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PsychedeliaDokholyan Laboratory
Plate VTwo ways of grouping

Families

A compound can be filed by what it is or by what it does, and the two answers disagree in interesting places. Both groupings are here, and neither is written by this project: the structural one is derived from the molecule, and the pharmacological one is quoted from MeSH. There is no hand-written taxonomy on this page.

I · Pharmacological class

What they do

Assigned by MeSH — the U.S. National Library of Medicine’s controlled vocabulary — and read from PubChem, never inferred here. Each class links to its MeSH descriptor and carries NLM’s own definition.

72 of 545 displayable compounds carry at least one MeSH pharmacological class, across 58 distinct classes. Membership is multi-label: LSD is filed as both a hallucinogen and a serotonin receptor agonist, so the counts below sum to more than the number of compounds. Percentages are stated against the classified set, not the archive.

  1. 0128% of classified

    Drugs capable of inducing illusions, hallucinations, delusions, paranoid ideations, and other alterations of mood and thinking. Despite the name, the feature that distinguishes these agents… from other classes of drugs is their capacity to induce states of altered perception, thought, and feeling that are not experienced otherwise.

  2. 0218% of classified

    Endogenous compounds and drugs that bind to and activate SEROTONIN RECEPTORS. Many serotonin receptor agonists are used as ANTIDEPRESSANTS; ANXIOLYTICS; and in the treatment of MIGRAINE… DISORDERS.

  3. 0310% of classified

    Drugs that bind to but do not activate excitatory amino acid receptors, thereby blocking the actions of agonists.

  4. 046% of classified

    Drugs intended to prevent damage to the brain or spinal cord from ischemia, stroke, convulsions, or trauma. Some must be administered before the event, but others may be effective for some… time after. They act by a variety of mechanisms, but often directly or indirectly minimize the damage produced by endogenous excitatory amino acids.

  5. 056% of classified

    Drugs that stimulate contraction of the myometrium. They are used to induce LABOR, OBSTETRIC at term, to prevent or control postpartum or postabortion hemorrhage, and to assess fetal status… in high risk pregnancies. They may also be used alone or with other drugs to induce abortions (ABORTIFACIENTS). Oxytocics used clinically include the neurohypophyseal hormone OXYTOCIN and certain prostaglandins and ergot alkaloids. (From AMA Drug Evaluations, 1994, p1157)

  6. 066% of classified

    Drugs used for their effects on serotonergic systems. Among these are drugs that affect serotonin receptors, the life cycle of serotonin, and the survival of serotonergic neurons.

  7. 076% of classified

    Drugs that bind to but do not activate serotonin receptors, thereby blocking the actions of serotonin or SEROTONIN RECEPTOR AGONISTS.

  8. 084% of classified

    Drugs that block the transport of adrenergic transmitters into axon terminals or into storage vesicles within terminals. The tricyclic antidepressants (ANTIDEPRESSIVE AGENTS, TRICYCLIC) and… amphetamines are among the therapeutically important drugs that may act via inhibition of adrenergic transport. Many of these drugs also block transport of serotonin.

  9. 094% of classified

    Compounds capable of relieving pain without the loss of CONSCIOUSNESS.

  10. 104% of classified

    A subclass of analgesic agents that typically do not bind to OPIOID RECEPTORS and are not addictive. Many non-narcotic analgesics are offered as NONPRESCRIPTION DRUGS.

  11. 114% of classified

    Intravenous anesthetics that induce a state of sedation, immobility, amnesia, and marked analgesia. Subjects may experience a strong feeling of dissociation from the environment. The… condition produced is similar to NEUROLEPTANALGESIA, but is brought about by the administration of a single drug. (From Gilman et al., Goodman and Gilman's The Pharmacological Basis of Therapeutics, 8th ed)

  12. 124% of classified

    Drugs used to prevent SEIZURES or reduce their severity.

  13. 134% of classified

    Drugs used to prevent NAUSEA or VOMITING.

  14. 144% of classified

    Compounds that interact with and stimulate the activity of CANNABINOID RECEPTORS.

  15. 154% of classified

    A loosely defined group of drugs that tend to increase behavioral alertness, agitation, or excitation. They work by a variety of mechanisms, but usually not by direct excitation of neurons.… The many drugs that have such actions as side effects to their main therapeutic use are not included here.

  16. 164% of classified

    Drugs that bind to but do not activate MUSCARINIC RECEPTORS, thereby blocking the actions of endogenous ACETYLCHOLINE or exogenous agonists. Muscarinic antagonists have widespread effects… including actions on the iris and ciliary muscle of the eye, the heart and blood vessels, secretions of the respiratory tract, GI system, and salivary glands, GI motility, urinary bladder tone, and the central nervous system.

  17. 174% of classified

    Agents that inhibit the actions of the parasympathetic nervous system. The major group of drugs used therapeutically for this purpose is the MUSCARINIC ANTAGONISTS.

  18. 184% of classified

    Endogenous compounds and drugs that specifically stimulate SEROTONIN 5-HT2 RECEPTORS. Included under this heading are agonists for one or more of the specific 5-HT2 receptor subtypes.

  19. 193% of classified

    Compounds that bind to and activate ADRENERGIC ALPHA-1 RECEPTORS.

  20. 203% of classified

    Agents used for the treatment or prevention of cardiac arrhythmias. They may affect the polarization-repolarization phase of the action potential, its excitability or refractoriness, or… impulse conduction or membrane responsiveness within cardiac fibers. Anti-arrhythmia agents are often classed into four main groups according to their mechanism of action: sodium channel blockade, beta-adrenergic blockade, repolarization prolongation, or calcium channel blockade.

  21. 213% of classified

    Anti-inflammatory agents that are non-steroidal in nature. In addition to anti-inflammatory actions, they have analgesic, antipyretic, and platelet-inhibitory actions. They act by blocking… the synthesis of prostaglandins by inhibiting cyclooxygenase, which converts arachidonic acid to cyclic endoperoxides, precursors of prostaglandins. Inhibition of prostaglandin synthesis accounts for their analgesic, antipyretic, and platelet-inhibitory actions; other mechanisms may contribute to their anti-inflammatory effects.

  22. 223% of classified

    Agents used in the treatment of Parkinson's disease. The most commonly used drugs act on the dopaminergic system in the striatum and basal ganglia or are centrally acting muscarinic… antagonists.

  23. 233% of classified

    Agents that suppress cough. They act centrally on the medullary cough center. EXPECTORANTS, also used in the treatment of cough, act locally.

  24. 243% of classified

    Drugs that bind to and activate dopamine receptors.

  25. 253% of classified

    A chemically heterogeneous group of drugs that have in common the ability to block oxidative deamination of naturally occurring monoamines. (From Gilman, et al., Goodman and Gilman's The… Pharmacological Basis of Therapeutics, 8th ed, p414)

  26. 263% of classified

    Chemical agents that increase the rate of genetic mutation by interfering with the function of nucleic acids. A clastogen is a specific mutagen that causes breaks in chromosomes.

  27. 273% of classified

    Toxic substances from microorganisms, plants or animals that interfere with the functions of the nervous system. Most venoms contain neurotoxic substances. Myotoxins are included in this… concept.

  28. 283% of classified

    Compounds that specifically inhibit the reuptake of serotonin in the brain.

  29. 293% of classified

    Drugs used to cause constriction of the blood vessels.

  30. 301% of classified

    Agents that are administered in association with anesthetics to increase effectiveness, improve delivery, or decrease required dosage.

  31. 311% of classified

    Drugs that selectively bind to and activate alpha adrenergic receptors.

  32. 321% of classified

    Gases or volatile liquids that vary in the rate at which they induce anesthesia; potency; the degree of circulation, respiratory, or neuromuscular depression they produce; and analgesic… effects. Inhalation anesthetics have advantages over intravenous agents in that the depth of anesthesia can be changed rapidly by altering the inhaled concentration. Because of their rapid elimination, any postoperative respiratory depression is of relatively short duration. (From AMA Drug Evaluations Annual, 1994, p173)

  33. 331% of classified

    Agents that alleviate ANXIETY, tension, and ANXIETY DISORDERS, promote sedation, and have a calming effect without affecting clarity of consciousness or neurologic conditions. ADRENERGIC… BETA-ANTAGONISTS are commonly used in the symptomatic treatment of anxiety but are not included here.

  34. 341% of classified

    Substances that prevent infectious agents or organisms from spreading or kill infectious agents in order to prevent the spread of infection.

  35. 351% of classified

    Substances used on humans and other animals that destroy harmful microorganisms or inhibit their activity. They are distinguished from DISINFECTANTS, which are used on inanimate objects.

  36. 361% of classified

    Agents that increase energy expenditure and weight loss by neural and metabolic regulation.

  37. 371% of classified

    Various agents with different action mechanisms used to treat or ameliorate PEPTIC ULCER or irritation of the gastrointestinal tract. This has included ANTIBIOTICS to treat HELICOBACTER… INFECTIONS; HISTAMINE H2 ANTAGONISTS to reduce GASTRIC ACID secretion; and ANTACIDS for symptomatic relief.

  38. 381% of classified

    Mood-stimulating drugs used primarily in the treatment of affective disorders and related conditions. Several MONOAMINE OXIDASE INHIBITORS are useful as antidepressants apparently as a… long-term consequence of their modulation of catecholamine levels. The tricyclic compounds useful as antidepressive agents (ANTIDEPRESSIVE AGENTS, TRICYCLIC) also appear to act through brain catecholamine systems. A third group (ANTIDEPRESSIVE AGENTS, SECOND-GENERATION) is a diverse group of drugs including some that act specifically on serotonergic systems.

  39. 391% of classified

    A structurally and mechanistically diverse group of drugs that are not tricyclics or monoamine oxidase inhibitors. The most clinically important appear to act selectively on serotonergic… systems, especially by inhibiting serotonin reuptake.

  40. 401% of classified

    Substances that destroy fungi by suppressing their ability to grow or reproduce. They differ from FUNGICIDES, INDUSTRIAL because they defend against fungi present in human or animal tissues.

  41. 411% of classified

    Naturally occurring or synthetic substances that inhibit or retard oxidation reactions. They counteract the damaging effects of oxidation in animal tissues.

  42. 421% of classified

    Agents that control agitated psychotic behavior, alleviate acute psychotic states, reduce psychotic symptoms, and exert a quieting effect. They are used in SCHIZOPHRENIA; senile dementia;… transient psychosis following surgery; or MYOCARDIAL INFARCTION; etc. These drugs are often referred to as neuroleptics alluding to the tendency to produce neurological side effects, but not all antipsychotics are likely to produce such effects. Many of these drugs may also be effective against nausea, emesis, and pruritus.

  43. 431% of classified

    A class of drugs that act by selective inhibition of calcium influx through cellular membranes.

  44. 441% of classified

    Compounds that inhibit or block the activity of CANNABINOID RECEPTORS.

  45. 451% of classified

    Drugs that bind to and activate cholinergic receptors.

  46. 461% of classified

    Drugs that bind to but do not activate CHOLINERGIC RECEPTORS, thereby blocking the actions of ACETYLCHOLINE or cholinergic agonists.

  47. 471% of classified

    Compounds or agents that combine with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction.

  48. 481% of classified

    Drugs that bind to and activate excitatory amino acid receptors.

  49. 491% of classified

    Substances that eliminate free radicals. Among other effects, they protect PANCREATIC ISLETS against damage by CYTOKINES and prevent myocardial and pulmonary REPERFUSION INJURY.

  50. 501% of classified

    Endogenous compounds and drugs that bind to and activate GABA-A RECEPTORS.

  51. 511% of classified

    Chemical substances which inhibit the function of the endocrine glands, the biosynthesis of their secreted hormones, or the action of hormones upon their specific sites.

  52. 521% of classified

    Agents that suppress immune function by one of several mechanisms of action. Classical cytotoxic immunosuppressants act by inhibiting DNA synthesis. Others may act through activation of… T-CELLS or by inhibiting the activation of HELPER CELLS. While immunosuppression has been brought about in the past primarily to prevent rejection of transplanted organs, new applications involving mediation of the effects of INTERLEUKINS and other CYTOKINES are emerging.

  53. 531% of classified

    Drugs that bind to and activate muscarinic cholinergic receptors (RECEPTORS, MUSCARINIC). Muscarinic agonists are most commonly used when it is desirable to increase smooth muscle tone,… especially in the GI tract, urinary bladder and the eye. They may also be used to reduce heart rate.

  54. 541% of classified

    Agents that dilate the pupil. They may be either sympathomimetics or parasympatholytics.

  55. 551% of classified

    Drugs that mimic the effects of parasympathetic nervous system activity. Included here are drugs that directly stimulate muscarinic receptors and drugs that potentiate cholinergic activity,… usually by slowing the breakdown of acetylcholine (CHOLINESTERASE INHIBITORS). Drugs that stimulate both sympathetic and parasympathetic postganglionic neurons (GANGLIONIC STIMULANTS) are not included here.

  56. 561% of classified

    Drugs that act principally at one or more sites within the peripheral neuroeffector systems, the autonomic system, and motor nerve-skeletal system. (From Smith and Reynard, Textbook of… Pharmacology, 1991, p75)

  57. 571% of classified

    A loosely defined grouping of drugs that have effects on psychological function. Here the psychotropic agents include the antidepressive agents, hallucinogens, and tranquilizing agents… (including the antipsychotics and anti-anxiety agents).

  58. 581% of classified

    Drugs used to cause dilation of the blood vessels.

Not indexed in MeSH

473 compounds have no MeSH pharmacological classification. Most are research chemicals and minor alkaloids that the vocabulary does not index. This is an absence of curation upstream, not a statement that these compounds are pharmacologically inert — which is exactly why they are listed here rather than swept into an “Other” tile.

II · Structural family

What they are

Compounds sharing a Bemis–Murcko scaffold, shown with the scaffold itself so the grouping can be checked rather than trusted.

Compounds here are not filed under curated class names like “tryptamine” or “phenethylamine”. Those are assertions someone has to stand behind. Instead each compound is reduced to its scaffold — strip the side chains, keep the ring systems and what links them — and compounds sharing one are shown together.

Bemis GW, Murcko MA. The properties of known drugs. 1. Molecular frameworks. J Med Chem. 1996;39(15):2887–93. doi:10.1021/jm9602928. Scaffolds computed with RDKit from the PubChem structure of each compound.

  1. Family 01

    136

    compounds

    c1ccccc1

  2. Family 02

    88

    compounds

    c1ccc2[nH]ccc2c1

  3. Family 03

    38

    compounds

    c1ccc2c(c1)OCO2

  4. Family 04

    30

    compounds

    C1=C2c3cccc4[nH]cc(c34)C[C@H]2NCC1

  5. Family 05

    23

    compounds

    c1ccc(CCNCc2ccccc2)cc1

  6. Family 06

    16

    compounds

    O=C1CCCCC1c1ccccc1

  7. Family 07

    15

    compounds

    c1ccc2occc2c1

  8. Family 08

    7

    compounds

    c1ccc(C2(N3CCCCC3)CCCCC2)cc1

  9. Family 09

    6

    compounds

    C1=C[C@H]2c3ccccc3OC[C@@H]2CC1

  10. Family 10

    6

    compounds

    c1ccc2c(c1)CCO2

  11. Family 11

    5

    compounds

    c1ccc(C2CCCCC2)cc1

  12. Family 12

    5

    compounds

    c1ccc(N2CCNCC2)cc1

  13. Family 13

    5

    compounds

    c1ccc2c(c1)CCC2

  14. Family 14

    5

    compounds

    c1ccc2c3c([nH]c2c1)[C@@H]1C[C@H]2CC[C@@H]1N(CC3)C2

  15. Family 15

    5

    compounds

    O=C(c1cccc2ccccc12)c1c[nH]c2ccccc12

  16. Family 16

    3

    compounds

    C1=C[C@@H](c2ccccc2)CCC1

  17. Family 17

    3

    compounds

    C1=NCCc2c1[nH]c1ccccc21

  18. Family 18

    3

    compounds

    c1cc2cc3c(cc2[nH]1)OCO3

  19. Family 19

    3

    compounds

    c1ccc(C2CC2)cc1

  20. Family 20

    3

    compounds

    c1ccc2c(c1)[nH]c1cnccc12

  21. Family 21

    3

    compounds

    c1ccc2c(c1)CCCC2

  22. Family 22

    3

    compounds

    c1ccc2c(CCN3CCCC3)c[nH]c2c1

  23. Family 23

    3

    compounds

    c1ccc2c3c([nH]c2c1)[C@@H]1CCCCN1CC3

  24. Family 24

    3

    compounds

    c1ccc2c3c([nH]c2c1)CNCC3

  25. Family 25

    3

    compounds

    O=C(C1CC1)n1cc2c3c(cccc31)C1=CCCN[C@@H]1C2

  26. Family 26

    2

    compounds

    C1=C[C@@H]2c3cccc4[nH]cc(c34)C[C@H]2NC1

  27. Family 27

    2

    compounds

    C1=CC[C@H]2c3ccccc3OC[C@@H]2C1

  28. Family 28

    2

    compounds

    C1=CCNCC1

  29. Family 29

    2

    compounds

    c1c2c(cc3c1OCC3)OCC2

  30. Family 30

    2

    compounds

    c1cc2c3c(c[nH]c3c1)CCC2

  31. Family 31

    2

    compounds

    c1cc2c3c(ccc2[nH]1)OCO3

  32. Family 32

    2

    compounds

    c1cc2cc3occc3cc2o1

  33. Family 33

    2

    compounds

    c1ccc(C2(N3CCCC3)CCCCC2)cc1

  34. Family 34

    2

    compounds

    c1ccc(CC(c2ccccc2)N2CCCCC2)cc1

  35. Family 35

    2

    compounds

    c1ccc(CNCCc2ccc3c(c2)OCO3)cc1

  36. Family 36

    2

    compounds

    c1ccc2[nH]ncc2c1

  37. Family 37

    2

    compounds

    c1ccc2c(C[C@H]3CCCN3)c[nH]c2c1

  38. Family 38

    2

    compounds

    c1ccc2c(c1)C[C@@H]1NCC[C@]23CCCC[C@H]13

  39. Family 39

    2

    compounds

    c1ccc2c(c1)CCNC2

  40. Family 40

    2

    compounds

    c1ccc2c3c([nH]c2c1)C1C[C@@H]2CC[C@@H]1N(CC3)C2

  41. Family 41

    2

    compounds

    c1csc(C2(N3CCCCC3)CCCCC2)c1

  42. Family 42

    2

    compounds

    O=C(Cc1ccccc1)OC1C[C@@H]2N[C@H](C1)[C@H]1O[C@H]12

  43. Family 43

    2

    compounds

    O=C(NC1OC2[C@@H]3CCCN3C(=O)[C@H](Cc3ccccc3)N2C1=O)[C@@H]1C=C2c3cccc4[nH]cc(c34)C[C@H]2NC1

  44. Family 44

    2

    compounds

    O=C(NN1CCCCC1)c1cc(-c2ccccc2)n(-c2ccccc2)n1

  45. Family 45

    2

    compounds

    O=C1CCCC2CC[C@H]3C(=O)O[C@H](c4ccoc4)CC3[C@@H]12

  46. Family 46

    2

    compounds

    O=c1cco[nH]1

Scaffolds held by a single compound

82 compounds have a framework no other compound in the archive shares. That is a statement about this archive’s contents, not about the chemistry.

No scaffold

A Murcko scaffold is a ring system. These compounds have none, so the derivation returns nothing and they are listed apart rather than placed in a family they do not belong to.