Natural Product: NPC61506

Natural Product IDNPC61506
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 (2R)-2-(3,4-Dihydroxyphenyl)-3,5,7-Trihydroxy-2,3-Dihydrochromen-4-One
IUPAC Name (2R)-2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-2,3-dihydrochromen-4-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1492383
PubChem CID 10185
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0000337] Flavans
          • [CHEMONTID:0001632] Flavanones
            • [CHEMONTID:0001362] Flavanonols

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 CXQWRCVTCMQVQX-YSSOQSIOSA-N
Standard InCHI InChI=1S/C15H12O7/c16-7-4-10(19)12-11(5-7)22-15(14(21)13(12)20)6-1-2-8(17)9(18)3-6/h1-5,14-19,21H/t14?,15-/m1/s1
SMILES c1cc(c(cc1[C@@H]1C(C(=O)c2c(cc(cc2O1)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   304.06 Volume:   285.403
?
Van der Waals volume.
Dense:   1.065 LogP:   1.068
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.357
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.4
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   18.0
TPSA:   127.45
?
Topological Polar Surface Area.
 H-Bond Acceptor:   7.0
H-Bond Donor:   5.0 Rings:   3.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.501 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.361 Fsp3:   0.133
MCE-18:   61.471
?
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:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   1
Chelating Alert:   1 PAINS Alert:   1
Colloidal aggregators:   0.601 Fluc inhibitor:   0.384
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.265
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.159
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.59 Promiscuous compounds:   0.348

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.13 MDCK Permeability:   -4.886
Pgp-inhibitor:   0.004 Pgp-substrate:   0.059
PAMPA:   0.715
?
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):   0.112
20% Bioavailability (F20%):   0.777 30% Bioavailability (F30%):   0.997
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.003 MRP1:   0.826
Plasma Protein Binding (PPB):   97.036% Volume Distribution (VD):   -0.522
Fu: 2.46%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.991
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.766
BSEP inhibitor:   0.007

ADMET: Metabolism

CYP1A2-inhibitor:   0.974 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.16 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.053 CYP2D6-substrate:   0.994
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.027
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.958
HLM stability:   0.105
?
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):  12.509 Half-life (T1/2):  1.916

ADMET: Toxicity

hERG Blockers:  0.078 hERG Blockers (10um):  0.632
Human Hepatotoxicity (H-HT):  0.495 Drug-induced Liver Injury (DILI):  0.189
AMES Toxicity:  0.534 Rat Oral Acute Toxicity:  0.47
Maximum Recommended Daily Dose:  0.703 Skin Sensitization:  0.954
Carcinogencity:  0.331 Eye Corrosion:  0.018
Eye Irritation:  0.971 Respiratory Toxicity:  0.58
Drug-induced Neurotoxicity:  0.066 Ototoxicity:  0.62
Hematotoxicity:  0.046 Drug-induced Nephrotoxicity:  0.096
Genotoxicity:  0.971 RPMI-8226 Immunitoxicity:  0.033
A549 Cytotoxicity:  0.685 Hek293 Cytotoxicity:  0.644
BCF:   1.057
?
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:   3.568
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.643
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.094
?
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
NPO21072 Rhododendron dauricum Species Ericaceae Eukaryota n.a. whole plant n.a. DOI[10.1007/BF02329610]
NPO3057 Polygonum aviculare Species Polygonaceae Eukaryota n.a. whole plant n.a. DOI[10.1016/S1572-557X(05)02007-6]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. cone n.a. PMID[10336650]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Leaves n.a. n.a. PMID[12088434]
NPO21072 Rhododendron dauricum Species Ericaceae Eukaryota n.a. n.a. n.a. PMID[15270561]
NPO12181 Albizia julibrissin Species Fabaceae Eukaryota n.a. bark n.a. PMID[15283458]
NPO12181 Albizia julibrissin Species Fabaceae Eukaryota n.a. stem n.a. PMID[15577257]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[15679315]
NPO25611 Smilax china Species Smilacaceae Eukaryota stems n.a. n.a. PMID[16252910]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[16252923]
NPO17782 Inula britannica Species Asteraceae Eukaryota flowers n.a. n.a. PMID[16643020]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. cone n.a. PMID[17624889]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[18611049]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[18768384]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[19476340]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. PMID[20815207]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. root n.a. PMID[21319773]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. leaf n.a. PMID[21319773]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. bark n.a. PMID[21319773]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[21707257]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[21912858]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. cone n.a. PMID[22111577]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. flower n.a. PMID[22166201]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. leaf n.a. PMID[22207282]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[23790907]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. root n.a. PMID[23806866]
NPO28265 Morus alba Species Moraceae Eukaryota root bark University of Veterinary and Pharmaceutical Sciences Brno (UVPS Brno), Brno, Czech Republic 2011-APR PMID[24901948]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. Konya, Turkey 2007-APR PMID[24901948]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[24948953]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[25564559]
NPO28265 Morus alba Species Moraceae Eukaryota leaves Chungbuk, Korea n.a. PMID[25935644]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. root n.a. PMID[25981820]
NPO25653 Spatholobus suberectus Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[26690274]
NPO9124 Inula japonica Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[27276091]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. latex n.a. PMID[27294120]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[29154541]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[29726697]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[30384263]
NPO28265 Morus alba Species Moraceae Eukaryota Root barks n.a. n.a. PMID[3097265]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[34443694]
NPO12935 Thymus quinquecostatus Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[34453492]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[34770961]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[35631245]
NPO3057 Polygonum aviculare Species Polygonaceae Eukaryota n.a. n.a. n.a. PMID[36558187]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36840093]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37020229]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37226152]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[37631012]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[38257205]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[38354824]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[38370080]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[38381096]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[38695450]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[39199155]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[39407547]
NPO12181 Albizia julibrissin Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[9051910]
NPO3057 Polygonum aviculare Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26378 Bistorta manshuriensis Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23213 Bistorta officinalis Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12935 Thymus quinquecostatus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25653 Spatholobus suberectus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25716 Persicaria orientalis Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21072 Rhododendron dauricum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12235 Trachelospermum jasminoides Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7132 Smilax glabra Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17782 Inula britannica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9124 Inula japonica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25611 Smilax china Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3057 Polygonum aviculare Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Essential Oil n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21072 Rhododendron dauricum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9124 Inula japonica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17782 Inula britannica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25653 Spatholobus suberectus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7132 Smilax glabra Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12235 Trachelospermum jasminoides Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12935 Thymus quinquecostatus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25611 Smilax china Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14834 Trachelospermum asiaticum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3057 Polygonum aviculare Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO17782 Inula britannica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3057 Polygonum aviculare Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25611 Smilax china Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12181 Albizia julibrissin Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9124 Inula japonica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7132 Smilax glabra Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23213 Bistorta officinalis Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21072 Rhododendron dauricum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12935 Thymus quinquecostatus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6826 Persicaria perfoliata Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25716 Persicaria orientalis Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12235 Trachelospermum jasminoides Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25653 Spatholobus suberectus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14834 Trachelospermum asiaticum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17782 Inula britannica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7132 Smilax glabra Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3057 Polygonum aviculare Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9124 Inula japonica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21072 Rhododendron dauricum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12181 Albizia julibrissin Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12235 Trachelospermum jasminoides Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25611 Smilax china Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25653 Spatholobus suberectus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7132 Smilax glabra Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9124 Inula japonica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12181 Albizia julibrissin Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21072 Rhododendron dauricum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12935 Thymus quinquecostatus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25611 Smilax china Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17782 Inula britannica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26378 Bistorta manshuriensis Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23213 Bistorta officinalis Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12235 Trachelospermum jasminoides Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25716 Persicaria orientalis Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO6826 Persicaria perfoliata Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3057 Polygonum aviculare Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25653 Spatholobus suberectus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14834 Trachelospermum asiaticum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12235 Trachelospermum jasminoides Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25611 Smilax china Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12181 Albizia julibrissin Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7132 Smilax glabra Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6826 Persicaria perfoliata Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14834 Trachelospermum asiaticum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17782 Inula britannica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21072 Rhododendron dauricum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12935 Thymus quinquecostatus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9124 Inula japonica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25653 Spatholobus suberectus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26378 Bistorta manshuriensis Species Polygonaceae 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
NPT199 Individual protein DNA polymerase kappa Homo sapiens Potency n.a. 1337.1 nM PubChem BioAssay data set
NPT197 Protein-protein interaction Menin/Histone-lysine N-methyltransferase MLL Homo sapiens Potency = 22387.2 nM PubChem BioAssay data set
NPT47 Individual protein ATP-dependent DNA helicase Q1 Homo sapiens Potency = 14125.4 nM PubChem BioAssay data set
NPT442 Individual protein Ferritin light chain Equus caballus Potency = 44668.4 nM PubChem BioAssay data set
NPT197 Protein-protein interaction Menin/Histone-lysine N-methyltransferase MLL Homo sapiens Potency = 25118.9 nM PubChem BioAssay data set
NPT49 Individual protein DNA-(apurinic or apyrimidinic site) lyase Homo sapiens Potency n.a. 15848.9 nM PubChem BioAssay data set

In vitro activity

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

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

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 NPC61506 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
1.0 High Similarity NPC36835
1.0 High Similarity NPC246162
1.0 High Similarity NPC9743
1.0 High Similarity NPC260491
1.0 High Similarity NPC240476
0.8125 Intermediate Similarity NPC62290
0.8125 Intermediate Similarity NPC142731
0.8125 Intermediate Similarity NPC326506
0.7959 Intermediate Similarity NPC19721
0.7551 Intermediate Similarity NPC21835
0.74 Intermediate Similarity NPC4152
0.7358 Intermediate Similarity NPC320825
0.7255 Intermediate Similarity NPC246328
0.7255 Intermediate Similarity NPC27532
0.717 Intermediate Similarity NPC611035
0.7115 Intermediate Similarity NPC44721
0.7115 Intermediate Similarity NPC211466
0.7115 Intermediate Similarity NPC605332
0.7091 Intermediate Similarity NPC326037
0.7091 Intermediate Similarity NPC13858
0.7059 Intermediate Similarity NPC279417
0.7059 Intermediate Similarity NPC49130
0.6981 Remote Similarity NPC250922
0.6792 Remote Similarity NPC306607
0.6792 Remote Similarity NPC606962
0.6731 Remote Similarity NPC208176
0.6719 Remote Similarity NPC186847
0.6415 Remote Similarity NPC261619
0.6415 Remote Similarity NPC61477
0.6415 Remote Similarity NPC78770
0.6415 Remote Similarity NPC219876
0.6415 Remote Similarity NPC126029
0.6415 Remote Similarity NPC15658
0.6182 Remote Similarity NPC321011
0.6182 Remote Similarity NPC294852
0.6182 Remote Similarity NPC188679
0.614 Remote Similarity NPC471744
0.6111 Remote Similarity NPC600246
0.6 Remote Similarity NPC160156
0.6 Remote Similarity NPC250963
0.6 Remote Similarity NPC325028
0.6 Remote Similarity NPC201837
0.6 Remote Similarity NPC274256
0.6 Remote Similarity NPC92565
0.6 Remote Similarity NPC109582
0.6 Remote Similarity NPC291220
0.6 Remote Similarity NPC256346
0.6 Remote Similarity NPC606550
0.5942 Remote Similarity NPC138688
0.5942 Remote Similarity NPC72787
0.5942 Remote Similarity NPC217795
0.5942 Remote Similarity NPC58223
0.5893 Remote Similarity NPC176869
0.5893 Remote Similarity NPC3779
0.5862 Remote Similarity NPC178054
0.5849 Remote Similarity NPC1940
0.5846 Remote Similarity NPC63438
0.5797 Remote Similarity NPC36916
0.5797 Remote Similarity NPC36
0.5797 Remote Similarity NPC7154
0.5797 Remote Similarity NPC125039
0.5797 Remote Similarity NPC7688
0.5758 Remote Similarity NPC270578
0.5758 Remote Similarity NPC52382
0.5735 Remote Similarity NPC607309
0.5672 Remote Similarity NPC163191
0.5667 Remote Similarity NPC150670
0.5634 Remote Similarity NPC279209
0.5634 Remote Similarity NPC102277
0.5634 Remote Similarity NPC479117
0.5556 Remote Similarity NPC75827
0.5556 Remote Similarity NPC601844
0.5507 Remote Similarity NPC22192
0.5507 Remote Similarity NPC606364
0.541 Remote Similarity NPC20907
0.5357 Remote Similarity NPC148011
0.5254 Remote Similarity NPC609065
0.5179 Remote Similarity NPC207179
0.5179 Remote Similarity NPC167571
0.5179 Remote Similarity NPC278552
0.5172 Remote Similarity NPC122828
0.5152 Remote Similarity NPC58190
0.5152 Remote Similarity NPC108811
0.5152 Remote Similarity NPC170103
0.5152 Remote Similarity NPC236202
0.5152 Remote Similarity NPC262911
0.5152 Remote Similarity NPC202742
0.5147 Remote Similarity NPC153342
0.5088 Remote Similarity NPC201227
0.5088 Remote Similarity NPC32441
0.5088 Remote Similarity NPC258474
0.5088 Remote Similarity NPC79943
0.5082 Remote Similarity NPC471515
0.5082 Remote Similarity NPC52530
0.5082 Remote Similarity NPC244250
0.5075 Remote Similarity NPC246202
0.5075 Remote Similarity NPC224161
0.5075 Remote Similarity NPC46335
0.5075 Remote Similarity NPC294558
0.5075 Remote Similarity NPC18185
0.5075 Remote Similarity NPC263940
0.5075 Remote Similarity NPC279406
0.5075 Remote Similarity NPC486519

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC61506 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
0.6415 Remote Similarity NPD1612 Clinical (unspecified phase)
0.6415 Remote Similarity NPD1613 Phase 4
0.5797 Remote Similarity NPD6166 Phase 2
0.5797 Remote Similarity NPD6167 Clinical (unspecified phase)
0.5797 Remote Similarity NPD6168 Clinical (unspecified phase)
0.5088 Remote Similarity NPD1552 Clinical (unspecified phase)

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