NPASS Compound

Natural Product: NPC508217

Natural Product ID	NPC508217
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	(2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[[(2~{R},3~{S},4~{S},5~{R},6~{R})-3,4,5-trihydroxy-6-[(1~{R},2~{S},4~{S},5'~{S},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S},18~{S},19~{S})-19-hydroxy-5',7,9,13-tetramethyl-spiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane-6,2'-tetrahydropyran]-16-yl]oxy-tetrahydropyran-2-yl]methoxy]tetrahydropyran-3,4,5-triol
IUPAC Name	(2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[[(2~{R},3~{S},4~{S},5~{R},6~{R})-3,4,5-trihydroxy-6-[(1~{R},2~{S},4~{S},5'~{S},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S},18~{S},19~{S})-19-hydroxy-5',7,9,13-tetramethyl-spiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane-6,2'-tetrahydropyran]-16-yl]oxy-tetrahydropyran-2-yl]methoxy]tetrahydropyran-3,4,5-triol
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001013] Steroidal glycosides [CHEMONTID:0002364] Steroidal saponins

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 117124 0 0 0 0 0 0 0 0999 V2000 -12.1795 0.2086 1.7537 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.5036 -0.2793 0.5136 C 0 0 1 0 0 0 0 0 0 0 0 0 -10.5807 0.8167 -0.0117 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.4787 0.1084 -0.7557 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6391 -0.7728 0.1639 C 0 0 1 0 0 0 0 0 0 0 0 0 -9.4494 -1.4393 1.0836 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.7590 -1.5803 0.6819 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.9297 -1.6081 -0.6478 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.6218 -1.6702 -0.3258 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.7121 -0.8997 -1.3095 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5418 -0.7492 -0.4359 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4179 0.1151 -0.8450 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.0089 -0.0783 -2.2717 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8169 0.8733 -2.4712 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.4709 0.9439 -3.8128 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7111 0.2549 -1.6503 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6499 0.7834 -2.0360 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6462 -0.2300 -1.4877 C 0 0 1 0 0 0 0 0 0 0 0 0 2.8355 0.3778 -1.1103 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9064 0.0807 -1.9291 C 0 0 2 0 0 0 0 0 0 0 0 0 4.8503 -0.6028 -1.1792 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0949 -0.0370 -1.1395 C 0 0 2 0 0 0 0 0 0 0 0 0 6.9954 -0.8173 -0.2019 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2689 -0.2558 -0.1438 O 0 0 0 0 0 0 0 0 0 0 0 0 9.1389 -0.9238 0.6812 C 0 0 2 0 0 0 0 0 0 0 0 0 9.5236 -0.1021 1.7393 O 0 0 0 0 0 0 0 0 0 0 0 0 10.6785 -0.6134 2.3364 C 0 0 2 0 0 0 0 0 0 0 0 0 10.8194 -0.0848 3.7303 C 0 0 0 0 0 0 0 0 0 0 0 0 9.7070 -0.4566 4.5160 O 0 0 0 0 0 0 0 0 0 0 0 0 11.8497 -0.2190 1.4957 C 0 0 1 0 0 0 0 0 0 0 0 0 13.0181 -0.9070 1.8280 O 0 0 0 0 0 0 0 0 0 0 0 0 11.5263 -0.4819 0.0638 C 0 0 2 0 0 0 0 0 0 0 0 0 11.1995 0.7513 -0.5387 O 0 0 0 0 0 0 0 0 0 0 0 0 10.3219 -1.3670 -0.1454 C 0 0 1 0 0 0 0 0 0 0 0 0 10.6472 -2.6659 0.2409 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0956 1.3985 -0.6937 C 0 0 1 0 0 0 0 0 0 0 0 0 7.2949 1.9581 -1.1667 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9797 2.1937 -1.3263 C 0 0 2 0 0 0 0 0 0 0 0 0 3.9846 2.3589 -0.3653 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4138 1.3967 -2.4707 C 0 0 1 0 0 0 0 0 0 0 0 0 5.2834 1.2682 -3.5378 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0699 -1.1771 -0.5048 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0668 -0.6536 0.4579 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9710 0.2820 -0.1882 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7059 1.6538 0.4298 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3044 -0.2558 0.1362 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.7451 0.0037 1.5417 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0929 -0.5413 1.9007 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1153 -0.1835 0.8474 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.2944 1.3109 0.7814 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4238 -0.8669 0.9557 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.6091 0.0371 0.8971 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.0921 0.4350 2.2805 C 0 0 0 0 0 0 0 0 0 0 0 0 -13.0976 -0.3851 2.0038 H 0 0 0 0 0 0 0 0 0 0 0 0 -12.5700 1.2399 1.5086 H 0 0 0 0 0 0 0 0 0 0 0 0 -11.5199 0.2978 2.6318 H 0 0 0 0 0 0 0 0 0 0 0 0 -12.2756 -0.4352 -0.2668 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.2136 1.4576 0.8030 H 0 0 0 0 0 0 0 0 0 0 0 0 -11.0856 1.4770 -0.7456 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.7961 0.7526 -1.3079 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.9626 -0.5837 -1.4852 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.8463 -2.1756 -0.2702 H 0 0 0 0 0 0 0 0 0 0 0 0 -11.2768 -2.1742 1.4614 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1859 -2.6747 -0.2525 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4730 -1.6368 -2.1236 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1840 0.0060 -1.6839 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1519 -1.7609 -0.1910 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5941 1.2061 -0.7112 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6535 -1.0948 -2.4949 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8059 0.2772 -2.9212 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0640 1.8940 -2.1352 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6833 0.0342 -4.1950 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6963 -0.8301 -1.9556 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6531 0.8217 -3.1562 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8531 1.8077 -1.7153 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9204 -0.8457 -2.3922 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6427 -0.5963 -2.7669 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5393 -0.1112 -2.1569 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5776 -0.8720 0.8183 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0869 -1.8545 -0.5890 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6297 -1.7938 1.1409 H 0 0 0 0 0 0 0 0 0 0 0 0 10.5848 -1.7324 2.4195 H 0 0 0 0 0 0 0 0 0 0 0 0 10.9371 1.0189 3.7622 H 0 0 0 0 0 0 0 0 0 0 0 0 11.6960 -0.5262 4.2357 H 0 0 0 0 0 0 0 0 0 0 0 0 9.7814 -1.4514 4.6133 H 0 0 0 0 0 0 0 0 0 0 0 0 12.0400 0.8553 1.6530 H 0 0 0 0 0 0 0 0 0 0 0 0 13.7603 -0.5766 1.2576 H 0 0 0 0 0 0 0 0 0 0 0 0 12.3661 -0.8790 -0.5426 H 0 0 0 0 0 0 0 0 0 0 0 0 11.4573 1.5099 0.0288 H 0 0 0 0 0 0 0 0 0 0 0 0 10.0501 -1.3544 -1.2101 H 0 0 0 0 0 0 0 0 0 0 0 0 10.3363 -3.3359 -0.4304 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1169 1.4366 0.4022 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8275 2.3793 -0.4404 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3333 3.1854 -1.6883 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3838 2.8120 0.4449 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5214 1.9668 -2.8244 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2907 2.1060 -4.0611 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6168 -2.0680 -1.0277 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9018 -1.6104 0.0881 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5548 -0.1563 1.3456 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4392 -1.5475 0.9110 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3748 2.4346 0.0770 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3777 1.8860 0.2526 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7501 1.5186 1.5507 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2317 -1.3857 0.0493 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6870 1.0463 1.8739 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0037 -0.5454 2.1994 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0590 -1.6077 2.1173 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4188 -0.0199 2.8441 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3530 1.8725 1.0554 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0054 1.5962 1.5841 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5645 1.6835 -0.2148 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5206 -1.5103 1.8487 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4219 0.9520 0.2654 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3010 0.1759 3.0099 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.2838 1.5066 2.2938 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.9783 -0.1735 2.5747 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 1 6 7 1 0 5 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 14 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 22 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 28 29 1 0 27 30 1 0 30 31 1 0 30 32 1 0 32 33 1 0 32 34 1 0 34 35 1 0 22 36 1 0 36 37 1 0 36 38 1 0 38 39 1 0 38 40 1 0 40 41 1 0 18 42 1 0 42 43 1 0 43 44 1 0 44 45 1 1 44 46 1 0 46 47 1 0 47 48 1 0 48 49 1 0 49 50 1 6 49 51 1 0 51 52 1 0 52 53 1 0 7 2 1 0 51 9 1 0 52 5 1 0 49 11 1 0 46 12 1 0 44 16 1 0 40 20 1 0 34 25 1 0 1 54 1 0 1 55 1 0 1 56 1 0 2 57 1 6 3 58 1 0 3 59 1 0 4 60 1 0 4 61 1 0 7 62 1 0 7 63 1 0 9 64 1 1 10 65 1 0 10 66 1 0 11 67 1 1 12 68 1 6 13 69 1 0 13 70 1 0 14 71 1 1 15 72 1 0 16 73 1 6 17 74 1 0 17 75 1 0 18 76 1 6 20 77 1 6 22 78 1 6 23 79 1 0 23 80 1 0 25 81 1 1 27 82 1 1 28 83 1 0 28 84 1 0 29 85 1 0 30 86 1 6 31 87 1 0 32 88 1 6 33 89 1 0 34 90 1 6 35 91 1 0 36 92 1 1 37 93 1 0 38 94 1 6 39 95 1 0 40 96 1 6 41 97 1 0 42 98 1 0 42 99 1 0 43100 1 0 43101 1 0 45102 1 0 45103 1 0 45104 1 0 46105 1 1 47106 1 0 47107 1 0 48108 1 0 48109 1 0 50110 1 0 50111 1 0 50112 1 0 51113 1 1 52114 1 6 53115 1 0 53116 1 0 53117 1 0 M END

Standard InCHIKey	GARIYKJPRDSJFN-UBXCSCSKSA-N
Standard InCHI	InChI=1S/C39H64O14/c1-17-5-10-39(49-15-17)18(2)28-25(53-39)13-22-20-12-24(41)23-11-19(6-8-37(23,3)21(20)7-9-38(22,28)4)50-36-34(47)32(45)30(43)27(52-36)16-48-35-33(46)31(44)29(42)26(14-40)51-35/h17-36,40-47H,5-16H2,1-4H3/t17-,18-,19-,20+,21-,22-,23+,24-,25-,26+,27+,28-,29+,30+,31-,32-,33+,34+,35+,36+,37+,38-,39+/m0/s1
SMILES	C[C@H]1CC[C@@]2(OC1)O[C@H]1C[C@H]3[C@@H]4C[C@H](O)[C@H]5C[C@@H](O[C@@H]6O[C@H](CO[C@@H]7O[C@H](CO)[C@@H](O)[C@H](O)[C@H]7O)[C@@H](O)[C@H](O)[C@H]6O)CC[C@]5(C)[C@H]4CC[C@]3(C)[C@H]1[C@@H]2C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	756.43	Volume:	737.711 ? Van der Waals volume.
Dense:	1.025	LogP:	2.502 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.894 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.253 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	6.0	Rigid Bonds:	42.0
TPSA:	217.22 ? Topological Polar Surface Area.	H-Bond Acceptor:	14.0
H-Bond Donor:	8.0	Rings:	8.0
Heavy Atoms:	14.0

MedChem Properties

QED Drug-Likeness Score:	0.173	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	6.335	Fsp³:	1.0
MCE-18:	203.846 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.667	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.075 ? 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:	0.206	Promiscuous compounds:	0.014

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.952	MDCK Permeability:	-5.069
Pgp-inhibitor:	0.001	Pgp-substrate:	0.49
PAMPA:	0.989 ? 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):	0.002
20% Bioavailability (F20%):	0.087	30% Bioavailability (F30%):	0.987
50% Bioavailability (F50%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.015	MRP1:	0.015
Plasma Protein Binding (PPB):	57.152%	Volume Distribution (VD):	-0.416
Fu:	33.308% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.687
BSEP inhibitor:	0.065

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	1.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.925
HLM stability:	0.004 ? 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):

0.908

Half-life (T1/2):

3.167

ADMET: Toxicity

hERG Blockers:	0.032	hERG Blockers (10um):	0.105
Human Hepatotoxicity (H-HT):	0.507	Drug-induced Liver Injury (DILI):	0.881
AMES Toxicity:	0.878	Rat Oral Acute Toxicity:	0.015
Maximum Recommended Daily Dose:	0.063	Skin Sensitization:	1.0
Carcinogencity:	0.169	Eye Corrosion:	0.0
Eye Irritation:	0.001	Respiratory Toxicity:	0.002
Drug-induced Neurotoxicity:	0.001	Ototoxicity:	0.994
Hematotoxicity:	0.158	Drug-induced Nephrotoxicity:	0.757
Genotoxicity:	0.002	RPMI-8226 Immunitoxicity:	0.234
A549 Cytotoxicity:	0.896	Hek293 Cytotoxicity:	0.836
BCF:	1.893 ? 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:	3.491 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.742 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.141 ? 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
NPO18141	Solanum torvum	Species	Solanaceae	Eukaryota	n.a.	fruit	n.a.	PMID[11830167]
NPO18141	Solanum torvum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO18141	Solanum torvum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18141	Solanum torvum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18141	Solanum torvum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18141	Solanum torvum	Species	Solanaceae	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 NPC508217 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	25205
0.1-0.2	20928
0.2-0.3	2975
0.3-0.4	525
0.4-0.5	113
0.5-0.6	75
0.6-0.7	31
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	Natural Product ID
0.7416	Intermediate Similarity	NPC211354
0.7416	Intermediate Similarity	NPC107188
0.7241	Intermediate Similarity	NPC177834
0.7011	Intermediate Similarity	NPC485594
0.6977	Remote Similarity	NPC172838
0.6966	Remote Similarity	NPC234352
0.6854	Remote Similarity	NPC297348
0.6854	Remote Similarity	NPC325828
0.6854	Remote Similarity	NPC249204
0.6854	Remote Similarity	NPC48339
0.6854	Remote Similarity	NPC141769
0.6854	Remote Similarity	NPC477547
0.6809	Remote Similarity	NPC485595
0.6667	Remote Similarity	NPC160426
0.6556	Remote Similarity	NPC181845
0.6526	Remote Similarity	NPC107962
0.6522	Remote Similarity	NPC477451
0.6476	Remote Similarity	NPC476112
0.6476	Remote Similarity	NPC307534
0.6437	Remote Similarity	NPC277715
0.6404	Remote Similarity	NPC485600
0.6404	Remote Similarity	NPC24960
0.6383	Remote Similarity	NPC206003
0.6383	Remote Similarity	NPC473610
0.6277	Remote Similarity	NPC250393
0.6275	Remote Similarity	NPC128572
0.6263	Remote Similarity	NPC475351
0.6222	Remote Similarity	NPC65550
0.6139	Remote Similarity	NPC475643
0.6122	Remote Similarity	NPC6295
0.6064	Remote Similarity	NPC294686
0.6058	Remote Similarity	NPC97700
0.6058	Remote Similarity	NPC30856
0.6042	Remote Similarity	NPC121453
0.602	Remote Similarity	NPC215408
0.5957	Remote Similarity	NPC137004
0.5905	Remote Similarity	NPC184617
0.5888	Remote Similarity	NPC473518
0.5872	Remote Similarity	NPC83137
0.5818	Remote Similarity	NPC132080
0.5816	Remote Similarity	NPC19400
0.5773	Remote Similarity	NPC222731
0.5769	Remote Similarity	NPC477809
0.5741	Remote Similarity	NPC475625
0.5732	Remote Similarity	NPC296734
0.57	Remote Similarity	NPC485601
0.5686	Remote Similarity	NPC113044
0.5686	Remote Similarity	NPC283829
0.5686	Remote Similarity	NPC14704
0.5686	Remote Similarity	NPC161676
0.5644	Remote Similarity	NPC125324
0.5636	Remote Similarity	NPC470864
0.5604	Remote Similarity	NPC144790
0.5604	Remote Similarity	NPC149400
0.56	Remote Similarity	NPC470591
0.56	Remote Similarity	NPC264101
0.5596	Remote Similarity	NPC116756
0.5591	Remote Similarity	NPC481420
0.5591	Remote Similarity	NPC473774
0.5591	Remote Similarity	NPC481419
0.5591	Remote Similarity	NPC481417
0.5591	Remote Similarity	NPC481421
0.5577	Remote Similarity	NPC473601
0.5567	Remote Similarity	NPC80191
0.5566	Remote Similarity	NPC51172
0.5566	Remote Similarity	NPC49032
0.5545	Remote Similarity	NPC232037
0.549	Remote Similarity	NPC470432
0.549	Remote Similarity	NPC230507
0.5472	Remote Similarity	NPC92890
0.5437	Remote Similarity	NPC195297
0.5435	Remote Similarity	NPC88962
0.5426	Remote Similarity	NPC481418
0.5421	Remote Similarity	NPC471464
0.5421	Remote Similarity	NPC300557
0.5421	Remote Similarity	NPC6806
0.5391	Remote Similarity	NPC470866
0.537	Remote Similarity	NPC480555
0.537	Remote Similarity	NPC150372
0.5357	Remote Similarity	NPC273290
0.5357	Remote Similarity	NPC232044
0.5349	Remote Similarity	NPC305808
0.5347	Remote Similarity	NPC54619
0.5288	Remote Similarity	NPC141433
0.5283	Remote Similarity	NPC202898
0.5273	Remote Similarity	NPC115165
0.5273	Remote Similarity	NPC475319
0.5253	Remote Similarity	NPC131693
0.5253	Remote Similarity	NPC475436
0.5242	Remote Similarity	NPC481190
0.5234	Remote Similarity	NPC485603
0.5234	Remote Similarity	NPC602423
0.5189	Remote Similarity	NPC485605
0.5179	Remote Similarity	NPC309278
0.5133	Remote Similarity	NPC194207
0.5133	Remote Similarity	NPC22779
0.513	Remote Similarity	NPC233433
0.513	Remote Similarity	NPC480553
0.513	Remote Similarity	NPC477811
0.5093	Remote Similarity	NPC470433
0.5093	Remote Similarity	NPC46190
0.5093	Remote Similarity	NPC171073
0.5078	Remote Similarity	NPC329807
0.5077	Remote Similarity	NPC481189
0.5059	Remote Similarity	NPC248944
0.5059	Remote Similarity	NPC7479
0.5059	Remote Similarity	NPC257296
0.5044	Remote Similarity	NPC475333
0.5044	Remote Similarity	NPC224098
0.5044	Remote Similarity	NPC208383

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC508217 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7510
0.1-0.2	1560
0.2-0.3	67
0.3-0.4	9
0.4-0.5	1
0.5-0.6	2
0.6-0.7	1
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
0.6854	Remote Similarity	NPD8171	Phase 2
0.596	Remote Similarity	NPD8170	Phase 2
0.5059	Remote Similarity	NPD6928	Phase 2

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