NPASS Compound

Natural Product: NPC313528

Natural Product ID	NPC313528
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	FEBLZLNTKCEFIT-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1599911
PubChem CID	3381
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001295] Hydroxysteroids [CHEMONTID:0003095] 21-hydroxysteroids

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

Chemical Representations

RDKit 3D 62 66 0 0 0 0 0 0 0 0999 V2000 -4.2527 1.8574 -0.7165 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9450 1.1642 -1.0712 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2317 -0.0188 -1.6868 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6158 -1.0281 -0.9575 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2491 -1.2463 -1.6253 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2180 -1.1474 -0.5589 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8191 -0.0672 -0.7558 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4708 -0.2139 -2.0811 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7190 0.6143 -2.2765 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6265 0.4739 -1.0797 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8805 0.1747 -1.2403 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8004 0.0244 -0.1158 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9952 -0.2603 -0.2728 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2134 0.2325 1.1946 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9448 0.5354 1.3396 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0133 0.6934 0.2271 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8263 -0.2496 0.3701 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2116 -0.0607 1.7100 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2801 -0.0085 1.6955 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9411 -0.9823 0.7751 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3050 -0.4328 0.3813 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1337 0.9281 0.0040 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3073 -0.5070 1.4127 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7596 0.5974 1.8021 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9015 -1.6609 2.0923 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9709 -1.2007 2.9051 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0536 -2.3555 1.3717 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5760 -1.1128 2.5798 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3237 -1.5357 0.2660 F 0 0 0 0 0 0 0 0 0 0 0 0 2.5245 2.1471 0.2968 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3826 0.2442 -3.4242 F 0 0 0 0 0 0 0 0 0 0 0 0 -2.2532 2.0838 -2.0756 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5876 2.3776 -1.6633 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0783 1.1275 -0.5252 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1480 2.6445 0.0251 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2521 -1.9031 -0.9669 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1043 -0.5894 -2.4901 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3058 -2.3104 -2.0061 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3796 -2.1086 -0.5426 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2980 0.9105 -0.6709 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7787 -0.0273 -2.9102 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8011 -1.2874 -2.2083 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4588 1.6853 -2.3285 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2397 0.0345 -2.2669 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8287 0.1390 2.1046 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5629 0.6807 2.3949 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5582 0.8674 2.2440 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6304 -0.2609 2.7380 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6547 1.0340 1.5302 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2231 -2.1443 2.8571 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2866 -2.4519 1.4607 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6038 -0.7446 2.2713 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9682 -2.8404 1.0020 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2142 -2.9734 0.9179 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9395 -2.3461 2.4793 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1707 -1.7515 2.1572 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3947 2.4802 1.3426 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3849 2.7554 -0.0999 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6767 2.3542 -0.3473 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8592 2.0564 -3.0129 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3591 3.1217 -1.6897 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2273 1.7877 -2.2823 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 2 0 12 14 1 0 14 15 2 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 21 23 1 0 23 24 2 0 23 25 1 0 25 26 1 0 20 27 1 0 18 28 1 0 17 29 1 0 16 30 1 0 9 31 1 0 2 32 1 0 22 2 1 0 21 4 1 0 20 6 1 0 17 7 1 0 16 10 1 0 1 33 1 0 1 34 1 0 1 35 1 0 4 36 1 0 5 37 1 0 5 38 1 0 6 39 1 0 7 40 1 0 8 41 1 0 8 42 1 0 9 43 1 0 11 44 1 0 14 45 1 0 15 46 1 0 18 47 1 0 19 48 1 0 19 49 1 0 25 50 1 0 25 51 1 0 26 52 1 0 27 53 1 0 27 54 1 0 27 55 1 0 28 56 1 0 30 57 1 0 30 58 1 0 30 59 1 0 32 60 1 0 32 61 1 0 32 62 1 0 M END

Standard InCHIKey	FEBLZLNTKCEFIT-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C24H30F2O6/c1-20(2)31-19-9-13-14-8-16(25)15-7-12(28)5-6-21(15,3)23(14,26)17(29)10-22(13,4)24(19,32-20)18(30)11-27/h5-7,13-14,16-17,19,27,29H,8-11H2,1-4H3
SMILES	CC1(OC2CC3C4CC(C5=CC(=O)C=CC5(C4(C(CC3(C2(O1)C(=O)CO)C)O)F)C)F)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	452.2	Volume:	435.208 ? Van der Waals volume.
Dense:	1.039	LogP:	2.267 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.657 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.54 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	2.0	Rigid Bonds:	26.0
TPSA:	93.06 ? Topological Polar Surface Area.	H-Bond Acceptor:	6.0
H-Bond Donor:	2.0	Rings:	5.0
Heavy Atoms:	8.0

MedChem Properties

QED Drug-Likeness Score:	0.668	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.023	Fsp³:	0.75
MCE-18:	99.524 ? 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:	0	PAINS Alert:	0
Colloidal aggregators:	0.026	Fluc inhibitor:	0.015 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.012 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.123 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.125	Promiscuous compounds:	0.06

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.846	MDCK Permeability:	-4.716
Pgp-inhibitor:	0.033	Pgp-substrate:	0.08
PAMPA:	0.637 ? 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):	0.37
20% Bioavailability (F20%):	0.82	30% Bioavailability (F30%):	0.99
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.999	MRP1:	0.971
Plasma Protein Binding (PPB):	61.114%	Volume Distribution (VD):	0.095
Fu:	34.537% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.009
OATP1B3 inhibitor:	0.266	BCRP inhibitor:	0.007
BSEP inhibitor:	0.995

ADMET: Metabolism

CYP1A2-inhibitor:	0.003	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.909	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.986	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.003	CYP2D6-substrate:	0.996
CYP3A4-inhibitor:	0.024	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.001	CYP2C8-inhibitor:	0.0
HLM stability:	0.763 ? 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):

11.013

Half-life (T1/2):

2.398

ADMET: Toxicity

hERG Blockers:	0.065	hERG Blockers (10um):	0.369
Human Hepatotoxicity (H-HT):	0.728	Drug-induced Liver Injury (DILI):	0.055
AMES Toxicity:	0.394	Rat Oral Acute Toxicity:	0.788
Maximum Recommended Daily Dose:	0.852	Skin Sensitization:	0.018
Carcinogencity:	0.725	Eye Corrosion:	0.0
Eye Irritation:	0.007	Respiratory Toxicity:	0.751
Drug-induced Neurotoxicity:	0.138	Ototoxicity:	0.927
Hematotoxicity:	0.045	Drug-induced Nephrotoxicity:	0.014
Genotoxicity:	0.883	RPMI-8226 Immunitoxicity:	0.035
A549 Cytotoxicity:	0.009	Hek293 Cytotoxicity:	0.628
BCF:	0.923 ? 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:	3.671 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.478 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.649 ? 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]
NPO25089	Cinchona calisaya	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11992775]
NPO21072	Rhododendron dauricum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15270561]
NPO25870	Vaccinium vitis-idaea	Species	Ericaceae	Eukaryota	n.a.	fruit	n.a.	PMID[16417304]
NPO4626	Pimpinella anisum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[36432786]
NPO4626	Pimpinella anisum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[36840093]
NPO4626	Pimpinella anisum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[37379658]
NPO4626	Pimpinella anisum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[37446712]
NPO19694	Senecio scandens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO366	Pyrus communis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25870	Vaccinium vitis-idaea	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO21072	Rhododendron dauricum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO4626	Pimpinella anisum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15565	Pinus resinosa	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25089	Cinchona calisaya	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO16481	Xanthium canadense	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11045	Paederia scandens	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO4626	Pimpinella anisum	Species	Apiaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO366	Pyrus communis	Species	Rosaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO25870	Vaccinium vitis-idaea	Species	Ericaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO4626	Pimpinella anisum	Species	Apiaceae	Eukaryota	Essential Oil	n.a.	n.a.	Database[FooDB]
NPO366	Pyrus communis	Species	Rosaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO366	Pyrus communis	Species	Rosaceae	Eukaryota	Pericarp	n.a.	n.a.	Database[FooDB]
NPO4626	Pimpinella anisum	Species	Apiaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO4626	Pimpinella anisum	Species	Apiaceae	Eukaryota	Tissue Culture	n.a.	n.a.	Database[FooDB]
NPO4626	Pimpinella anisum	Species	Apiaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO25870	Vaccinium vitis-idaea	Species	Ericaceae	Eukaryota	Fruits	n.a.		Database[FooDB]
NPO366	Pyrus communis	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[FooDB]
NPO8886	Protea mellifera	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15565	Pinus resinosa	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23604	Fructus choerospondiatis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[HerDing]
NPO29385	Nidus vespae	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[HerDing]
NPO25870	Vaccinium vitis-idaea	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO366	Pyrus communis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4626	Pimpinella anisum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21072	Rhododendron dauricum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16481	Xanthium canadense	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19694	Senecio scandens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11045	Paederia scandens	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO366	Pyrus communis	Species	Rosaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO366	Pyrus communis	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[Phenol-Explorer]
NPO23604	Fructus choerospondiatis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO16481	Xanthium canadense	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19694	Senecio scandens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25089	Cinchona calisaya	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25870	Vaccinium vitis-idaea	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21072	Rhododendron dauricum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4626	Pimpinella anisum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29385	Nidus vespae	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO11045	Paederia scandens	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15565	Pinus resinosa	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO366	Pyrus communis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8886	Protea mellifera	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15565	Pinus resinosa	Species	Pinaceae	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]
NPO11045	Paederia scandens	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21072	Rhododendron dauricum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO19694	Senecio scandens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO19694	Senecio scandens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25870	Vaccinium vitis-idaea	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16481	Xanthium canadense	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO366	Pyrus communis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4626	Pimpinella anisum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25089	Cinchona calisaya	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15565	Pinus resinosa	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8886	Protea mellifera	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11045	Paederia scandens	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21072	Rhododendron dauricum	Species	Ericaceae	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

Activity Type	# Activity
Potency	14

Activity Type	# Activity
Individual protein	5
Organism	4
Nucleic acid	2
Others	3

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT135	Individual protein	Chromobox protein homolog 1	Homo sapiens	Potency	n.a.	89125.1	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
NPT483	Individual protein	Prelamin-A/C	Homo sapiens	Potency	=	316.2	nM	PubChem BioAssay data set
NPT861	Individual protein	Isocitrate dehydrogenase [NADP] cytoplasmic	Homo sapiens	Potency	n.a.	290.9	nM	PubChem BioAssay data set
NPT536	Nucleic acid	microRNA 21	Homo sapiens	Potency	=	1.6	nM	PubChem BioAssay data set
NPT64	Individual protein	ATPase family AAA domain-containing protein 5	Homo sapiens	Potency	n.a.	25918.5	nM	PubChem BioAssay data set

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Potency	n.a.	13459.1	nM	PubChem BioAssay data set
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Potency	n.a.	5858.4	nM	PubChem BioAssay data set
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Potency	n.a.	10417.9	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	354.8	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	2818.4	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	22387.2	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
-	Mus musculus	LD50	=	3.6427756	mg/kg	TOXRIC

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

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 NPC313528 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	18662
0.1-0.2	30838
0.2-0.3	355
0.3-0.4	3
0.4-0.5	0
0.5-0.6	0
0.6-0.7	0
0.7-0.8	2
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
		NPC

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC313528 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6887
0.1-0.2	2151
0.2-0.3	42
0.3-0.4	32
0.4-0.5	14
0.5-0.6	19
0.6-0.7	1
0.7-0.8	2
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD5988	Phase 4
0.8108	Intermediate Similarity	NPD6616	Phase 4
0.7534	Intermediate Similarity	NPD5956	Phase 4
0.7534	Intermediate Similarity	NPD6015	Phase 4
0.6711	Remote Similarity	NPD6016	Phase 4
0.5952	Remote Similarity	NPD7492	Phase 4
0.5867	Remote Similarity	NPD5168	Approved
0.5867	Remote Similarity	NPD5173	Phase 4
0.5823	Remote Similarity	NPD6313	Phase 4
0.5823	Remote Similarity	NPD6314	Approved
0.5556	Remote Similarity	NPD6059	Phase 4
0.5556	Remote Similarity	NPD6336	Discontinued
0.5513	Remote Similarity	NPD5174	Approved
0.5513	Remote Similarity	NPD5175	Phase 2
0.5488	Remote Similarity	NPD6617	Phase 4
0.5422	Remote Similarity	NPD6317	Phase 4
0.5385	Remote Similarity	NPD5127	Approved
0.5366	Remote Similarity	NPD6868	Phase 4
0.5349	Remote Similarity	NPD7604	Phase 2
0.5309	Remote Similarity	NPD6054	Phase 4
0.5172	Remote Similarity	NPD6847	Phase 4
0.5111	Remote Similarity	NPD7078	Phase 4
0.506	Remote Similarity	NPD5134	Clinical (unspecified phase)
0.506	Remote Similarity	NPD5135	Approved

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