jmbi.1993.1335. PMID 8515458.
^Painter, CA; Negroni MP (2011). "Conformational Liability in Class II MHC 3/10-Helix". Proc Natl Acad Sci USA. 108 (48): 19329–19338. doi:10.1073/pnas.1108074108. PMC 3228433. PMID 22084083.
^Rahuel, J; Gay B (1996). "Structural basis for specificity of GRB-2-SH2 revealed by a novel ligand binding mode". Nat Struct Biol. 90 (7): 586–589. doi:10.1038/nsb0796-586. PMID 8673601. S2CID 1899970.
AmideRings are small motifs in proteins and polypeptides. They consist of 9-atom or 11-atom rings formed by two CO...HN hydrogen bonds between a side...
nicotinamide consists of a pyridine ring to which a primary amide group is attached in the meta position. It is an amide of nicotinic acid. As an aromatic...
cyclic amide, formally derived from an amino alkanoic acid through cyclization reactions. The term is a portmanteau of the words lactone + amide. Greek...
of the ring nitrogen and slow down the sorption on sodium amide, (2) these electron-withdrawing groups can also form complexes with sodium amide, and (3)...
hydrogen bond arrangement in parallel beta sheet resembles that in an amidering motif with 11 atoms. Finally, an individual strand may exhibit a mixed...
bicyclic ring systems containing a β-lactam moiety fused with a five-member thiazolidine ring. Due to ring strain and limitations on amide resonance...
benzene molecule is composed of six carbon atoms joined in a planar hexagonal ring with one hydrogen atom attached to each. Because it contains only carbon...
alpha-helices as asx turns and asx motifs, and in similar turn motifs, or as amiderings, in beta sheets. Its role can be thought as "capping" the hydrogen bond...
rearrangement also occurs without stereospecificity; the regioisomer formed has the amide nitrogen substituted with the group possessing the greatest migratory aptitude...
Chymotrypsin preferentially cleaves peptide amide bonds where the side chain of the amino acid N-terminal to the scissile amide bond (the P1 position) is a large...
amide – imidic acid: H−N−C=O ⇌ N=C−O−H (e.g., the latter is encountered during nitrile hydrolysis reactions) lactam – lactim, a cyclic form of amide-imidic...
of the amide bond reverses at each bond, all nylon 6 amide bonds lie in the same direction (see figure: note the N to C orientation of each amide bond)...
cyclohexene rings A and C that are connected by two short bridges creating an 8 membered ring in the middle (ring B). The third pre-assembled part is an amide tail...
name refers to the presence of aromatic rings of six carbon atoms. In aramids these rings are connected via amide linkages each comprising a CO group attached...
mechanism has been extensively studied in reactions of metal amide nucleophiles (such as sodium amide) and substituted pyrimidines (for instance 4-phenyl-6-bromopyrimidine...
carbonyl at the second position of the 5-member indoline ring. Classified as a cyclic amide, it is a pale yellow solid. Oxindole is derived in nature...
This loop is connected on its other end to the peripheral propionic amide group at ring D and consists of structural elements derived from aminopropanol...
Articaine is a dental amide-type local anesthetic. It is the most widely used local anesthetic in a number of European countries and is available in many...
substitution of one amine or amide anion on an amine or ammonium salt. For example, the attack of a primary amine by a primary amide anion can be used to prepare...
but usually either an alkoxide base or an amine to yield an ester or an amide, respectively. α,α'-Dihaloketones eliminate HX under the reaction conditions...
In organic chemistry, the phenyl group, or phenyl ring, is a cyclic group of atoms with the formula C6H5, and is often represented by the symbol Ph (archaically...
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