Structure

Physi-Chem Properties

Molecular Weight:  306.15
Volume:  310.324
LogP:  2.018
LogD:  1.483
LogS:  -2.301
# Rotatable Bonds:  2
TPSA:  72.83
# H-Bond Aceptor:  5
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.747
Synthetic Accessibility Score:  4.757
Fsp3:  0.647
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.626
MDCK Permeability:  8.308538963319734e-05
Pgp-inhibitor:  0.829
Pgp-substrate:  0.016
Human Intestinal Absorption (HIA):  0.031
20% Bioavailability (F20%):  0.467
30% Bioavailability (F30%):  0.974

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.953
Plasma Protein Binding (PPB):  28.930116653442383%
Volume Distribution (VD):  1.067
Pgp-substrate:  59.782039642333984%

ADMET: Metabolism

CYP1A2-inhibitor:  0.101
CYP1A2-substrate:  0.082
CYP2C19-inhibitor:  0.023
CYP2C19-substrate:  0.576
CYP2C9-inhibitor:  0.005
CYP2C9-substrate:  0.031
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.04
CYP3A4-inhibitor:  0.448
CYP3A4-substrate:  0.302

ADMET: Excretion

Clearance (CL):  9.786
Half-life (T1/2):  0.574

ADMET: Toxicity

hERG Blockers:  0.043
Human Hepatotoxicity (H-HT):  0.666
Drug-inuced Liver Injury (DILI):  0.4
AMES Toxicity:  0.013
Rat Oral Acute Toxicity:  0.925
Maximum Recommended Daily Dose:  0.395
Skin Sensitization:  0.508
Carcinogencity:  0.337
Eye Corrosion:  0.084
Eye Irritation:  0.051
Respiratory Toxicity:  0.979

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  Natural Product: NPC192978

Natural Product ID:  NPC192978
Common Name*:   SYTRJRUSWMMZLV-AHWDLOTJSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  SYTRJRUSWMMZLV-AHWDLOTJSA-N
Standard InCHI:  InChI=1S/C17H22O5/c1-8-7-12(21-10(3)18)13-9(2)16(19)22-15(13)14-11(8)5-6-17(14,4)20/h5-6,9,12-15,20H,7H2,1-4H3/t9-,12-,13+,14-,15-,17-/m0/s1
SMILES:  CC1=C2C=C[C@@](C)([C@@H]2[C@@H]2[C@H]([C@H](C)C(=O)O2)[C@H](C1)OC(=O)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000050] Lactones
        • [CHEMONTID:0001245] Gamma butyrolactones

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO17790 Trigonostemon reidioides Species Euphorbiaceae Eukaryota roots Rat Buri Province, Thailand 1988-DEC PMID[14987064]
NPO17790 Trigonostemon reidioides Species Euphorbiaceae Eukaryota n.a. root n.a. PMID[16204992]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota Fruits n.a. n.a. PMID[16309325]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. Seoul, Korea 2000-Jun PMID[16643034]
NPO8524 Pithecellobium clypearia Species Fabaceae Eukaryota leaves n.a. n.a. PMID[16724853]
NPO8524 Pithecellobium clypearia Species Fabaceae Eukaryota n.a. leaf n.a. PMID[16724853]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota fruit n.a. n.a. PMID[18505286]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota fruit n.a. n.a. PMID[19650637]
NPO16660 Phomopsis archeri Species Valsaceae Eukaryota n.a. mycelium n.a. PMID[21341709]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota fruits n.a. n.a. PMID[23305920]
NPO28626 Isodon rubescens Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[25590529]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[32141747]
NPO2733 Sarcomelicope argyrophylla Species Rutaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO17706 Caragana tibetica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10436 Aristolochia maxima Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13180 Jasminum officinale Species Oleaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16620 Malus asiatica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13856 Bergenia purpurascens Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17637 Pimpinella saxifraga Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10436 Aristolochia maxima Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17244 Montrouziera sphaeroidea Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17637 Pimpinella saxifraga Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13180 Jasminum officinale Species Oleaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28626 Isodon rubescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17790 Trigonostemon reidioides Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13856 Bergenia purpurascens Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17706 Caragana tibetica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13180 Jasminum officinale Species Oleaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28626 Isodon rubescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11925 Mola mola Species Molidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16253 Rapanea myricoides Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17870 Euphorbia ferganensis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28626 Isodon rubescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22469 Tropaeolum speciosum Species Tropaeolaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13180 Jasminum officinale Species Oleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14408 Chrysolina fastuosa Species Chrysomelidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8524 Pithecellobium clypearia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21802 Julocroton camporum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO16374 Crataegus sinaica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17029 Tridacna gigas Species Tridacnidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15079 Polygala myrtifolia Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11559 Betula mandshurica Species Betulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11831 Achillea collina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1148 Phalium undulatum Species Cassidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9523 Nephroma antarcticum Species Nephromataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2589 Solanum bahamense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17244 Montrouziera sphaeroidea Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15814 Rhodiola krylovii Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15667 Ligularia platyglossa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17175 Lasiocephalus ovatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16620 Malus asiatica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17637 Pimpinella saxifraga Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2733 Sarcomelicope argyrophylla Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12559 Mikania obtusata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17790 Trigonostemon reidioides Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15964 Tropiometra afra Species Tropiometridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16510 Ganoderma australe Species Ganodermataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18962 Actinobacillus pleuropneumoniae Species Pasteurellaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO6939 Vatica diospyroides Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16660 Phomopsis archeri Species Valsaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17739 Macrotyloma axillare Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11420 Dolichospermum affine Species Aphanizomenonaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO17945 Arachniodes dimorphophylla Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17100 Artemisia vachanica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11020 Streptomyces purpeofuscus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO10436 Aristolochia maxima Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17327 Cotoneaster orbicularis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14698 Phyllospongia madagascarensis Species Thorectidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18709 Discaria crenata Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12733 Pentapora fascialis Species Bitectiporidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26487 Tinospora smilacina Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13856 Bergenia purpurascens Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18027 Oreosolen wattii Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9428 Annona rensoniana Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17355 Bischofia trifoliata Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13422 Amoora yunnanensis n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO17706 Caragana tibetica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5634 Wallago attu Species Siluridae Eukaryota n.a. n.a. n.a. Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  NP Quantity Composition/Concentration

Organism ID NP ID Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  Biological Activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC192978 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC192978 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage

  Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data