NPASS Compound

Natural Product: NPC66654

Natural Product ID	NPC66654
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	ginsenoside ck
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	9852086
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0001580] Triterpene glycosides [CHEMONTID:0002358] Triterpene 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 106110 0 0 0 0 0 0 0 0999 V2000 -3.5118 5.1189 0.0405 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0717 4.5121 1.3069 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5100 3.3301 1.6815 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4569 2.4868 0.9193 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0815 1.0778 0.6806 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8542 0.7506 -0.0835 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.8095 1.2848 -1.4742 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6137 1.0955 0.7175 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6203 0.2601 1.9720 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4899 -0.7863 1.7476 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5284 0.1491 1.1668 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3384 0.7192 0.0251 C 0 0 2 0 0 0 0 0 0 0 0 0 0.4772 1.8073 -0.5547 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6131 1.0849 -1.3093 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4650 0.4731 -0.2348 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7365 -0.5222 0.5854 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5987 -0.9876 1.7519 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9115 -1.5209 1.2645 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5977 -0.3813 0.5089 C 0 0 2 0 0 0 0 0 0 0 0 0 3.8359 0.0323 -0.7174 C 0 0 2 0 0 0 0 0 0 0 0 0 4.4986 1.3075 -1.2260 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9595 1.2819 -1.3057 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6668 0.0729 -0.8348 C 0 0 1 0 0 0 0 0 0 0 0 0 6.0458 -0.6153 0.3397 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4109 -2.1024 0.2139 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7538 -0.1731 1.6338 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9414 -0.8552 -1.8701 O 0 0 0 0 0 0 0 0 0 0 0 0 3.7924 -0.9289 -1.8400 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3131 -1.7626 -0.1373 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1379 2.7686 -1.2836 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8259 1.1669 2.2217 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7397 -0.6599 -0.2377 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7636 -1.2853 -0.8656 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.2433 -2.1655 -1.9769 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.4317 -2.9232 -2.5927 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.9555 -3.8415 -1.5193 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.3404 -2.9183 -0.3540 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2700 -2.2020 0.0998 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.7885 -3.8257 0.7732 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7445 -4.6878 1.1350 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.1342 -4.4773 -1.9025 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0421 -3.6720 -3.6777 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6499 -1.5029 -3.0192 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1204 5.2517 2.1693 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7095 5.8544 -0.2771 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3923 5.7768 0.2391 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6730 4.4282 -0.7816 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1146 2.9632 2.6611 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8431 3.0102 0.0135 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3858 2.4474 1.5835 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1475 0.5717 1.6958 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0056 0.5929 0.1795 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6989 0.9271 -2.0203 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8404 2.3878 -1.5538 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9224 0.8549 -1.9850 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5519 2.1691 0.9867 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3561 0.9003 2.8389 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5404 -0.2477 2.2207 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2071 -1.2463 2.6920 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9480 -1.4790 1.0128 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5457 -0.0732 -0.6882 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0288 2.3396 0.2785 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1223 1.8560 -1.8760 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1217 0.3489 -1.9657 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7092 1.3381 0.4556 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9993 -1.7952 2.2554 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7895 -0.2183 2.4949 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8702 -2.4474 0.7038 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5404 -1.7095 2.1643 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4806 0.5012 1.2145 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0777 1.4472 -2.2663 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1072 2.1910 -0.6595 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3569 2.1736 -0.7319 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3245 1.4880 -2.3580 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7051 0.3892 -0.5105 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8763 -2.7245 0.9289 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5021 -2.1737 0.5030 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3778 -2.4438 -0.8328 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0664 -0.3895 2.4611 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6901 -0.7081 1.7907 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8947 0.9400 1.6282 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4931 -0.3238 -2.5256 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7284 -0.9388 -2.2293 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1855 -1.9274 -1.6489 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3599 -0.5604 -2.7492 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1857 -2.4166 -0.4327 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8028 -2.4153 0.6328 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7312 -1.6160 -1.0418 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4402 3.5687 -1.3239 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6520 0.7200 3.2487 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1479 2.0430 2.0828 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8336 1.5634 2.2617 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5821 -0.6815 -1.2641 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5781 -2.9390 -1.5385 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2495 -2.2106 -2.8329 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1982 -4.5562 -1.1441 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2125 -2.2967 -0.6391 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0104 -3.2176 1.6883 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7192 -4.3720 0.5267 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0852 -4.1780 1.6802 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3011 -5.2424 -1.2974 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7925 -4.5816 -3.3407 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3566 -1.1577 -3.6300 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1243 5.2307 1.6513 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9653 4.7198 3.1244 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3962 6.3102 2.3074 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 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 19 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 24 25 1 0 24 26 1 0 23 27 1 0 20 28 1 6 16 29 1 6 13 30 1 0 11 31 1 1 6 32 1 6 32 33 1 0 33 34 1 0 34 35 1 0 35 36 1 0 36 37 1 0 37 38 1 0 37 39 1 0 39 40 1 0 36 41 1 0 35 42 1 0 34 43 1 0 2 44 1 0 12 8 1 0 16 11 1 0 20 15 1 0 24 19 1 0 38 33 1 0 1 45 1 0 1 46 1 0 1 47 1 0 3 48 1 0 4 49 1 0 4 50 1 0 5 51 1 0 5 52 1 0 7 53 1 0 7 54 1 0 7 55 1 0 8 56 1 1 9 57 1 0 9 58 1 0 10 59 1 0 10 60 1 0 12 61 1 6 13 62 1 1 14 63 1 0 14 64 1 0 15 65 1 1 17 66 1 0 17 67 1 0 18 68 1 0 18 69 1 0 19 70 1 1 21 71 1 0 21 72 1 0 22 73 1 0 22 74 1 0 23 75 1 1 25 76 1 0 25 77 1 0 25 78 1 0 26 79 1 0 26 80 1 0 26 81 1 0 27 82 1 0 28 83 1 0 28 84 1 0 28 85 1 0 29 86 1 0 29 87 1 0 29 88 1 0 30 89 1 0 31 90 1 0 31 91 1 0 31 92 1 0 33 93 1 6 34 94 1 1 35 95 1 6 36 96 1 1 37 97 1 6 39 98 1 0 39 99 1 0 40100 1 0 41101 1 0 42102 1 0 43103 1 0 44104 1 0 44105 1 0 44106 1 0 M END

Standard InCHIKey	FVIZARNDLVOMSU-IRFFNABBSA-N
Standard InCHI	InChI=1S/C36H62O8/c1-20(2)10-9-14-36(8,44-31-30(42)29(41)28(40)23(19-37)43-31)21-11-16-35(7)27(21)22(38)18-25-33(5)15-13-26(39)32(3,4)24(33)12-17-34(25,35)6/h10,21-31,37-42H,9,11-19H2,1-8H3/t21-,22+,23+,24-,25+,26-,27-,28+,29-,30+,31-,33-,34+,35+,36-/m0/s1
SMILES	CC(=CCC[C@@](C)([C@H]1CC[C@@]2([C@@H]1[C@@H](C[C@H]3[C@]2(CC[C@@H]4[C@@]3(CC[C@@H](C4(C)C)O)C)C)O)C)O[C@H]5[C@@H]([C@H]([C@@H]([C@H](O5)CO)O)O)O)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	622.44	Volume:	656.115 ? Van der Waals volume.
Dense:	0.949	LogP:	3.405 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.613 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.006 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	7.0	Rigid Bonds:	27.0
TPSA:	139.84 ? Topological Polar Surface Area.	H-Bond Acceptor:	8.0
H-Bond Donor:	6.0	Rings:	5.0
Heavy Atoms:	8.0

MedChem Properties

QED Drug-Likeness Score:	0.231	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.404	Fsp³:	0.944
MCE-18:	110.4 ? 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:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.911	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:	0.227	Promiscuous compounds:	0.247

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.956	MDCK Permeability:	-5.148
Pgp-inhibitor:	0.002	Pgp-substrate:	0.649
PAMPA:	0.996 ? 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):	0.021
20% Bioavailability (F20%):	0.484	30% Bioavailability (F30%):	0.477
50% Bioavailability (F50%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.897	MRP1:	0.827
Plasma Protein Binding (PPB):	84.804%	Volume Distribution (VD):	-0.436
Fu:	10.925% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.05
BSEP inhibitor:	0.019

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.868	CYP2C19-substrate:	0.038
CYP2C9-inhibitor:	0.001	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.004
CYP3A4-inhibitor:	0.16	CYP3A4-substrate:	0.573
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.957
HLM stability:	0.565 ? 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):

3.355

Half-life (T1/2):

1.968

ADMET: Toxicity

hERG Blockers:	0.031	hERG Blockers (10um):	0.097
Human Hepatotoxicity (H-HT):	0.598	Drug-induced Liver Injury (DILI):	0.219
AMES Toxicity:	0.755	Rat Oral Acute Toxicity:	0.087
Maximum Recommended Daily Dose:	0.055	Skin Sensitization:	1.0
Carcinogencity:	0.423	Eye Corrosion:	0.0
Eye Irritation:	0.134	Respiratory Toxicity:	0.319
Drug-induced Neurotoxicity:	0.032	Ototoxicity:	0.951
Hematotoxicity:	0.622	Drug-induced Nephrotoxicity:	0.918
Genotoxicity:	0.138	RPMI-8226 Immunitoxicity:	0.125
A549 Cytotoxicity:	0.87	Hek293 Cytotoxicity:	0.435
BCF:	1.705 ? 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:	3.8 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.253 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.546 ? 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
NPO41952	A new engineered strain of Nicotiana tabacum [LMS]	Strain	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17057703]
NPO41950	A new engineered strain of Nicotiana tabacum [n.a.]	Strain	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22158354]
NPO41950	A new engineered strain of Nicotiana tabacum [n.a.]	Strain	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24499788]
NPO41661	Corynebacterium glutamicum strain RML5; Corynebacterium glutamicum strain RML6 [rosB, rosA, RFK]	Strain	Corynebacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[31451111]

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
Inhibition	2
Activity	1

Activity Type	# Activity
Organism	1
Individual protein	2

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT692	Individual protein	Histone deacetylase 6	Homo sapiens	Inhibition	=	-6.74	%	HDAC6 screening dataset using tau-based substrate in an enzymatic assay yields selective inhibitors and activators
NPT692	Individual protein	Histone deacetylase 6	Homo sapiens	Inhibition	=	-3.19	%	HDAC6 screening dataset using tau-based substrate in an enzymatic assay yields selective inhibitors and activators

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
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	76.0	%	PMID[29353722]

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 NPC66654 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	21236
0.1-0.2	23038
0.2-0.3	4694
0.3-0.4	756
0.4-0.5	73
0.5-0.6	31
0.6-0.7	17
0.7-0.8	0
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.831	Intermediate Similarity	NPC160734
0.8082	Intermediate Similarity	NPC114874
0.7917	Intermediate Similarity	NPC31907
0.7237	Intermediate Similarity	NPC309425
0.7195	Intermediate Similarity	NPC127801
0.7195	Intermediate Similarity	NPC152584
0.7125	Intermediate Similarity	NPC208477
0.7037	Intermediate Similarity	NPC69737
0.6951	Remote Similarity	NPC213190
0.6923	Remote Similarity	NPC157659
0.686	Remote Similarity	NPC208594
0.6829	Remote Similarity	NPC181467
0.6629	Remote Similarity	NPC160816
0.6538	Remote Similarity	NPC43912
0.65	Remote Similarity	NPC8431
0.6477	Remote Similarity	NPC208650
0.6353	Remote Similarity	NPC131479
0.6341	Remote Similarity	NPC274833
0.6333	Remote Similarity	NPC220427
0.6279	Remote Similarity	NPC269627
0.6129	Remote Similarity	NPC14946
0.6129	Remote Similarity	NPC159005
0.6129	Remote Similarity	NPC63368
0.6105	Remote Similarity	NPC6931
0.6	Remote Similarity	NPC131466
0.5938	Remote Similarity	NPC135369
0.5895	Remote Similarity	NPC246124
0.5806	Remote Similarity	NPC65167
0.5773	Remote Similarity	NPC180183
0.5732	Remote Similarity	NPC82955
0.573	Remote Similarity	NPC472719
0.57	Remote Similarity	NPC241381
0.5663	Remote Similarity	NPC47566
0.5663	Remote Similarity	NPC129372
0.5663	Remote Similarity	NPC609286
0.5588	Remote Similarity	NPC488292
0.5588	Remote Similarity	NPC146868
0.5488	Remote Similarity	NPC234287
0.5488	Remote Similarity	NPC88000
0.5488	Remote Similarity	NPC4831
0.5488	Remote Similarity	NPC472023
0.5435	Remote Similarity	NPC472717
0.5422	Remote Similarity	NPC7341
0.5417	Remote Similarity	NPC64081
0.5385	Remote Similarity	NPC488294
0.5352	Remote Similarity	NPC282454
0.5244	Remote Similarity	NPC280825
0.5244	Remote Similarity	NPC473198
0.5238	Remote Similarity	NPC136816
0.5229	Remote Similarity	NPC488291
0.5222	Remote Similarity	NPC473020
0.5222	Remote Similarity	NPC229801
0.5109	Remote Similarity	NPC472252
0.5109	Remote Similarity	NPC245280
0.5068	Remote Similarity	NPC80530
0.5068	Remote Similarity	NPC273410

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC66654 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7635
0.1-0.2	1440
0.2-0.3	69
0.3-0.4	6
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