NPASS Compound

Natural Product: NPC491676

Natural Product ID	NPC491676
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	alpha-Cryptoxanthin
IUPAC Name	(1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-2-en-1-ol
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds]

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 97 98 0 0 0 0 0 0 0 0999 V2000 -3.8767 2.2521 1.2022 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2772 1.9224 0.8274 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0959 2.9847 0.6638 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4837 2.6836 0.2927 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.2807 3.7791 0.5763 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.0003 1.5481 1.1675 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1987 0.3046 0.8736 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4268 -0.7048 1.9787 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7600 -0.3100 -0.3884 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7100 0.5416 0.6156 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9077 -0.5125 1.2906 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2926 -1.4168 0.5474 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4995 -2.5488 0.6247 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3602 -3.2070 1.9723 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9045 -3.0916 -0.3974 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0649 -4.3138 -0.4178 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3969 -4.3499 -1.5721 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4943 -5.1280 -2.2659 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0317 -6.4666 -2.1104 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1357 -4.4151 -3.2451 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0838 -4.6181 -4.2511 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6593 -3.4460 -4.6210 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5299 -2.7201 -5.3934 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8791 -1.4929 -4.8374 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9579 -1.6664 -3.3822 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1556 -0.1567 -4.8406 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6894 0.2345 -3.6475 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1758 1.2945 -2.8752 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7369 0.8137 -1.7074 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8671 -0.5584 -1.3547 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8452 1.9510 -0.6317 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3355 1.5515 0.4858 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5210 2.3793 1.6866 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1229 1.6932 2.6818 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5007 0.2800 2.4876 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3727 2.3471 3.9901 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5966 3.8423 3.8347 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4284 4.4416 3.1168 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8879 3.6667 1.9818 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5875 4.6232 0.8832 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4006 3.2931 2.4794 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7630 3.3487 1.4130 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1641 2.0681 0.3411 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5200 1.6344 2.0418 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7246 3.9670 0.8041 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6313 2.3694 -0.7403 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.2461 3.5021 0.6000 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.9131 1.8710 2.2303 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.0546 1.3405 0.9668 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.2712 -0.3643 2.6530 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5892 -0.8665 2.6640 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6925 -1.7093 1.5561 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9634 -0.2986 -1.1822 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.0116 -1.3724 -0.1746 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.6835 0.1833 -0.7391 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6038 0.3869 -0.5158 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6732 -0.5729 2.3140 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5416 -1.1586 -0.5672 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4754 -3.8303 2.0396 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3378 -3.7333 2.2038 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2462 -2.3713 2.7341 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1425 -2.6390 -1.3800 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9162 -5.0377 0.2655 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8873 -3.5084 -2.2907 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0433 -7.1409 -2.9576 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1760 -6.3660 -1.8274 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3420 -6.9629 -1.1814 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3783 -3.3625 -3.2522 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4755 -5.4105 -4.7891 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7623 -2.7005 -4.2353 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0605 -2.7956 -6.3057 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2427 -0.8111 -2.8084 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3053 -2.5660 -3.0241 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9912 -1.4788 -3.8481 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0992 0.6682 -5.4814 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7752 -0.8288 -3.1002 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2046 2.3073 -3.0182 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8932 -0.7210 -0.8213 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0595 -1.2548 -2.2560 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0856 -0.9086 -0.7051 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5484 2.8743 -0.9157 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6068 0.4810 0.5197 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5928 -0.3619 2.6699 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0501 0.0411 1.5904 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1836 0.0005 3.3478 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6678 2.0427 4.7526 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3662 1.9453 4.3268 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5314 3.9884 3.2106 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7989 4.2616 4.8173 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6014 4.4311 3.9214 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5488 5.5130 2.9160 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8420 4.3171 0.1437 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4457 5.0874 0.3783 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9922 5.5001 1.3976 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0561 2.4531 1.8843 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5048 3.0228 3.5419 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7904 4.2217 2.4224 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 4 6 1 0 6 7 1 0 7 8 1 0 7 9 1 0 7 10 1 0 10 11 1 0 11 12 2 0 12 13 1 0 13 14 1 0 13 15 2 0 15 16 1 0 16 17 2 0 17 18 1 0 18 19 1 0 18 20 2 0 20 21 1 0 21 22 2 0 22 23 1 0 23 24 2 0 24 25 1 0 24 26 1 0 26 27 2 0 27 28 1 0 28 29 2 0 29 30 1 0 29 31 1 0 31 32 2 0 32 33 1 0 33 34 2 0 34 35 1 0 34 36 1 0 36 37 1 0 37 38 1 0 38 39 1 0 39 40 1 0 39 41 1 0 10 2 1 0 39 33 1 0 1 42 1 0 1 43 1 0 1 44 1 0 3 45 1 0 4 46 1 6 5 47 1 0 6 48 1 0 6 49 1 0 8 50 1 0 8 51 1 0 8 52 1 0 9 53 1 0 9 54 1 0 9 55 1 0 10 56 1 0 11 57 1 0 12 58 1 0 14 59 1 0 14 60 1 0 14 61 1 0 15 62 1 0 16 63 1 0 17 64 1 0 19 65 1 0 19 66 1 0 19 67 1 0 20 68 1 0 21 69 1 0 22 70 1 0 23 71 1 0 25 72 1 0 25 73 1 0 25 74 1 0 26 75 1 0 27 76 1 0 28 77 1 0 30 78 1 0 30 79 1 0 30 80 1 0 31 81 1 0 32 82 1 0 35 83 1 0 35 84 1 0 35 85 1 0 36 86 1 0 36 87 1 0 37 88 1 0 37 89 1 0 38 90 1 0 38 91 1 0 40 92 1 0 40 93 1 0 40 94 1 0 41 95 1 0 41 96 1 0 41 97 1 0 M END

Standard InCHIKey	ORAKUVXRZWMARG-DWADUKLPSA-N
Standard InCHI	InChI=1S/C40H56O/c1-30(18-13-20-32(3)23-25-37-34(5)22-15-27-39(37,7)8)16-11-12-17-31(2)19-14-21-33(4)24-26-38-35(6)28-36(41)29-40(38,9)10/h11-14,16-21,23-26,28,36,38,41H,15,22,27,29H2,1-10H3/b12-11+,18-13+,19-14+,25-23+,26-24+,30-16+,31-17+,32-20+,33-21+/t36-,38?/m0/s1
SMILES	CC1=C[C@H](O)CC(C)(C)C1/C=C/C(C)=C/C=C/C(C)=C/C=C/C=C(C)/C=C/C=C(C)/C=C/C1=C(C)CCCC1(C)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	552.43	Volume:	663.072 ? Van der Waals volume.
Dense:	0.833	LogP:	5.566 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.225 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-6.438 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	10.0	Rigid Bonds:	21.0
TPSA:	20.23 ? Topological Polar Surface Area.	H-Bond Acceptor:	1.0
H-Bond Donor:	1.0	Rings:	2.0
Heavy Atoms:	1.0

MedChem Properties

QED Drug-Likeness Score:	0.211	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.691	Fsp³:	0.45
MCE-18:	47.793 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	1.0	Fluc inhibitor:	0.543 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.236 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.04 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.619	Promiscuous compounds:	0.082

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.983	MDCK Permeability:	-4.776
Pgp-inhibitor:	0.098	Pgp-substrate:	0.991
PAMPA:	0.739 ? 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%):	0.013	30% Bioavailability (F30%):	0.077
50% Bioavailability (F50%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.884
Plasma Protein Binding (PPB):	93.864%	Volume Distribution (VD):	0.313
Fu:	7.25% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	0.629	BCRP inhibitor:	0.006
BSEP inhibitor:	1.0

ADMET: Metabolism

CYP1A2-inhibitor:	1.0	CYP1A2-substrate:	0.968
CYP2C19-inhibitor:	0.998	CYP2C19-substrate:	0.032
CYP2C9-inhibitor:	1.0	CYP2C9-substrate:	0.013
CYP2D6-inhibitor:	0.952	CYP2D6-substrate:	0.816
CYP3A4-inhibitor:	1.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.007	CYP2C8-inhibitor:	1.0
HLM stability:	0.999 ? 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):

8.647

Half-life (T1/2):

0.397

ADMET: Toxicity

hERG Blockers:	0.129	hERG Blockers (10um):	0.509
Human Hepatotoxicity (H-HT):	0.515	Drug-induced Liver Injury (DILI):	0.376
AMES Toxicity:	0.823	Rat Oral Acute Toxicity:	0.861
Maximum Recommended Daily Dose:	0.949	Skin Sensitization:	0.934
Carcinogencity:	0.851	Eye Corrosion:	0.0
Eye Irritation:	0.227	Respiratory Toxicity:	0.882
Drug-induced Neurotoxicity:	0.852	Ototoxicity:	0.721
Hematotoxicity:	0.402	Drug-induced Nephrotoxicity:	0.811
Genotoxicity:	0.679	RPMI-8226 Immunitoxicity:	0.156
A549 Cytotoxicity:	0.492	Hek293 Cytotoxicity:	0.609
BCF:	3.322 ? 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:	5.333 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	7.077 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	7.262 ? 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
NPO25443	Citrus reticulata	Species	Rutaceae	Eukaryota	n.a.	fruit	n.a.	PMID[10606547]
NPO27261	Carica papaya	Species	Caricaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22305790]
NPO25443	Citrus reticulata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[34771092]
NPO27261	Carica papaya	Species	Caricaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[36235241]
NPO25443	Citrus reticulata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[38786901]
NPO27261	Carica papaya	Species	Caricaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[38986200]
NPO27261	Carica papaya	Species	Caricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Article]
NPO57747	Rosa gallica officinalis	Genus	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO59935	Capsicum annuum var. lycopersiciforme flavum	Genus	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO27261	Carica papaya	Species	Caricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3949	Ceramium rubrum	Species	Ceramiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25443	Citrus reticulata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO60928	Gymnogobius castaneus	Species	Gobiidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO55756	Protousnea sp.	Genus	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO27261	Carica papaya	Species	Caricaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO27261	Carica papaya	Species	Caricaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO25443	Citrus reticulata	Species	Rutaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO27261	Carica papaya	Species	Caricaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO27261	Carica papaya	Species	Caricaceae	Eukaryota	Latex Exudate	n.a.	n.a.	Database[FooDB]
NPO25443	Citrus reticulata	Species	Rutaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO27261	Carica papaya	Species	Caricaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO25443	Citrus reticulata	Species	Rutaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO27261	Carica papaya	Species	Caricaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO27261	Carica papaya	Species	Caricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25443	Citrus reticulata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25443	Citrus reticulata	Species	Rutaceae	Eukaryota	Fruits	n.a.		Database[Phenol-Explorer]
NPO25443	Citrus reticulata	Species	Rutaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO27261	Carica papaya	Species	Caricaceae	Eukaryota	Fruits	n.a.		Database[Phenol-Explorer]
NPO27261	Carica papaya	Species	Caricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25443	Citrus reticulata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27261	Carica papaya	Species	Caricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO25443	Citrus reticulata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO25443	Citrus reticulata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO27261	Carica papaya	Species	Caricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3949	Ceramium rubrum	Species	Ceramiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25443	Citrus reticulata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	Organism Name	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

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

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

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 NPC491676 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	24456
0.1-0.2	24800
0.2-0.3	565
0.3-0.4	11
0.4-0.5	12
0.5-0.6	8
0.6-0.7	4
0.7-0.8	1
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
0.7551	Intermediate Similarity	NPC171148
0.7551	Intermediate Similarity	NPC313179
0.7551	Intermediate Similarity	NPC69383
0.6279	Remote Similarity	NPC17810
0.6279	Remote Similarity	NPC606095
0.617	Remote Similarity	NPC55412
0.617	Remote Similarity	NPC249645
0.56	Remote Similarity	NPC95863
0.5323	Remote Similarity	NPC38841
0.5306	Remote Similarity	NPC22019
0.5306	Remote Similarity	NPC281986
0.5306	Remote Similarity	NPC321568
0.5185	Remote Similarity	NPC226066
0.5179	Remote Similarity	NPC607338
0.5102	Remote Similarity	NPC45782

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC491676 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7882
0.1-0.2	1206
0.2-0.3	50
0.3-0.4	1
0.4-0.5	7
0.5-0.6	1
0.6-0.7	2
0.7-0.8	1
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
0.7551	Intermediate Similarity	NPD8264	Approved
0.6279	Remote Similarity	NPD8262	Phase 4
0.617	Remote Similarity	NPD4219	Phase 4
0.5185	Remote Similarity	NPD5325	Clinical (unspecified phase)

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