Natural Product: NPC96835

Natural Product IDNPC96835
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Phenanthrene
IUPAC Name phenanthrene
Synonyms Phenanthrene
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL46730
PubChem CID 995
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0000025] Phenanthrenes and derivatives

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 YNPNZTXNASCQKK-UHFFFAOYSA-N
Standard InCHI InChI=1S/C14H10/c1-3-7-13-11(5-1)9-10-12-6-2-4-8-14(12)13/h1-10H
SMILES c1ccc2c(c1)c1ccccc1cc2

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   178.08 Volume:   206.576
?
Van der Waals volume.
Dense:   0.862 LogP:   4.459
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.852
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -5.178
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   0.0 Rigid Bonds:   16.0
TPSA:   0.0
?
Topological Polar Surface Area.
 H-Bond Acceptor:   0.0
H-Bond Donor:   0.0 Rings:   3.0
Heavy Atoms:   0.0

MedChem Properties

QED Drug-Likeness Score:   0.456 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   1.197 Fsp3:   0.0
MCE-18:   13.0
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Accepted GSK Rule:   Accepted
Golden Triangle Rule:   Accepted BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.385 Fluc inhibitor:   0.659
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.192
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.002
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.996 Promiscuous compounds:   0.806

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.193 MDCK Permeability:   -4.509
Pgp-inhibitor:   0.328 Pgp-substrate:   0.341
PAMPA:   0.098
?
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):   0.005
20% Bioavailability (F20%):   0.088 30% Bioavailability (F30%):   0.583
50% Bioavailability (F50%):   0.809

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.933 MRP1:   0.488
Plasma Protein Binding (PPB):   97.514% Volume Distribution (VD):   0.136
Fu: 1.47%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.843
OATP1B3 inhibitor:   0.933 BCRP inhibitor:   0.573
BSEP inhibitor:   0.961

ADMET: Metabolism

CYP1A2-inhibitor:   0.946 CYP1A2-substrate:   0.885
CYP2C19-inhibitor:   0.988 CYP2C19-substrate:   0.713
CYP2C9-inhibitor:   0.999 CYP2C9-substrate:   0.624
CYP2D6-inhibitor:   0.998 CYP2D6-substrate:   0.16
CYP3A4-inhibitor:   0.132 CYP3A4-substrate:   0.999
CYP2B6-substrate:   0.999 CYP2C8-inhibitor:   0.827
HLM stability:   0.944
?
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):  7.853 Half-life (T1/2):  1.778

ADMET: Toxicity

hERG Blockers:  0.245 hERG Blockers (10um):  0.649
Human Hepatotoxicity (H-HT):  0.642 Drug-induced Liver Injury (DILI):  0.682
AMES Toxicity:  0.806 Rat Oral Acute Toxicity:  0.471
Maximum Recommended Daily Dose:  0.531 Skin Sensitization:  0.607
Carcinogencity:  0.815 Eye Corrosion:  0.252
Eye Irritation:  0.983 Respiratory Toxicity:  0.807
Drug-induced Neurotoxicity:  0.854 Ototoxicity:  0.301
Hematotoxicity:  0.447 Drug-induced Nephrotoxicity:  0.458
Genotoxicity:  0.221 RPMI-8226 Immunitoxicity:  0.059
A549 Cytotoxicity:  0.25 Hek293 Cytotoxicity:  0.367
BCF:   3.091
?
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:   4.452
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.328
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.226
?
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
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. root n.a. DOI[10.1007/s11418-007-0221-0]
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/0031-9422(83)80138-1]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. DOI[10.1172/JCI16309]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. DOI[10.1371/journal.pone.0115359]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[10557354]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[11034610]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[11419736]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[11530998]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[1175644]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[12391014]
NPO11421 Arnebia euchroma Species Boraginaceae Eukaryota n.a. n.a. n.a. PMID[12502328]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[12812989]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[12840027]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[12878451]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[15084647]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[1521032]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[15230696]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[15314235]
NPO10780 Bletilla striata Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[15686910]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[16112079]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[16770722]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[1687010]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[17116739]
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. n.a. n.a. PMID[17157006]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[17190852]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[17875433]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[18311922]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[18544912]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[18799520]
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. n.a. n.a. PMID[19217780]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[19425150]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[19961175]
NPO15890 Cimicifuga foetida Species Ranunculaceae Eukaryota Roots n.a. n.a. PMID[20121210]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[20506249]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[20601097]
NPO8256 Zanthoxylum armatum Species Rutaceae Eukaryota n.a. seed n.a. PMID[20628994]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. faeces n.a. PMID[20708442]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. urine n.a. PMID[20708442]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. bile n.a. PMID[20708442]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[20876113]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[21798258]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[2268561]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[22711758]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23315938]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23717534]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23752203]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23810710]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23811455]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23868375]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23919613]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24101735]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24399466]
NPO8256 Zanthoxylum armatum Species Rutaceae Eukaryota n.a. stem n.a. PMID[24412550]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24494566]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24558969]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24816727]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[25114169]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[25181601]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[25293588]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[25644343]
NPO10780 Bletilla striata Species Orchidaceae Eukaryota Fibrous Roots n.a. n.a. PMID[25760525]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[26236990]
NPO21305 Carpesium macrocephalum Species Asteraceae Eukaryota Whole Plant n.a. n.a. PMID[26394911]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[27471436]
NPO1085 Peganum harmala Species Nitrariaceae Eukaryota Seeds n.a. n.a. PMID[28128938]
NPO15373 Actaea dahurica Species Ranunculaceae Eukaryota Roots n.a. n.a. PMID[28558206]
NPO10780 Bletilla striata Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[31415170]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[3179836]
NPO15373 Actaea dahurica Species Ranunculaceae Eukaryota n.a. n.a. n.a. PMID[32031796]
NPO43854 Ononis alba Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[33096945]
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. n.a. n.a. PMID[3373224]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[347637]
NPO55200 Sitophilus granarius Species Curculionidae Eukaryota n.a. n.a. n.a. PMID[35638325]
NPO8256 Zanthoxylum armatum Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[36500729]
NPO8256 Zanthoxylum armatum Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[37029634]
NPO1085 Peganum harmala Species Nitrariaceae Eukaryota n.a. n.a. n.a. PMID[38971075]
NPO21305 Carpesium macrocephalum Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[39407585]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[4696527]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[5432584]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[6121420]
NPO1085 Peganum harmala Species Nitrariaceae Eukaryota n.a. n.a. n.a. PMID[6736972]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[6780563]
NPO11421 Arnebia euchroma Species Boraginaceae Eukaryota n.a. n.a. n.a. PMID[7775984]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[8600370]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[8987136]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[9192820]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[9800648]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15373 Actaea dahurica Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO389 Actaea heracleifolia Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2727 Actaea simplex Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4702 Trichosanthes rosthornii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11421 Arnebia euchroma Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8256 Zanthoxylum armatum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1085 Peganum harmala Species Nitrariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20297 Arnebia guttata Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10780 Bletilla striata Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6326 Morus serrata Species Moraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9225 Bursera graveolens Species Burseraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5854 Cerasus lusitanica n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO1085 Peganum harmala Species Nitrariaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11421 Arnebia euchroma Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4702 Trichosanthes rosthornii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20297 Arnebia guttata Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6326 Morus serrata Species Moraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10780 Bletilla striata Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9225 Bursera graveolens Species Burseraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO20297 Arnebia guttata Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10780 Bletilla striata Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2727 Actaea simplex Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4702 Trichosanthes rosthornii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15890 Cimicifuga foetida Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15373 Actaea dahurica Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11421 Arnebia euchroma Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1085 Peganum harmala Species Nitrariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6326 Morus serrata Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9225 Bursera graveolens Species Burseraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO389 Actaea heracleifolia Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8256 Zanthoxylum armatum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20297 Arnebia guttata Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10780 Bletilla striata Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11421 Arnebia euchroma Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4702 Trichosanthes rosthornii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1085 Peganum harmala Species Nitrariaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO389 Actaea heracleifolia Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15373 Actaea dahurica Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2727 Actaea simplex Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11421 Arnebia euchroma Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15890 Cimicifuga foetida Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4702 Trichosanthes rosthornii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10780 Bletilla striata Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20297 Arnebia guttata Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15890 Cimicifuga foetida Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21305 Carpesium macrocephalum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9225 Bursera graveolens Species Burseraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11421 Arnebia euchroma Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20297 Arnebia guttata Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO389 Actaea heracleifolia Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4702 Trichosanthes rosthornii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10780 Bletilla striata Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15373 Actaea dahurica Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2215 Guarea grandiflora Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1085 Peganum harmala Species Nitrariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2727 Actaea simplex Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5854 Cerasus lusitanica n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO6326 Morus serrata Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8256 Zanthoxylum armatum Species Rutaceae 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
NPO21305 Carpesium macrocephalum Oil Aerial parts 0.1 n.a. n.a. % PMID[39407585]
NPO43854 Ononis alba Oil n.a. 0.1 n.a. n.a. % PMID[33096945]
NPO55200 Sitophilus granarius Oil n.a. 0.7 n.a. n.a. % PMID[35638325]

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
NPT240 Individual protein Cytochrome P450 2A6 Homo sapiens IC50 = 97000.0 nM PMID[15658857]
NPT1420 Individual protein Cytochrome P450 2A5 Mus musculus IC50 = 26000.0 nM PMID[15658857]
NPT1420 Individual protein Cytochrome P450 2A5 Mus musculus IC50 = 26001.6 nM PMID[19110342]
NPT240 Individual protein Cytochrome P450 2A6 Homo sapiens IC50 = 97051.0 nM PMID[19110342]
NPT149 Individual protein Endoplasmic reticulum-associated amyloid beta-peptide-binding protein Homo sapiens Potency = 39810.7 nM PubChem BioAssay data set
NPT210 Individual protein Thyroid stimulating hormone receptor Homo sapiens Potency = 1000.0 nM PubChem BioAssay data set
NPT135 Individual protein Chromobox protein homolog 1 Homo sapiens Potency n.a. 79432.8 nM PubChem BioAssay data set
NPT152 Individual protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Potency n.a. 74978.0 nM PubChem BioAssay data set
NPT102 Individual protein Interleukin-8 Homo sapiens Potency n.a. 74978.0 nM PubChem BioAssay data set
NPT50 Individual protein Tyrosyl-DNA phosphodiesterase 1 Homo sapiens Potency = 1995.3 nM PubChem BioAssay data set
NPT540 Individual protein Bile acid receptor FXR Homo sapiens Potency n.a. 56234.1 nM PubChem BioAssay data set
NPT94 Individual protein Aldehyde dehydrogenase 1A1 Homo sapiens Potency = 35481.3 nM PubChem BioAssay data set
NPT98 Individual protein HERG Homo sapiens Potency n.a. 28183.8 nM PubChem BioAssay data set
NPT74 Individual protein Proto-oncogene c-JUN Homo sapiens Potency n.a. 53465.5 nM PubChem BioAssay data set
NPT532 Individual protein Lysine-specific demethylase 4A Homo sapiens Potency n.a. 39810.7 nM PubChem BioAssay data set
NPT546 Individual protein Retinoid X receptor alpha Homo sapiens Potency n.a. 50118.7 nM PubChem BioAssay data set

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT347 Cell line Lymphoblastoid cells Homo sapiens Potency = 1.6 nM PubChem BioAssay data set
NPT1970 Cell line THP-1 Homo sapiens FC = 1.4 n.a. PMID[23933533]
NPT1970 Cell line THP-1 Homo sapiens FC = 1.3 n.a. PMID[23933533]
NPT1970 Cell line THP-1 Homo sapiens FC = 1.2 n.a. PMID[23933533]
NPT1970 Cell line THP-1 Homo sapiens FC = 1.1 n.a. PMID[23933533]
NPT1970 Cell line THP-1 Homo sapiens Inhibition = 0.0 % PMID[23933533]
NPT1970 Cell line THP-1 Homo sapiens Inhibition = 6.0 % PMID[23933533]
NPT1970 Cell line THP-1 Homo sapiens Inhibition = 8.5 % PMID[23933533]
NPT1819 Organism Microsporum canis Arthroderma otae MIC > 50.0 ug.mL-1 PMID[10543891]
NPT327 Organism Microsporum gypseum Microsporum gypseum MIC > 50.0 ug.mL-1 PMID[10543891]
NPT330 Organism Trichophyton mentagrophytes Trichophyton mentagrophytes MIC > 50.0 ug.mL-1 PMID[10543891]
NPT329 Organism Trichophyton rubrum Trichophyton rubrum MIC > 50.0 ug.mL-1 PMID[10543891]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 > 100.0 ug.mL-1 PMID[23933533]
NPT328 Organism Epidermophyton floccosum Epidermophyton floccosum MIC > 50.0 ug.mL-1 PMID[10543891]
NPT1 Others Radical scavenging activity n.a. IC50 > 100.0 ug.mL-1 PMID[23933533]
NPT2 Others Unspecified n.a. Potency n.a. 12299.8 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 189.7 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 59455.9 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 68589.6 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 66710.6 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 61644.8 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 37850.7 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 47227.5 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 30637.9 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 23669.8 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 13800.6 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 15484.5 nM PubChem BioAssay data set

In vivo activity

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





 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
- Rattus norvegicus NOEL = 1.0 mg ToxVal
- Rattus norvegicus NOEL = 150.0 mg/kg-day ToxVal
- Rattus norvegicus NOEL = 1.0 mg/10 g bdwt ToxVal
- Rattus norvegicus LOEL = 100.0 mg/kg-day ToxVal
- Rattus norvegicus LOEL = 150.0 mg/kg-day ToxVal
- Rattus norvegicus NOEL = 100.0 mg/kg-day ToxVal
- Mus musculus LD50 = 2.405892514 mg/kg TOXRIC
- Mus musculus NOEL = 50.0 mg/kg-day ToxVal
- Mus musculus LOEL = 100.0 mg/kg-day ToxVal
- Mus musculus LD50 = 700.0 mg/kg ToxVal
- Homo sapiens Medium-Specific Concentration = 1.1 mg/L ToxVal
- Homo sapiens RfD = 0.3 mg/kg-day ToxVal
- Homo sapiens PAC-3 = 76.0 mg/m3 ToxVal
- Homo sapiens PAC-2 = 13.0 mg/m3 ToxVal
- Homo sapiens PAC-1 = 1.1 mg/m3 ToxVal
- Homo sapiens MEG = 2800.0 mg/kg ToxVal
- Homo sapiens MEG = 6.0 mg/m3 ToxVal
- Homo sapiens MEG = 20.0 mg/m3 ToxVal
- Homo sapiens RfD = 0.228 mg/kg-day ToxVal

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 NPC96835 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
0.8667 High Similarity NPC66270
0.5714 Remote Similarity NPC291066

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC96835 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