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3-D interactive structures of Biological molecules

in JSMol format _

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CARBOHYDRATES
Monosaccharides
hexoses glucose alpha and beta glucose
fructose glucose-galactose comparison
pentoses ribose deoxyribose
glucose derivatives glucosamine N acetyl glucosamine
Disaccharides
glucose dimers maltose cellobiose
trehalose
mixed dimers sucrose lactose
hyaluronic acid
Oligosaccharides
fructo-oligosaccharides nystose inulin
Polysaccharides
storage compounds - animal glycogen
storage compounds - plants amylose [another form of amylose] amylopectin
structural compounds - plants cellulose
structural compounds - fungi and arthropods chitin
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 proteinsCollagenKeratin
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  
nucleotidesAMP, 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
Medicinal compounds Salicin and Aspirin Non Steroidal Anti Inflammatory Drugs (NSAIDs)
Opiates, opioids
and cannabinoids		 Oxycodone (OxyContin)
Antimalarial compounds  Anti-Tuberculosis Drugs
Paracetamol Taxol
Salbutamol, terbutamine,
adrenaline and triamcinolone		 A fungal product
Category C Capsaicin Carotene
Caffeine Chlorophyll
Sweet stuff Artificial sweeteners Stevioside
Others Acetyl choline AZT
AND MORE Blank Canvas Phenoxy herbicide molecules
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.

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




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