NPASS Compound

Natural Product: NPC269058

Natural Product ID	NPC269058
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	DATCMCBQCCLKRF-HMSDPZTLSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL258445
PubChem CID	24770660
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0002321] Cycloartanols 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

RDKit 3D 83 87 0 0 0 0 0 0 0 0999 V2000 8.7191 0.7911 -0.5500 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2749 0.7798 -0.2319 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7963 -0.0865 0.6406 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3479 -0.1422 0.9990 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7676 -1.5142 0.6646 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2955 -1.5799 1.0279 C 0 0 1 0 0 0 0 0 0 0 0 0 3.2489 -1.3159 2.5148 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4722 -0.6125 0.2324 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5817 -0.8546 -1.2538 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1866 -0.8481 -1.8328 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4051 -0.1437 -0.7742 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6834 1.3309 -0.8922 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0587 -0.3705 -0.8245 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6013 0.5963 -1.8926 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0809 0.2570 -2.0374 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7257 0.7788 -0.7734 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.2201 0.5848 -0.7797 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6702 -0.2015 -2.0087 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9804 1.8880 -0.8007 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7000 -0.1999 0.4230 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.2433 0.4092 1.7170 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.7776 0.8278 1.6696 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.1765 0.1465 0.4612 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.9793 -1.3026 0.5961 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7857 -0.2970 0.4536 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.0075 -0.0152 1.6710 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4586 0.0606 1.6059 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0021 -0.7548 0.4824 C 0 0 2 0 0 0 0 0 0 0 0 0 0.6557 -2.2073 0.5260 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6308 2.2015 1.6174 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0435 1.4771 2.1141 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.1065 -0.1384 0.4034 O 0 0 0 0 0 0 0 0 0 0 0 0 6.3633 1.7420 -0.8929 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1764 -0.2209 -0.5191 H 0 0 0 0 0 0 0 0 0 0 0 0 9.3162 1.4311 0.1329 H 0 0 0 0 0 0 0 0 0 0 0 0 8.8356 1.1741 -1.5868 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4600 -0.7905 1.1243 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8377 0.6359 0.4100 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2769 -0.0293 2.0815 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2783 -2.2345 1.3403 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9800 -1.8192 -0.3580 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9820 -2.6277 0.8756 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2320 -1.6887 2.9463 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2362 -0.2421 2.7745 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4468 -1.8722 3.0438 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8238 0.4094 0.4709 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1195 -1.7653 -1.5120 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1209 0.0017 -1.7410 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1493 -0.3298 -2.8185 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8690 -1.9030 -1.9682 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0195 1.9630 -0.2808 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7375 1.6089 -0.7557 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4561 1.5997 -1.9667 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2240 -1.3850 -1.2984 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5354 1.6475 -1.5569 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1285 0.3824 -2.8518 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4491 0.8631 -2.8872 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2615 -0.8139 -2.1280 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5270 1.8695 -0.7297 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7829 -0.2506 -1.9435 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4319 0.3670 -2.9218 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2582 -1.2250 -1.9972 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4619 2.0755 -1.8002 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3525 2.7677 -0.5894 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8385 1.8771 -0.0807 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4360 -1.2717 0.3449 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3457 -0.3694 2.5001 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2750 0.4963 2.6254 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0533 -1.7604 1.5928 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1171 -2.0031 -0.2493 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2916 -0.7695 2.4552 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3773 0.9642 2.0986 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8920 -0.1880 2.5923 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7568 1.1165 1.4211 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7970 -2.6594 1.5230 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2880 -2.7947 -0.1915 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3790 -2.4508 0.2121 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1883 2.6040 2.3214 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6741 1.2172 2.8500 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5167 -0.9597 0.0730 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5516 1.2447 -1.4601 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9049 2.4028 -1.5877 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8908 2.4183 -0.1357 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 3 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 6 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 1 11 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 17 19 1 0 17 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 6 25 24 1 1 25 26 1 0 26 27 1 0 27 28 1 0 28 29 1 1 22 30 1 0 21 31 1 0 20 32 1 0 2 33 1 0 28 8 1 0 28 11 1 0 25 13 1 0 23 16 1 0 25 23 1 0 1 34 1 0 1 35 1 0 1 36 1 0 3 37 1 0 4 38 1 0 4 39 1 0 5 40 1 0 5 41 1 0 6 42 1 1 7 43 1 0 7 44 1 0 7 45 1 0 8 46 1 6 9 47 1 0 9 48 1 0 10 49 1 0 10 50 1 0 12 51 1 0 12 52 1 0 12 53 1 0 13 54 1 6 14 55 1 0 14 56 1 0 15 57 1 0 15 58 1 0 16 59 1 1 18 60 1 0 18 61 1 0 18 62 1 0 19 63 1 0 19 64 1 0 19 65 1 0 20 66 1 6 21 67 1 1 22 68 1 1 24 69 1 0 24 70 1 0 26 71 1 0 26 72 1 0 27 73 1 0 27 74 1 0 29 75 1 0 29 76 1 0 29 77 1 0 30 78 1 0 31 79 1 0 32 80 1 0 33 81 1 0 33 82 1 0 33 83 1 0 M END

Standard InCHIKey	DATCMCBQCCLKRF-HMSDPZTLSA-N
Standard InCHI	InChI=1S/C30H50O3/c1-18(2)9-8-10-19(3)20-13-14-28(7)22-12-11-21-26(4,5)24(32)23(31)25(33)30(21)17-29(22,30)16-15-27(20,28)6/h9,19-25,31-33H,8,10-17H2,1-7H3/t19-,20-,21+,22+,23+,24-,25+,27-,28+,29+,30-/m1/s1
SMILES	CC(=CCC[C@@H](C)[C@H]1CC[C@@]2(C)[C@@H]3CC[C@H]4C(C)(C)[C@@H]([C@@H]([C@@H]([C@]54C[C@@]35CC[C@]12C)O)O)O)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	458.38	Volume:	508.388 ? Van der Waals volume.
Dense:	0.902	LogP:	4.821 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.264 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.304 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	4.0	Rigid Bonds:	23.0
TPSA:	60.69 ? Topological Polar Surface Area.	H-Bond Acceptor:	3.0
H-Bond Donor:	3.0	Rings:	5.0
Heavy Atoms:	3.0

MedChem Properties

QED Drug-Likeness Score:	0.445	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.839	Fsp³:	0.933
MCE-18:	137.586 ? 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:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.78	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.006 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.0 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.358	Promiscuous compounds:	0.135

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.622	MDCK Permeability:	-5.168
Pgp-inhibitor:	0.001	Pgp-substrate:	0.044
PAMPA:	0.798 ? 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):	0.013
20% Bioavailability (F20%):	0.14	30% Bioavailability (F30%):	0.532
50% Bioavailability (F50%):	0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.332	MRP1:	0.062
Plasma Protein Binding (PPB):	93.059%	Volume Distribution (VD):	-0.213
Fu:	7.303% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	0.998	BCRP inhibitor:	0.61
BSEP inhibitor:	0.001

ADMET: Metabolism

CYP1A2-inhibitor:	0.001	CYP1A2-substrate:	0.087
CYP2C19-inhibitor:	0.991	CYP2C19-substrate:	0.005
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.002
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.01
CYP3A4-inhibitor:	0.293	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.972
HLM stability:	0.987 ? 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):

9.927

Half-life (T1/2):

1.078

ADMET: Toxicity

hERG Blockers:	0.094	hERG Blockers (10um):	0.446
Human Hepatotoxicity (H-HT):	0.47	Drug-induced Liver Injury (DILI):	0.09
AMES Toxicity:	0.441	Rat Oral Acute Toxicity:	0.333
Maximum Recommended Daily Dose:	0.123	Skin Sensitization:	0.99
Carcinogencity:	0.618	Eye Corrosion:	0.035
Eye Irritation:	0.745	Respiratory Toxicity:	0.912
Drug-induced Neurotoxicity:	0.054	Ototoxicity:	0.58
Hematotoxicity:	0.704	Drug-induced Nephrotoxicity:	0.744
Genotoxicity:	0.175	RPMI-8226 Immunitoxicity:	0.093
A549 Cytotoxicity:	0.715	Hek293 Cytotoxicity:	0.228
BCF:	3.324 ? 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:	5.303 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.731 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	6.307 ? 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
NPO11707	Ruta chalepensis	Species	Rutaceae	Eukaryota	roots	northern Saudi desert	n.a.	PMID[10924184]
NPO6831	Commiphora opobalsamum	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18177010]
NPO6831	Commiphora opobalsamum	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11707	Ruta chalepensis	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9036	Dipteryx lacunifera	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9883	Allium giganteum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO7260	Angelica genuflexa	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10085	Aspergillus varians	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3693	Calpurnia aurea	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO29336	Corynandra chelidonii	Species	Cleomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO4463	Cytisus canariensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO6022	Cytisus supinus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO24891	Elmerina caryae	Species	Aporpiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25831	Siphonoglossa sessilis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]
NPO5284	Ramalina hierrensis	Species	Ramalinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9639	Prunus puddum	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8810	Pinus austriaca	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO2328	Lagochilus setulosus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8297	Hydnellum caeruleum	Species	Thelephoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO1586	Gorgonocephalus chilensis	Species	Gorgonocephalidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8985	Gazania rigens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO5886	Fossombronia alaskana	Species	Fossombroniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO817	Dictamnus angustifolius	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO7260	Angelica genuflexa	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11707	Ruta chalepensis	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO817	Dictamnus angustifolius	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO817	Dictamnus angustifolius	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7260	Angelica genuflexa	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11707	Ruta chalepensis	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8297	Hydnellum caeruleum	Species	Thelephoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11707	Ruta chalepensis	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO10085	Aspergillus varians	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2328	Lagochilus setulosus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7260	Angelica genuflexa	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8985	Gazania rigens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24891	Elmerina caryae	Species	Aporpiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5284	Ramalina hierrensis	Species	Ramalinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1586	Gorgonocephalus chilensis	Species	Gorgonocephalidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8810	Pinus austriaca	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29336	Corynandra chelidonii	Species	Cleomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO817	Dictamnus angustifolius	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9036	Dipteryx lacunifera	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6022	Cytisus supinus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4463	Cytisus canariensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9639	Prunus puddum	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25831	Siphonoglossa sessilis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO3693	Calpurnia aurea	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9883	Allium giganteum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11707	Ruta chalepensis	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6831	Commiphora opobalsamum	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5886	Fossombronia alaskana	Species	Fossombroniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8297	Hydnellum caeruleum	Species	Thelephoraceae	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
IC50	2

Activity Type	# Activity
Cell line	2

Molecular-level activity

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

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT306	Cell line	PC-3	Homo sapiens	IC50	>	50000.0	nM	PMID[18177010]
NPT90	Cell line	DU-145	Homo sapiens	IC50	>	50000.0	nM	PMID[18177010]

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

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 NPC269058 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	28390
0.1-0.2	19187
0.2-0.3	2038
0.3-0.4	171
0.4-0.5	56
0.5-0.6	6
0.6-0.7	5
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC71520
0.75	Intermediate Similarity	NPC275671
0.7358	Intermediate Similarity	NPC113978
0.6481	Remote Similarity	NPC85346
0.6481	Remote Similarity	NPC65897
0.6481	Remote Similarity	NPC80237
0.629	Remote Similarity	NPC300179
0.6	Remote Similarity	NPC289670
0.5965	Remote Similarity	NPC302041
0.5873	Remote Similarity	NPC102426
0.541	Remote Similarity	NPC89747
0.5254	Remote Similarity	NPC214770
0.5254	Remote Similarity	NPC477856
0.5085	Remote Similarity	NPC604180

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC269058 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	8283
0.1-0.2	843
0.2-0.3	24
0.3-0.4	0
0.4-0.5	0
0.5-0.6	0
0.6-0.7	0
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
		NPD

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