NPASS Compound

Natural Product: NPC589992

Natural Product ID	NPC589992
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Dioscoreside I
IUPAC Name	1-[(3~{S},8~{R},9~{S},10~{R},13~{S},14~{S})-3-[(2~{R},3~{R},4~{S},5~{R},6~{R})-5-hydroxy-6-(hydroxymethyl)-4-[(2~{S},3~{R},4~{S},5~{S},6~{R})-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-3-[(2~{S},3~{R},4~{R},5~{R},6~{S})-3,4,5-trihydroxy-6-methyl-tetrahydropyran-2-yl]oxy-tetrahydropyran-2-yl]oxy-10,13-dimethyl-2,3,4,7,8,9,11,12,14,15-decahydro-1~{H}-cyclopenta[a]phenanthren-17-yl]ethanone
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 115121 0 0 0 0 0 0 0 0999 V2000 10.5752 -0.3292 -0.5541 C 0 0 0 0 0 0 0 0 0 0 0 0 9.4266 -0.1843 0.3450 C 0 0 0 0 0 0 0 0 0 0 0 0 9.4248 0.7552 1.1838 O 0 0 0 0 0 0 0 0 0 0 0 0 8.2798 -1.0869 0.3080 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1929 -2.0999 -0.5335 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8838 -2.8276 -0.3088 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -1.7132 0.2113 C 0 0 1 0 0 0 0 0 0 0 0 0 4.8955 -2.0478 1.0804 C 0 0 2 0 0 0 0 0 0 0 0 0 3.9608 -3.0554 0.5637 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5547 -2.6601 0.4938 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0594 -1.6607 1.1625 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6327 -1.2963 1.0611 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5707 0.0067 0.3453 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6286 0.6371 0.2555 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0961 0.8409 -1.0164 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.0521 2.2158 -1.3293 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2365 2.4140 -2.6993 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.3282 3.8673 -3.0517 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1608 4.5527 -2.6805 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4771 1.6956 -3.1840 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.0594 0.5550 -3.8572 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3107 1.2345 -1.9849 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.5858 2.3153 -1.1942 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9112 2.6804 -1.0806 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.9815 4.0224 -1.4070 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.1906 4.6289 -1.2172 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.9759 6.1134 -1.5591 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1574 6.8072 -1.3940 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.6880 4.5614 0.2307 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.0330 4.9970 0.1856 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.7085 3.0782 0.5823 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.0966 2.8732 1.8947 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.3087 2.5374 0.3745 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.3662 1.1705 0.6613 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4738 0.2574 -1.1545 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5162 -1.0198 -1.6718 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0339 -2.0068 -0.9010 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.1079 -3.0685 -0.7288 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5673 -3.9540 0.2393 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5559 -3.3532 1.6291 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9053 -4.5502 -0.0457 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.7976 -5.7885 -0.7170 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8732 -3.6443 -0.7296 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.7530 -3.0124 0.1467 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1958 -2.6420 -1.6368 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1108 -1.7053 -2.0502 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6406 0.9445 0.8781 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2374 0.4903 2.1805 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9450 -0.8430 2.0413 C 0 0 1 0 0 0 0 0 0 0 0 0 3.0164 -1.4707 3.4071 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2669 -0.6769 1.3762 C 0 0 1 0 0 0 0 0 0 0 0 0 5.2149 0.1325 2.1807 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5667 0.2954 1.4820 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0873 -1.0578 1.1436 C 0 0 2 0 0 0 0 0 0 0 0 0 7.3601 -1.9086 2.3624 C 0 0 0 0 0 0 0 0 0 0 0 0 11.3385 -0.9825 -0.0996 H 0 0 0 0 0 0 0 0 0 0 0 0 10.3209 -0.7605 -1.5480 H 0 0 0 0 0 0 0 0 0 0 0 0 11.0473 0.6630 -0.7407 H 0 0 0 0 0 0 0 0 0 0 0 0 8.8937 -2.4353 -1.2975 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4887 -3.1133 -1.3111 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9876 -3.7103 0.3126 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8311 -0.9847 -0.5738 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3028 -2.3584 2.0883 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9892 -3.9607 1.2537 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3054 -3.4845 -0.4160 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9233 -3.2862 -0.1831 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0970 -2.1085 0.5528 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2340 -1.2559 2.0967 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8965 -0.2101 -0.7175 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4348 0.3695 -1.7718 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3665 1.9788 -3.2152 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4258 3.9873 -4.1501 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1722 4.3826 -2.5589 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5728 3.8857 -2.5034 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0086 2.3408 -3.8720 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8045 0.1488 -4.3369 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2378 0.8179 -2.3816 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6076 2.0384 -1.6582 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9842 4.2035 -1.8456 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6280 6.2320 -2.5908 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2168 6.5498 -0.8815 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.8229 6.4177 -2.0226 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0863 5.1598 0.9191 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.2948 5.4327 1.0344 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3712 2.5869 -0.1476 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.0678 3.0571 1.9431 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5553 3.0054 1.0392 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1140 0.8099 0.0826 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8978 0.1989 -0.1321 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3942 -1.7256 0.0945 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8312 -4.8053 0.2484 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1246 -4.0740 2.3648 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0183 -2.3907 1.6357 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6083 -3.1332 1.9217 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3647 -4.8043 0.9554 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9733 -5.7569 -1.2740 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5304 -4.2814 -1.3958 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6334 -2.8292 -0.2842 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8125 -3.1996 -2.5331 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6383 -1.3615 -1.2904 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1642 1.9284 1.0687 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4575 1.1314 0.1600 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8345 1.2893 2.6050 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3887 0.3134 2.9051 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0841 -0.7268 4.2261 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0580 -2.0485 3.5327 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8186 -2.2446 3.4817 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0873 -0.1954 0.3907 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3182 -0.2324 3.2133 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8317 1.1882 2.2667 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2301 0.8229 2.2037 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4078 0.8723 0.5738 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2467 -2.9879 2.1957 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8048 -1.6163 3.2598 H 0 0 0 0 0 0 0 0 0 0 0 0 8.4541 -1.7649 2.6086 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 2 4 1 0 4 5 2 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 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 17 20 1 0 20 21 1 0 20 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 26 29 1 0 29 30 1 0 29 31 1 0 31 32 1 0 31 33 1 0 33 34 1 0 22 35 1 0 35 36 1 0 36 37 1 0 37 38 1 0 38 39 1 0 39 40 1 0 39 41 1 0 41 42 1 0 41 43 1 0 43 44 1 0 43 45 1 0 45 46 1 0 13 47 1 0 47 48 1 0 48 49 1 0 49 50 1 1 49 51 1 0 51 52 1 0 52 53 1 0 53 54 1 0 54 55 1 1 54 4 1 0 54 7 1 0 51 8 1 0 49 11 1 0 35 15 1 0 45 37 1 0 33 24 1 0 1 56 1 0 1 57 1 0 1 58 1 0 5 59 1 0 6 60 1 0 6 61 1 0 7 62 1 6 8 63 1 1 9 64 1 0 9 65 1 0 10 66 1 0 12 67 1 0 12 68 1 0 13 69 1 6 15 70 1 6 17 71 1 6 18 72 1 0 18 73 1 0 19 74 1 0 20 75 1 6 21 76 1 0 22 77 1 6 24 78 1 6 26 79 1 6 27 80 1 0 27 81 1 0 28 82 1 0 29 83 1 1 30 84 1 0 31 85 1 6 32 86 1 0 33 87 1 1 34 88 1 0 35 89 1 1 37 90 1 1 39 91 1 1 40 92 1 0 40 93 1 0 40 94 1 0 41 95 1 1 42 96 1 0 43 97 1 6 44 98 1 0 45 99 1 6 46100 1 0 47101 1 0 47102 1 0 48103 1 0 48104 1 0 50105 1 0 50106 1 0 50107 1 0 51108 1 6 52109 1 0 52110 1 0 53111 1 0 53112 1 0 55113 1 0 55114 1 0 55115 1 0 M END

Standard InCHIKey	VZYCYPQHUZOSIT-BXJPREBZSA-N
Standard InCHI	InChI=1S/C39H60O16/c1-16(42)21-7-8-22-20-6-5-18-13-19(9-11-38(18,3)23(20)10-12-39(21,22)4)51-37-34(55-35-31(48)29(46)26(43)17(2)50-35)33(28(45)25(15-41)53-37)54-36-32(49)30(47)27(44)24(14-40)52-36/h5,7,17,19-20,22-37,40-41,43-49H,6,8-15H2,1-4H3/t17-,19-,20-,22-,23-,24+,25+,26-,27+,28+,29+,30-,31+,32+,33-,34+,35-,36-,37+,38-,39+/m0/s1
SMILES	CC(=O)C1=CC[C@H]2[C@@H]3CC=C4C[C@@H](O[C@@H]5O[C@H](CO)[C@@H](O)[C@H](O[C@@H]6O[C@H](CO)[C@@H](O)[C@H](O)[C@H]6O)[C@H]5O[C@@H]5O[C@@H](C)[C@H](O)[C@@H](O)[C@H]5O)CC[C@]4(C)[C@H]3CC[C@]12C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	784.39	Volume:	755.939 ? Van der Waals volume.
Dense:	1.038	LogP:	1.199 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.041 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.963 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	9.0	Rigid Bonds:	39.0
TPSA:	254.52 ? Topological Polar Surface Area.	H-Bond Acceptor:	16.0
H-Bond Donor:	9.0	Rings:	7.0
Heavy Atoms:	16.0

MedChem Properties

QED Drug-Likeness Score:	0.126	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.837	Fsp³:	0.872
MCE-18:	135.589 ? 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:	0.748	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.005 ? 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:	0.277	Promiscuous compounds:	0.18

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.513	MDCK Permeability:	-5.09
Pgp-inhibitor:	0.0	Pgp-substrate:	0.619
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):	0.001
20% Bioavailability (F20%):	0.004	30% Bioavailability (F30%):	0.826
50% Bioavailability (F50%):	0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.006	MRP1:	0.018
Plasma Protein Binding (PPB):	62.004%	Volume Distribution (VD):	-0.424
Fu:	31.992% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.054
BSEP inhibitor:	0.011

ADMET: Metabolism

CYP1A2-inhibitor:	0.019	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.015	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.83	CYP3A4-substrate:	0.953
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.495
HLM stability:	0.417 ? 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):

0.472

Half-life (T1/2):

2.942

ADMET: Toxicity

hERG Blockers:	0.011	hERG Blockers (10um):	0.029
Human Hepatotoxicity (H-HT):	0.489	Drug-induced Liver Injury (DILI):	0.893
AMES Toxicity:	0.922	Rat Oral Acute Toxicity:	0.003
Maximum Recommended Daily Dose:	0.005	Skin Sensitization:	1.0
Carcinogencity:	0.078	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.001
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	0.999
Hematotoxicity:	0.48	Drug-induced Nephrotoxicity:	0.677
Genotoxicity:	0.111	RPMI-8226 Immunitoxicity:	0.159
A549 Cytotoxicity:	0.641	Hek293 Cytotoxicity:	0.532
BCF:	0.863 ? 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:	3.31 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.681 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.847 ? 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
NPO10541	Dioscorea spongiosa	Species	Dioscoreaceae	Eukaryota	rhizomes	n.a.	n.a.	PMID[12762799]
NPO4863	Dioscorea futschauensis	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10541	Dioscorea spongiosa	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9089	Dioscorea panthaica	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10541	Dioscorea spongiosa	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4863	Dioscorea futschauensis	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9089	Dioscorea panthaica	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9089	Dioscorea panthaica	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4863	Dioscorea futschauensis	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10541	Dioscorea spongiosa	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4863	Dioscorea futschauensis	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4863	Dioscorea futschauensis	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9089	Dioscorea panthaica	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9089	Dioscorea panthaica	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4863	Dioscorea futschauensis	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10541	Dioscorea spongiosa	Species	Dioscoreaceae	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 NPC589992 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	20467
0.1-0.2	24918
0.2-0.3	3257
0.3-0.4	1053
0.4-0.5	98
0.5-0.6	50
0.6-0.7	12
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
0.7683	Intermediate Similarity	NPC165439
0.6701	Remote Similarity	NPC48886
0.6701	Remote Similarity	NPC300557
0.6701	Remote Similarity	NPC94881
0.6633	Remote Similarity	NPC150057
0.6633	Remote Similarity	NPC147753
0.6566	Remote Similarity	NPC102016
0.6566	Remote Similarity	NPC95051
0.6535	Remote Similarity	NPC309278
0.6495	Remote Similarity	NPC602423
0.625	Remote Similarity	NPC218571
0.625	Remote Similarity	NPC487615
0.6238	Remote Similarity	NPC308459
0.5816	Remote Similarity	NPC306991
0.5816	Remote Similarity	NPC94272
0.5673	Remote Similarity	NPC475182
0.5517	Remote Similarity	NPC22140
0.5517	Remote Similarity	NPC243728
0.5517	Remote Similarity	NPC158088
0.5484	Remote Similarity	NPC486114
0.5455	Remote Similarity	NPC600456
0.5437	Remote Similarity	NPC40440
0.5437	Remote Similarity	NPC486388
0.5405	Remote Similarity	NPC477811
0.5393	Remote Similarity	NPC282669
0.5392	Remote Similarity	NPC470748
0.5377	Remote Similarity	NPC480555
0.5377	Remote Similarity	NPC150372
0.537	Remote Similarity	NPC486386
0.5345	Remote Similarity	NPC477808
0.5327	Remote Similarity	NPC73243
0.5327	Remote Similarity	NPC244086
0.5327	Remote Similarity	NPC84956
0.5312	Remote Similarity	NPC272015
0.5288	Remote Similarity	NPC98696
0.5283	Remote Similarity	NPC124677
0.5273	Remote Similarity	NPC194207
0.5273	Remote Similarity	NPC197003
0.5273	Remote Similarity	NPC22779
0.5273	Remote Similarity	NPC254255
0.5243	Remote Similarity	NPC305423
0.5243	Remote Similarity	NPC113044
0.5243	Remote Similarity	NPC283829
0.5243	Remote Similarity	NPC161676
0.5243	Remote Similarity	NPC600116
0.5229	Remote Similarity	NPC247037
0.5182	Remote Similarity	NPC13193
0.5158	Remote Similarity	NPC296686
0.5143	Remote Similarity	NPC42482
0.5133	Remote Similarity	NPC480553
0.5128	Remote Similarity	NPC609635
0.5114	Remote Similarity	NPC473890
0.5098	Remote Similarity	NPC295980
0.5094	Remote Similarity	NPC470433
0.5094	Remote Similarity	NPC46190
0.5094	Remote Similarity	NPC265275
0.5094	Remote Similarity	NPC171073
0.5089	Remote Similarity	NPC249265
0.5047	Remote Similarity	NPC248746
0.5047	Remote Similarity	NPC122819
0.5044	Remote Similarity	NPC23808
0.5044	Remote Similarity	NPC87998
0.5043	Remote Similarity	NPC232054

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC589992 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7147
0.1-0.2	1869
0.2-0.3	118
0.3-0.4	13
0.4-0.5	1
0.5-0.6	1
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
0.6633	Remote Similarity	NPD8450	Suspended
0.5047	Remote Similarity	NPD8449	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