NPASS Compound

Natural Product: NPC116717

Natural Product ID	NPC116717
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Nimbin
IUPAC Name	n.a.
Synonyms	Nimbin
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1774397
PubChem CID	108058
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids [CHEMONTID:0002380] Limonoids

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 75 79 0 0 0 0 0 0 0 0999 V2000 4.0457 0.9613 1.8884 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3306 -0.2015 1.2729 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0262 -0.2573 1.1012 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7326 -1.5676 0.4628 C 0 0 1 0 0 0 0 0 0 0 0 0 2.9345 -2.4456 0.7475 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0251 -1.4105 0.8142 C 0 0 1 0 0 0 0 0 0 0 0 0 4.7294 -1.3094 -0.4548 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2453 -0.8134 -1.6351 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2483 -0.9103 -2.5793 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2865 -1.4377 -2.0011 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0426 -1.6977 -0.7384 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6519 -1.9972 1.1540 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1467 -0.8979 1.4828 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.5130 -0.9633 0.9379 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.9792 0.0122 -0.0551 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4454 0.2781 -0.0706 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.0785 0.7334 1.2067 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8110 1.2004 -1.1759 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9312 1.8621 -1.8998 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4793 1.7136 -1.6361 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6743 1.9507 -2.5173 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1387 1.2629 -0.2451 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.5771 2.3911 0.6433 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3021 0.8958 -0.1040 C 0 0 1 0 0 0 0 0 0 0 0 0 1.3321 1.7256 -0.7410 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4926 3.1259 -0.4241 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0743 3.5662 0.5950 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9967 4.1087 -1.2576 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1617 5.4731 -0.9377 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6474 0.3530 1.2478 C 0 0 2 0 0 0 0 0 0 0 0 0 0.5489 1.2186 2.4229 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1640 -1.0040 -0.4460 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0624 -1.5069 0.2694 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.8422 -1.6692 -1.6156 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5132 -2.8590 -1.9661 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7174 -2.3134 0.5100 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5064 -3.2320 1.1373 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1060 -2.8728 2.1806 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7023 -4.6243 0.6699 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7552 1.3187 1.0909 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3877 1.7807 2.1528 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7018 0.6216 2.7237 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6397 -1.5541 -0.6228 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8255 -3.0365 1.6592 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1730 -3.1301 -0.0922 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7344 -1.7969 1.6142 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2812 -0.4009 -1.8827 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1931 -0.6023 -3.6304 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7556 -2.1348 -0.0690 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2173 -1.0252 2.6074 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2156 -0.8876 1.8251 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8243 -0.5299 -1.0610 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4201 1.8033 1.0611 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5111 0.5987 2.1178 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0659 0.2082 1.4021 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8975 1.3250 -1.3873 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2197 2.5105 -2.6835 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8070 3.1860 0.5725 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4801 2.8655 0.1494 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7669 2.1508 1.6805 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3342 -0.0714 -0.7366 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3781 1.5003 -1.8398 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3302 1.2345 -0.4170 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1989 5.8098 -0.9699 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5023 6.0445 -1.6507 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6898 5.6584 0.0713 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5140 2.2819 2.3493 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3319 0.8877 3.0687 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4119 0.9604 3.1154 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9608 -3.4616 -2.7033 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6927 -3.4988 -1.0900 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5074 -2.5780 -2.3809 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5840 -4.6549 -0.4420 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7641 -4.8895 0.8862 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0064 -5.3359 1.1573 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 2 0 9 10 1 0 10 11 1 0 4 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 1 16 18 1 0 18 19 2 0 19 20 1 0 20 21 2 0 20 22 1 0 22 23 1 1 22 24 1 0 24 25 1 0 25 26 1 0 26 27 2 0 26 28 1 0 28 29 1 0 24 30 1 0 30 31 1 1 16 32 1 0 32 33 2 0 32 34 1 0 34 35 1 0 14 36 1 0 36 37 1 0 37 38 2 0 37 39 1 0 6 2 1 0 11 7 2 0 30 13 1 0 30 3 1 0 22 15 1 0 1 40 1 0 1 41 1 0 1 42 1 0 4 43 1 6 5 44 1 0 5 45 1 0 6 46 1 1 8 47 1 0 9 48 1 0 11 49 1 0 13 50 1 1 14 51 1 1 15 52 1 6 17 53 1 0 17 54 1 0 17 55 1 0 18 56 1 0 19 57 1 0 23 58 1 0 23 59 1 0 23 60 1 0 24 61 1 6 25 62 1 0 25 63 1 0 29 64 1 0 29 65 1 0 29 66 1 0 31 67 1 0 31 68 1 0 31 69 1 0 35 70 1 0 35 71 1 0 35 72 1 0 39 73 1 0 39 74 1 0 39 75 1 0 M END

Standard InCHIKey	NHOIBRJOQAYBJT-IMGVWCFESA-N
Standard InCHI	InChI=1S/C30H36O9/c1-15-18(17-9-11-37-14-17)12-19-23(15)30(5)20(13-22(33)35-6)29(4)21(32)8-10-28(3,27(34)36-7)25(29)24(26(30)39-19)38-16(2)31/h8-11,14,18-20,24-26H,12-13H2,1-7H3/t18-,19-,20-,24-,25+,26-,28-,29+,30-/m1/s1
SMILES	CC1=C2[C@@H](C[C@H]1c1ccoc1)O[C@@H]1[C@@H]([C@H]3[C@@](C)(C=CC(=O)[C@]3(C)[C@@H](CC(=O)OC)[C@]21C)C(=O)OC)OC(=O)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	540.24	Volume:	542.674 ? Van der Waals volume.
Dense:	0.996	LogP:	2.226 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.447 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.26 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	8.0	Rigid Bonds:	28.0
TPSA:	118.34 ? Topological Polar Surface Area.	H-Bond Acceptor:	9.0
H-Bond Donor:	0.0	Rings:	5.0
Heavy Atoms:	9.0

MedChem Properties

QED Drug-Likeness Score:	0.311	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.314	Fsp³:	0.6
MCE-18:	126.417 ? 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:	Accepted	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.743	Fluc inhibitor:	0.002 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.086 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.001 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.17	Promiscuous compounds:	0.315

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.083	MDCK Permeability:	-4.714
Pgp-inhibitor:	0.881	Pgp-substrate:	0.592
PAMPA:	0.173 ? 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):	0.0
20% Bioavailability (F20%):	0.493	30% Bioavailability (F30%):	0.553
50% Bioavailability (F50%):	0.968

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.27	MRP1:	1.0
Plasma Protein Binding (PPB):	77.024%	Volume Distribution (VD):	-0.131
Fu:	23.207% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.707
OATP1B3 inhibitor:	0.529	BCRP inhibitor:	0.096
BSEP inhibitor:	0.999

ADMET: Metabolism

CYP1A2-inhibitor:	0.48	CYP1A2-substrate:	0.685
CYP2C19-inhibitor:	0.118	CYP2C19-substrate:	0.03
CYP2C9-inhibitor:	0.001	CYP2C9-substrate:	0.059
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.645
CYP3A4-inhibitor:	0.988	CYP3A4-substrate:	0.24
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.994
HLM stability:	0.963 ? 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):

9.623

Half-life (T1/2):

1.07

ADMET: Toxicity

hERG Blockers:	0.099	hERG Blockers (10um):	0.106
Human Hepatotoxicity (H-HT):	0.625	Drug-induced Liver Injury (DILI):	0.921
AMES Toxicity:	0.593	Rat Oral Acute Toxicity:	0.877
Maximum Recommended Daily Dose:	0.983	Skin Sensitization:	0.923
Carcinogencity:	0.823	Eye Corrosion:	0.0
Eye Irritation:	0.069	Respiratory Toxicity:	0.888
Drug-induced Neurotoxicity:	0.733	Ototoxicity:	0.589
Hematotoxicity:	0.666	Drug-induced Nephrotoxicity:	0.975
Genotoxicity:	0.988	RPMI-8226 Immunitoxicity:	0.201
A549 Cytotoxicity:	0.529	Hek293 Cytotoxicity:	0.207
BCF:	0.675 ? 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:	3.416 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.219 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.587 ? 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
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1007/s12038-008-0027-6]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12193038]
NPO7202	Goniothalamus giganteus	Species	Annonaceae	Eukaryota	bark	n.a.	n.a.	PMID[1479382]
NPO7202	Goniothalamus giganteus	Species	Annonaceae	Eukaryota	n.a.	bark	n.a.	PMID[1479382]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1593280]
NPO7202	Goniothalamus giganteus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1791471]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18816111]
NPO5587	Chisocheton ceramicus	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19081726]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19299148]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	fruits	n.a.	n.a.	PMID[20669933]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[21381696]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	seed	n.a.	PMID[21381696]
NPO5587	Chisocheton ceramicus	Species	Meliaceae	Eukaryota	n.a.	bark	n.a.	PMID[21428417]
NPO5587	Chisocheton ceramicus	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21428417]
NPO5587	Chisocheton ceramicus	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23395661]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2607354]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2614419]
NPO7202	Goniothalamus giganteus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2614426]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26339153]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[28493718]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[37151484]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	leaf	n.a.	PMID[9134742]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	bark	n.a.	PMID[9134742]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	fruit	n.a.	PMID[9134742]
NPO7202	Goniothalamus giganteus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9322367]
NPO7202	Goniothalamus giganteus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9917277]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO2006	Centaurea sinaica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO5587	Chisocheton ceramicus	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO774	Cleome pungens	Species	Cleomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9217	Daphniphyllum angustifolium	Species	Daphniphyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO7202	Goniothalamus giganteus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8249	Marcetella moquiniana	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3846	Melia indica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO2423	Melochia corchorifolia	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO1058	Pestalotiopsis heterocornis	Species	Sporocadaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15379	Phalaenopsis schilleriana	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8783	Stachys palustris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO26224	Walsura piscidia	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO1594	[enterobacter] aerogenes	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]
NPO7202	Goniothalamus giganteus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3846	Melia indica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7202	Goniothalamus giganteus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3846	Melia indica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8783	Stachys palustris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26224	Walsura piscidia	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8783	Stachys palustris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7202	Goniothalamus giganteus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7202	Goniothalamus giganteus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15379	Phalaenopsis schilleriana	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2006	Centaurea sinaica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8249	Marcetella moquiniana	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26224	Walsura piscidia	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1058	Pestalotiopsis heterocornis	Species	Sporocadaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5587	Chisocheton ceramicus	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO774	Cleome pungens	Species	Cleomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3846	Melia indica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2423	Melochia corchorifolia	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1594	[enterobacter] aerogenes	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO9217	Daphniphyllum angustifolium	Species	Daphniphyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8783	Stachys palustris	Species	Lamiaceae	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	4
AFI	1
Survival	5

Activity Type	# Activity
Cell line	2
Non-molecular	2
Organism	6

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
NPT81	Cell line	A549	Homo sapiens	IC50	>	20000.0	nM	PMID[21381696]
NPT134	Cell line	SK-BR-3	Homo sapiens	IC50	>	20000.0	nM	PMID[21381696]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	IC50	=	15900.0	nM	PMID[21381696]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	IC50	>	20000.0	nM	PMID[21381696]
NPT1175	Organism	Spodoptera litura	Spodoptera litura	AFI	=	33.7	%	PMID[12137465]

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT847	Organism	Reticulitermes speratus	Reticulitermes speratus	Survival	=	80.5	%	DOI[10.1271/bbb.56.1835]
NPT847	Organism	Reticulitermes speratus	Reticulitermes speratus	Survival	=	83.0	%	DOI[10.1271/bbb.56.1835]
NPT847	Organism	Reticulitermes speratus	Reticulitermes speratus	Survival	=	84.5	%	DOI[10.1271/bbb.56.1835]
NPT847	Organism	Reticulitermes speratus	Reticulitermes speratus	Survival	=	84.0	%	DOI[10.1271/bbb.56.1835]

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 NPC116717 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	9687
0.1-0.2	38376
0.2-0.3	1624
0.3-0.4	139
0.4-0.5	16
0.5-0.6	9
0.6-0.7	4
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9296	High Similarity	NPC5180
0.7662	Intermediate Similarity	NPC291150
0.7125	Intermediate Similarity	NPC197137
0.619	Remote Similarity	NPC470118
0.618	Remote Similarity	NPC308205
0.6067	Remote Similarity	NPC322546
0.6044	Remote Similarity	NPC475226
0.5895	Remote Similarity	NPC61967
0.5789	Remote Similarity	NPC475641
0.5714	Remote Similarity	NPC475237
0.5699	Remote Similarity	NPC214495
0.5699	Remote Similarity	NPC470119
0.5682	Remote Similarity	NPC604850
0.5591	Remote Similarity	NPC488535
0.5275	Remote Similarity	NPC182427
0.5217	Remote Similarity	NPC29695

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC116717 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3164
0.1-0.2	5936
0.2-0.3	50
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