Natural Product: NPC119224

Natural Product IDNPC119224
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Garcinone E
IUPAC Name 2,3,6,8-tetrahydroxy-1,4,7-tris(3-methylbut-2-enyl)xanthen-9-one
Synonyms Garcinone E
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL454580
PubChem CID 10298511
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000123] Benzopyrans
        • [CHEMONTID:0003410] 1-benzopyrans
          • [CHEMONTID:0002817] Dibenzopyrans
            • [CHEMONTID:0000200] Xanthenes
              • [CHEMONTID:0000204] Xanthones
                • [CHEMONTID:0003519] 8-prenylated xanthones

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

  Chemical Representations

Standard InCHIKey WVJYEKGQSBGNRP-UHFFFAOYSA-N
Standard InCHI InChI=1S/C28H32O6/c1-14(2)7-10-17-20(29)13-21-23(24(17)30)27(33)22-18(11-8-15(3)4)25(31)26(32)19(28(22)34-21)12-9-16(5)6/h7-9,13,29-32H,10-12H2,1-6H3
SMILES CC(=CCc1c(cc2c(c1O)c(=O)c1c(CC=C(C)C)c(c(c(CC=C(C)C)c1o2)O)O)O)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   464.22 Volume:   493.551
?
Van der Waals volume.
Dense:   0.941 LogP:   5.945
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.185
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -5.363
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   6.0 Rigid Bonds:   20.0
TPSA:   111.13
?
Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   4.0 Rings:   3.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.194 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.452 Fsp3:   0.321
MCE-18:   24.0
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   1 PAINS Alert:   1
Colloidal aggregators:   0.995 Fluc inhibitor:   0.608
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.976
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.68
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.546 Promiscuous compounds:   0.304

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.112 MDCK Permeability:   -4.748
Pgp-inhibitor:   0.985 Pgp-substrate:   0.076
PAMPA:   0.311
?
The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).
 Human Intestinal Absorption (HIA):   0.372
20% Bioavailability (F20%):   0.992 30% Bioavailability (F30%):   0.999
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.981
Plasma Protein Binding (PPB):   93.872% Volume Distribution (VD):   0.127
Fu: 7.458%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.915 BCRP inhibitor:   0.99
BSEP inhibitor:   0.928

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   1.0
CYP2C19-inhibitor:   1.0 CYP2C19-substrate:   1.0
CYP2C9-inhibitor:   0.018 CYP2C9-substrate:   0.006
CYP2D6-inhibitor:   0.838 CYP2D6-substrate:   0.033
CYP3A4-inhibitor:   0.992 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   1.0
?
Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):  5.811 Half-life (T1/2):  1.263

ADMET: Toxicity

hERG Blockers:  0.009 hERG Blockers (10um):  0.584
Human Hepatotoxicity (H-HT):  0.545 Drug-induced Liver Injury (DILI):  0.545
AMES Toxicity:  0.739 Rat Oral Acute Toxicity:  0.967
Maximum Recommended Daily Dose:  0.63 Skin Sensitization:  0.994
Carcinogencity:  0.277 Eye Corrosion:  0.0
Eye Irritation:  0.276 Respiratory Toxicity:  0.999
Drug-induced Neurotoxicity:  0.132 Ototoxicity:  0.342
Hematotoxicity:  0.089 Drug-induced Nephrotoxicity:  0.526
Genotoxicity:  0.995 RPMI-8226 Immunitoxicity:  0.049
A549 Cytotoxicity:  0.577 Hek293 Cytotoxicity:  0.816
BCF:   2.021
?
Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].
 IGC50:   5.208
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   7.074
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   6.691
?
96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11240-015-0798-z]
NPO5276 Zanthoxylum decaryi Species Rutaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/0031-9422(74)80113-5]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.fitote.2006.01.011]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jarmap.2018.11.004]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.plaphy.2005.07.013]
NPO3806 Garcinia morella Species Clusiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0040-4039(00)90246-6]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. DOI[10.1078/0176-1617-00195]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. DOI[10.1155/2014/609649]
NPO7811 Scleronephthya pallida Species Nephtheidae Eukaryota n.a. n.a. n.a. PMID[10075773]
NPO6775 Cistanche salsa Species Orobanchaceae Eukaryota n.a. whole plant n.a. PMID[10361686]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[10757735]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[14735439]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. callus n.a. PMID[15715262]
NPO11471 Garcinia oblongifolia Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[16724839]
NPO10376 Arcyria denudata Species Trichiidae Eukaryota n.a. n.a. n.a. PMID[16933891]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[18220354]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[18464091]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[18558747]
NPO11471 Garcinia oblongifolia Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[19113969]
NPO7920 Pentadesma butyracea Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[19296616]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota stem bark Pangradin village, Jasinga, West Java, Indonesia 2005-AUG PMID[19839614]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[20817450]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. pericarp n.a. PMID[24555285]
NPO11471 Garcinia oblongifolia Species Clusiaceae Eukaryota leaves Bobai, Guangxi Province, China 2005-Dec PMID[24679044]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[24717154]
NPO11471 Garcinia oblongifolia Species Clusiaceae Eukaryota Barks n.a. n.a. PMID[24754786]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[28445039]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota Roots n.a. n.a. PMID[30024167]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[32560389]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[36336219]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[38217369]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota fruit hulls Madras, Tamil Nadu, India 1993-MAR PMID[9213587]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3707 Chromatium okenii Species Chromatiaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO9741 Actinopyga agassizi Species Holothuriidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8560 Aplidium tabascum Species Polyclinidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10376 Arcyria denudata Species Trichiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8354 Aster bellidiastrum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10391 Dolomiaea souliei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4064 Halimodendron halodendron Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7534 Leptogorgia sarmentosa Species Gorgoniidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3449 Lonicera hypoleuca Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24931 Myelochroa aurulenta Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10056 Nicotiana sylvestris Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7920 Pentadesma butyracea Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8927 Poria selecta Species Coccinellidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7811 Scleronephthya pallida Species Nephtheidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25216 Senecio vellereus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27924 Serpocaulon triseriale Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10221 Streptomyces alboniger Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO12600 Trametes cinnabarina Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9717 Wibelia divaricata Species Davalliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3806 Garcinia morella Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11471 Garcinia oblongifolia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10228 Ascochyta viciae Species Didymellaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6775 Cistanche salsa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6948 Davidsoniella virescens Species Ceratocystidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2812 Lecanora kukunorensis Species Lecanoraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1154 Neomeris annulata Species Dasycladaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9298 Piper wightii Species Piperaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15242 Setosphaeria holmii Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26341 Trifolium resupinatum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5276 Zanthoxylum decaryi Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3806 Garcinia morella Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6775 Cistanche salsa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10849 Eucalyptus camaldulensis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5276 Zanthoxylum decaryi Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10391 Dolomiaea souliei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3806 Garcinia morella Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6775 Cistanche salsa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5276 Zanthoxylum decaryi Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10849 Eucalyptus camaldulensis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3806 Garcinia morella Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10391 Dolomiaea souliei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8560 Aplidium tabascum Species Polyclinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9741 Actinopyga agassizi Species Holothuriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3707 Chromatium okenii Species Chromatiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27924 Serpocaulon triseriale Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10391 Dolomiaea souliei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4064 Halimodendron halodendron Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10376 Arcyria denudata Species Trichiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8354 Aster bellidiastrum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12600 Trametes cinnabarina Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3449 Lonicera hypoleuca Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3806 Garcinia morella Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10221 Streptomyces alboniger Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO6775 Cistanche salsa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10056 Nicotiana sylvestris Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7534 Leptogorgia sarmentosa Species Gorgoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24931 Myelochroa aurulenta Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10849 Eucalyptus camaldulensis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8927 Poria selecta Species Coccinellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10228 Ascochyta viciae Species Didymellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1154 Neomeris annulata Species Dasycladaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11471 Garcinia oblongifolia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7811 Scleronephthya pallida Species Nephtheidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25216 Senecio vellereus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6948 Davidsoniella virescens Species Ceratocystidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9717 Wibelia divaricata Species Davalliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15242 Setosphaeria holmii Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9298 Piper wightii Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5276 Zanthoxylum decaryi Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26341 Trifolium resupinatum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2812 Lecanora kukunorensis Species Lecanoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7920 Pentadesma butyracea Species Clusiaceae 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 Organism Name 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

Molecular-level activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT1387 Individual protein Genome polyprotein Hepatitis C virus IC50 > 49751.0 nM PubChem BioAssay data set
NPT282 Individual protein MAP kinase ERK2 Homo sapiens Potency = 14125.4 nM PubChem BioAssay data set
NPT1254 Individual protein Streptokinase A Streptococcus pyogenes serotype M1 EC50 = 828.0 nM PubChem BioAssay data set
NPT152 Individual protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Potency n.a. 25929.0 nM PubChem BioAssay data set
NPT2892 Individual protein X-box-binding protein 1 Homo sapiens IC50 = 5240.0 nM PubChem BioAssay data set
NPT2893 Individual protein DNA damage-inducible transcript 3 protein Mus musculus IC50 > 9670.0 nM PubChem BioAssay data set
NPT199 Individual protein DNA polymerase kappa Homo sapiens Potency n.a. 79432.8 nM PubChem BioAssay data set
NPT154 Individual protein Mothers against decapentaplegic homolog 3 Homo sapiens Potency n.a. 6309.6 nM PubChem BioAssay data set
NPT2971 Individual protein DNA dC->dU-editing enzyme APOBEC-3F Homo sapiens Potency n.a. 35481.3 nM PubChem BioAssay data set
NPT10 Individual protein Geminin Homo sapiens Potency n.a. 25929.0 nM PubChem BioAssay data set
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens Potency n.a. 31622.8 nM PubChem BioAssay data set
NPT11 Individual protein Guanine nucleotide-binding protein G(s), subunit alpha Homo sapiens Potency n.a. 7079.5 nM PubChem BioAssay data set
NPT1043 Individual protein Glycoprotein hormones alpha chain Homo sapiens Potency n.a. 3981.1 nM PubChem BioAssay data set
NPT11 Individual protein Guanine nucleotide-binding protein G(s), subunit alpha Homo sapiens Potency n.a. 31622.8 nM PubChem BioAssay data set
NPT531 Individual protein Nuclear receptor ROR-gamma Mus musculus Potency = 35481.3 nM PubChem BioAssay data set
NPT55 Individual protein Putative fructose-1,6-bisphosphate aldolase Giardia intestinalis Potency = 17740.7 nM PubChem BioAssay data set
NPT58 Individual protein Bloom syndrome protein Homo sapiens Potency = 28183.8 nM PubChem BioAssay data set
NPT531 Individual protein Nuclear receptor ROR-gamma Mus musculus Potency = 19952.6 nM PubChem BioAssay data set
NPT9 Individual protein DNA polymerase eta Homo sapiens Potency n.a. 39810.7 nM PubChem BioAssay data set
NPT48 Individual protein Lysine-specific demethylase 4D-like Homo sapiens Potency = 28183.8 nM PubChem BioAssay data set
NPT54 Individual protein Nonstructural protein 1 Influenza A virus Potency = 19952.6 nM PubChem BioAssay data set
NPT446 Individual protein Rap guanine nucleotide exchange factor 3 Homo sapiens Potency n.a. 56234.1 nM PubChem BioAssay data set
NPT51 Individual protein Microtubule-associated protein tau Homo sapiens Potency = 14125.4 nM PubChem BioAssay data set
NPT51 Individual protein Microtubule-associated protein tau Homo sapiens Potency = 22387.2 nM PubChem BioAssay data set
NPT59 Individual protein DNA polymerase beta Homo sapiens Potency = 44668.4 nM PubChem BioAssay data set
NPT63 Individual protein Bromodomain adjacent to zinc finger domain protein 2B Homo sapiens Potency n.a. 50118.7 nM PubChem BioAssay data set
NPT8 Individual protein DNA polymerase iota Homo sapiens Potency n.a. 12589.3 nM PubChem BioAssay data set
NPT478 Individual protein Ataxin-2 Homo sapiens Potency n.a. 16833.6 nM PubChem BioAssay data set
NPT755 Individual protein Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 Homo sapiens Potency n.a. 50118.7 nM PubChem BioAssay data set
NPT861 Individual protein Isocitrate dehydrogenase [NADP] cytoplasmic Homo sapiens Potency n.a. 16360.1 nM PubChem BioAssay data set
NPT535 Individual protein Parathyroid hormone receptor Homo sapiens Potency n.a. 31622.8 nM PubChem BioAssay data set
NPT441 Individual protein Cytochrome P450 19A1 Homo sapiens Activity = 23.9 % PMID[18558747]
NPT441 Individual protein Cytochrome P450 19A1 Homo sapiens IC50 = 25100.0 nM PMID[18558747]
NPT441 Individual protein Cytochrome P450 19A1 Homo sapiens Activity = 32.3 % PMID[18558747]
NPT865 Individual protein Fatty acid synthase Homo sapiens IC50 = 3300.0 nM PMID[20817450]
NPT536 Nucleic acid microRNA 21 Homo sapiens Potency = 23280.9 nM PubChem BioAssay data set
NPT532 Individual protein Lysine-specific demethylase 4A Homo sapiens Potency n.a. 50118.7 nM PubChem BioAssay data set
NPT64 Individual protein ATPase family AAA domain-containing protein 5 Homo sapiens Potency n.a. 32629.4 nM PubChem BioAssay data set
NPT49 Individual protein DNA-(apurinic or apyrimidinic site) lyase Homo sapiens Potency n.a. 22387.2 nM PubChem BioAssay data set

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT116 Cell line HL-60 Homo sapiens IC50 = 15000.0 nM PMID[12932141]
NPT83 Cell line MCF7 Homo sapiens IC50 = 1.5 ug.mL-1 PMID[19296616]
NPT71 Cell line HEK293 Homo sapiens IC50 = 6768.81 nM PubChem BioAssay data set
NPT71 Cell line HEK293 Homo sapiens IC50 = 4649.0 nM PubChem BioAssay data set
NPT71 Cell line HEK293 Homo sapiens EC50 = 4780.0 nM PubChem BioAssay data set
NPT71 Cell line HEK293 Homo sapiens IC50 > 20000.0 nM PubChem BioAssay data set
NPT65 Cell line HepG2 Homo sapiens Potency n.a. 8912.5 nM PubChem BioAssay data set
NPT1225 Organism Plasmodium falciparum (isolate FcB1 / Columbia) Plasmodium falciparum FcB1/Columbia IC50 = 2.8 ug.mL-1 PMID[19296616]
NPT174 Organism Streptococcus Streptococcus EC50 = 3017.0 nM PubChem BioAssay data set
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 13115.4 nM PubChem BioAssay data set
NPT29229 Organism Vibrio campbellii Vibrio campbellii MIC = 31.2 ug.mL-1 PMID[35308024]
NPT1252 Organism Streptococcus sp. 'group A' Streptococcus sp. 'group A' EC50 = 813.0 nM PubChem BioAssay data set
NPT5711 Organism Vibrio vulnificus Vibrio vulnificus MIC = 15.6 ug.mL-1 PMID[35308024]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 25.0 ug.mL-1 PMID[35308024]
NPT19 Organism Escherichia coli Escherichia coli MIC = 25.0 ug.mL-1 PMID[35308024]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 12.5 ug.mL-1 PMID[35308024]
NPT2 Others Unspecified n.a. Ratio IC50 = 0.54 n.a. PMID[19296616]
NPT2 Others Unspecified n.a. Potency = 29092.9 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. IC50 = 3460.0 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. IC50 = 2790.0 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 14125.4 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 8912.5 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 10000.0 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 23109.3 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 28183.8 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 22387.2 nM PubChem BioAssay data set
NPT29882 Organism Vibrio rotiferianus Vibrio rotiferianus MIC = 15.6 ug.mL-1 PMID[35308024]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT134 Cell line SK-BR-3 Homo sapiens Survival = 52.3 % PMID[18558747]





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference





 Experimental Toxicity

Quantitative toxicity

Experiment Model Experiment Organism Toxicity Type Toxicity Relation Toxicity Value Toxicity Unit Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption
Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption

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 toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]


  Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

●  The left chart: Distribution of similarity level between NPC119224 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
0.7288 Intermediate Similarity NPC142339
0.6769 Remote Similarity NPC236132
0.6613 Remote Similarity NPC100123
0.6308 Remote Similarity NPC602307
0.6232 Remote Similarity NPC236796
0.6197 Remote Similarity NPC37870
0.6061 Remote Similarity NPC228785
0.6056 Remote Similarity NPC207690
0.5694 Remote Similarity NPC320359
0.5692 Remote Similarity NPC186397
0.5652 Remote Similarity NPC217677
0.5588 Remote Similarity NPC45146
0.5556 Remote Similarity NPC25152
0.5484 Remote Similarity NPC602367
0.5479 Remote Similarity NPC189473
0.5479 Remote Similarity NPC61010
0.5429 Remote Similarity NPC172770
0.5417 Remote Similarity NPC136674
0.5263 Remote Similarity NPC40491
0.5263 Remote Similarity NPC278052
0.5147 Remote Similarity NPC227122
0.5147 Remote Similarity NPC157784
0.5143 Remote Similarity NPC235018
0.5075 Remote Similarity NPC89474
0.5072 Remote Similarity NPC69769
0.5072 Remote Similarity NPC3825
0.507 Remote Similarity NPC304295
0.5067 Remote Similarity NPC310349

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC119224 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
NPD

Bioactivity similarity

  Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by 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