3-D interactive structures of Biological molecules

in JSMol format

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CARBOHYDRATES
Monosaccharides
hexoses	glucose	alpha and beta glucose
hexoses	fructose	glucose-galactose comparison
pentoses	ribose	deoxyribose
glucose derivatives	glucosamine	N acetyl glucosamine
Disaccharides
glucose dimers	maltose	cellobiose
mixed dimers	sucrose	lactose
Oligosaccharides
fructo-oligosaccharides	nystose	inulin
Polysaccharides
storage compounds - animal	glycogen
storage compounds - plants	amylose [another form of amylose]	amylopectin
structural compounds - plants	cellulose
starch-iodine test	amylose-iodide complex
AMINO ACIDS
All shown on one page	20 amino acids
Individual amino acids - seen a little larger	glycine, alanine, valine, leucine, isoleucine, serine, threonine, lysine, histidine, arginine, phenylalanine, tyrosine, tryptophan, cysteine, methionine, aspartic acid, asparagine, glutamic acid, glutamine, proline
DIPEPTIDE
Special request	Leucine-alanine
PROTEINS
Levels of protein structure	General principles	as shown by Insulin
	as shown by Glucagon, Fibroin	as shown by hCG
	as shown by Haemoglobin	as shown by Myoglobin
Enzyme structure	Amylase as an example Pepsin Pepsinogen	More to be added soon
Fibrous proteins	Collagen	Keratin
LIPIDS (FATS and OILS)
Sub-units	glycerol	saturated and unsaturated fatty acids
Polyunsaturated fatty acids	alpha-linolenic acid	gamma-linolenic acid
More about functional foods	plant sterols and stanols and their esters
Neutral fats	triglycerides	monoglycerides and diglycerides
	phospholipids	phospholipid bilayer
	cardiolipin
Sterols and steroids	cholesterol	More to follow
NUCLEIC ACIDS
Section	DNA
nucleotides	AMP, TMP pair	GMP, CMP pair
bases	DNA bases	RNA bases
co-enzymes	ATP Coenzyme A	NAD and reduced NAD
Nucleoside analogues	Emtricitabine Tenofovir	AZT Fialuridine XXX
Base analogues	5-FluoroUracil (5FU)
Nucleotide analogues	Remdesivir	Molnupiravir
Non-nucleoside reverse transcriptase inhibitor ( NNRTI)	Efavirenz
Coronavirus protease inhibitors	Paxlovid	Ritonavir

VITAMINS
Fat Soluble	Vitamin A	Water Soluble	Vitamin B1
	Retinal		Vitamin B2
			Vitamin B3
	Vitamin D		Vitamin B5
			Vitamin B6
	Vitamin E		Vitamin B7
			Vitamin B9
	Vitamin K		Vitamin B12
			Vitamin C

ANTIBIOTICS

Beta Lactams	Examples
Penicillins (Penems)	Penicillin G Amoxicillin Ampicillin Methicillin
Cephalosporins (Cephems)	Cephalexin
Monolactams	Aztreonam
Carbapenems	Meropenem
Beta-lactamase inhibitors	Clavulanic acid

Other categories of antibiotic	Examples
Macrolides	Erythromycin
Tetracyclines	Lymecycline
Quinolones	Ciprofloxacin
Aminoglycosides	Streptomycin
Sulfonamides	Sulfamethoxazole
Diaminopyrimidine	Trimethoprim
Glycopeptide	Vancomycin
Oxazolidinone	Linezolid
Lipopeptide	Daptomycin
Depsipeptide	Teixobactin
Cyclic peptide	Lugdunin
2-Amino-1,3,4-thiadiazole	Halicin

*Other molecules of biological interest*
Carotene	Caffeine	A fungal product
Antimalarial compounds	Taxol	Anti-Tuberculosis Drugs
Chlorophyll	Artificial sweeteners	Stevioside
Paracetamol	Opiates, opioids and cannabinoids	Oxycodone (OxyContin)
Salicin and Aspirin	Capsaicin	Salbutamol, terbutamine, adrenaline and triamcinolone
Acetyl choline	AZT	Blank Canvas

*Water*
Water molecule	Hydrogen bonds in water	Water - moving molecules	Structure of ice

More molecules to be added in the near future
Please get in touch with any suggestions for candidate compounds (or categories)

Web references and useful websites
The Protein Data Bank (PDB; https://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules, now containing more than 100,000 structures.

Structural View of Biology is a portion of the PDB, focusing on the biological function of the molecules.

Orientations of Proteins in Membranes (OPM) database "provides spatial arrangements of membrane proteins with respect to the hydrocarbon core of the lipid bilayer."

FirstGlance in Jmol is a simple tool for macromolecular visualization.

ChemInteractive is a free site designed to promote active learning of Chemistry. It is targeted at students learning Organic Chemistry in the early years of College or University programmes.

The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.

ChemSpider is a free chemical structure database owned by the Royal Society of Chemistry.

Jmol/JSmol interactive scripting documentation

An Introduction to Jmol* Scripting Nathan Silva and David Marcey

Possibly relevant
material available online
(from Amazon.com)

Possibly relevant
material available online
(from Amazon.co.uk)

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3-D interactive structures of Biological molecules

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Web references and useful websites