NPASS Compound

Natural Product: NPC13554

Natural Product ID	NPC13554
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	(20S)-Dammarane-24(25)-Ene-3Beta,20,21-Tetrol
IUPAC Name	(2S)-2-[(3S,5R,8R,9R,10R,13R,14R,17S)-3-hydroxy-4,4,8,10,14-pentamethyl-2,3,5,6,7,9,11,12,13,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-17-yl]-6-methylhept-5-ene-1,2-diol
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL2313414
PubChem CID	60201377
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

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 85 88 0 0 0 0 0 0 0 0999 V2000 4.3119 -3.7549 -0.5700 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1041 -2.9946 -0.3641 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4309 -1.5409 -0.8181 C 0 0 1 0 0 0 0 0 0 0 0 0 2.3049 -0.6799 -0.4158 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5231 0.7802 -0.7963 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1745 1.3064 -1.3149 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2483 0.3551 -0.6424 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9601 -0.9571 -0.9971 C 0 0 2 0 0 0 0 0 0 0 0 0 0.2194 -2.1475 -0.6009 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2600 -2.0973 -0.4724 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7856 -0.7433 -0.2639 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.1377 0.2941 -1.1850 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.0561 -0.2514 -2.6088 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8048 1.6041 -1.2094 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1611 1.7354 -0.6388 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5910 0.6938 0.3190 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3020 -0.6516 -0.2753 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.9231 -0.9195 -1.5970 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7806 -1.7418 0.6676 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2288 -1.6268 1.0091 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5451 -0.2875 1.5585 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.9748 0.8845 0.8084 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9560 1.3551 -0.2524 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9479 2.0184 1.8442 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9204 -0.0770 1.6938 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2967 0.6253 0.8432 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6929 -1.2689 -0.0491 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4099 -0.0032 -0.2225 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6710 0.0077 0.6243 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8086 0.9216 1.5356 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7524 1.9422 1.7507 C 0 0 0 0 0 0 0 0 0 0 0 0 8.0192 1.0096 2.4169 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7268 -1.5796 -2.1763 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7619 -3.9391 0.2761 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4037 -3.4964 -1.0129 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9150 -3.0737 0.6908 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2727 -0.6825 0.7006 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8214 1.3969 0.0827 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1965 0.8117 -1.6549 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1473 1.3816 -2.3886 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0651 2.3279 -0.9002 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0633 -0.9514 -2.1123 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3858 -2.9239 -1.4274 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6835 -2.6047 0.3207 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8005 -2.6930 -1.2489 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5129 -2.6843 0.4697 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5205 -0.4649 0.7809 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9764 0.0337 -3.2012 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9730 -1.3405 -2.6356 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2344 0.1632 -3.1986 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8736 1.9963 -2.2720 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0997 2.3545 -0.7333 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9586 1.8019 -1.4394 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2293 2.7253 -0.1278 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9218 0.7774 1.2286 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9096 -1.4631 -1.4846 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3003 -1.6691 -2.1679 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1496 -0.0614 -2.2249 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6475 -2.7056 0.0951 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1708 -1.8260 1.5693 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9225 -1.9536 0.2086 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4062 -2.3691 1.8449 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1412 -0.2620 2.6135 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9450 1.4441 0.2876 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1173 0.6390 -1.0508 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7223 2.3803 -0.5969 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5080 1.6184 2.7938 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3630 2.8782 1.5418 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9889 2.3263 2.0700 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0458 0.5921 2.4220 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1666 1.2389 1.1596 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5811 1.2661 1.1614 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3803 -0.3026 1.4524 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4555 -2.0994 -0.2619 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5037 -1.4678 1.0689 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8069 0.0400 -1.2700 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8787 0.9346 -0.0694 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3983 -0.7423 0.4342 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7933 1.4071 1.9064 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9301 2.5554 2.6618 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6780 2.5660 0.8465 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8133 0.6574 3.4462 H 0 0 0 0 0 0 0 0 0 0 0 0 8.8139 0.3224 2.0099 H 0 0 0 0 0 0 0 0 0 0 0 0 8.3844 2.0607 2.4797 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0208 -1.1851 -2.7451 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 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 6 12 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 6 17 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 22 24 1 0 21 25 1 0 7 26 1 1 3 27 1 0 27 28 1 0 28 29 1 0 29 30 2 3 30 31 1 0 30 32 1 0 3 33 1 6 8 4 1 0 17 11 1 0 12 7 1 0 22 16 1 0 1 34 1 0 2 35 1 0 2 36 1 0 4 37 1 1 5 38 1 0 5 39 1 0 6 40 1 0 6 41 1 0 8 42 1 6 9 43 1 0 9 44 1 0 10 45 1 0 10 46 1 0 11 47 1 1 13 48 1 0 13 49 1 0 13 50 1 0 14 51 1 0 14 52 1 0 15 53 1 0 15 54 1 0 16 55 1 1 18 56 1 0 18 57 1 0 18 58 1 0 19 59 1 0 19 60 1 0 20 61 1 0 20 62 1 0 21 63 1 1 23 64 1 0 23 65 1 0 23 66 1 0 24 67 1 0 24 68 1 0 24 69 1 0 25 70 1 0 26 71 1 0 26 72 1 0 26 73 1 0 27 74 1 0 27 75 1 0 28 76 1 0 28 77 1 0 29 78 1 0 31 79 1 0 31 80 1 0 31 81 1 0 32 82 1 0 32 83 1 0 32 84 1 0 33 85 1 0 M END

Standard InCHIKey	ARYNZYKWUXIZOG-AYHBXSNGSA-N
Standard InCHI	InChI=1S/C30H52O3/c1-20(2)9-8-15-30(33,19-31)22-12-17-28(6)21(22)10-11-24-27(5)16-14-25(32)26(3,4)23(27)13-18-29(24,28)7/h9,21-25,31-33H,8,10-19H2,1-7H3/t21-,22+,23+,24-,25+,27+,28-,29-,30-/m1/s1
SMILES	OC[C@@]([C@H]1CC[C@@]2([C@@H]1CC[C@H]1[C@@]2(C)CC[C@@H]2[C@]1(C)CC[C@@H](C2(C)C)O)C)(CCC=C(C)C)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	460.39	Volume:	516.944 ? Van der Waals volume.
Dense:	0.891	LogP:	4.768 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.268 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.714 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	5.0	Rigid Bonds:	21.0
TPSA:	60.69 ? Topological Polar Surface Area.	H-Bond Acceptor:	3.0
H-Bond Donor:	3.0	Rings:	4.0
Heavy Atoms:	3.0

MedChem Properties

QED Drug-Likeness Score:	0.41	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.842	Fsp³:	0.933
MCE-18:	85.345 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted	GSK Rule:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.625	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.002 ? 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:	0.623	Promiscuous compounds:	0.319

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.025	MDCK Permeability:	-4.921
Pgp-inhibitor:	0.183	Pgp-substrate:	0.355
PAMPA:	0.94 ? 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):	0.004
20% Bioavailability (F20%):	0.89	30% Bioavailability (F30%):	0.407
50% Bioavailability (F50%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.914	MRP1:	0.966
Plasma Protein Binding (PPB):	97.449%	Volume Distribution (VD):	-0.021
Fu:	3.039% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	0.983	BCRP inhibitor:	0.318
BSEP inhibitor:	0.854

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.001
CYP2C19-inhibitor:	0.956	CYP2C19-substrate:	0.004
CYP2C9-inhibitor:	0.031	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.006	CYP2D6-substrate:	0.005
CYP3A4-inhibitor:	0.025	CYP3A4-substrate:	0.255
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.813
HLM stability:	0.063 ? 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):

10.725

Half-life (T1/2):

0.673

ADMET: Toxicity

hERG Blockers:	0.12	hERG Blockers (10um):	0.356
Human Hepatotoxicity (H-HT):	0.541	Drug-induced Liver Injury (DILI):	0.024
AMES Toxicity:	0.209	Rat Oral Acute Toxicity:	0.197
Maximum Recommended Daily Dose:	0.391	Skin Sensitization:	0.97
Carcinogencity:	0.513	Eye Corrosion:	0.084
Eye Irritation:	0.757	Respiratory Toxicity:	0.694
Drug-induced Neurotoxicity:	0.131	Ototoxicity:	0.578
Hematotoxicity:	0.221	Drug-induced Nephrotoxicity:	0.691
Genotoxicity:	0.072	RPMI-8226 Immunitoxicity:	0.051
A549 Cytotoxicity:	0.338	Hek293 Cytotoxicity:	0.243
BCF:	1.845 ? 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:	3.941 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.32 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.662 ? 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
NPO12934	Gynostemma pentaphyllum	Species	Cucurbitaceae	Eukaryota	Stems	n.a.	n.a.	PMID[20104880]
NPO12934	Gynostemma pentaphyllum	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22342101]
NPO12934	Gynostemma pentaphyllum	Species	Cucurbitaceae	Eukaryota	aerial parts	n.a.	n.a.	PMID[25895106]
NPO16506	Synotis alata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO4305	Pertusaria wulfenii	Species	Pertusariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12934	Gynostemma pentaphyllum	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO918	Dahlia pinnata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11990	Coleostephus myconis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12934	Gynostemma pentaphyllum	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11990	Coleostephus myconis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO918	Dahlia pinnata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11990	Coleostephus myconis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12934	Gynostemma pentaphyllum	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO918	Dahlia pinnata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11990	Coleostephus myconis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12934	Gynostemma pentaphyllum	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4305	Pertusaria wulfenii	Species	Pertusariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11990	Coleostephus myconis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO918	Dahlia pinnata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16506	Synotis alata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12934	Gynostemma pentaphyllum	Species	Cucurbitaceae	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	1

Activity Type	# Activity
Individual protein	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT178	Individual protein	Protein-tyrosine phosphatase 1B	Homo sapiens	IC50	=	15200.0	nM	PMID[23177789]

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 NPC13554 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	23644
0.1-0.2	21200
0.2-0.3	4296
0.3-0.4	565
0.4-0.5	108
0.5-0.6	31
0.6-0.7	4
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
0.8077	Intermediate Similarity	NPC285761
0.8077	Intermediate Similarity	NPC34930
0.6607	Remote Similarity	NPC245869
0.6491	Remote Similarity	NPC237460
0.6102	Remote Similarity	NPC80530
0.6102	Remote Similarity	NPC273410
0.5965	Remote Similarity	NPC606606
0.5932	Remote Similarity	NPC488511
0.5789	Remote Similarity	NPC480925
0.5789	Remote Similarity	NPC48079
0.5781	Remote Similarity	NPC131665
0.5781	Remote Similarity	NPC255387
0.5667	Remote Similarity	NPC42853
0.5574	Remote Similarity	NPC296701
0.5574	Remote Similarity	NPC218616
0.55	Remote Similarity	NPC91573
0.5484	Remote Similarity	NPC215843
0.5424	Remote Similarity	NPC192638
0.5424	Remote Similarity	NPC25511
0.5424	Remote Similarity	NPC600137
0.541	Remote Similarity	NPC248830
0.541	Remote Similarity	NPC231256
0.541	Remote Similarity	NPC212241
0.541	Remote Similarity	NPC178383
0.5397	Remote Similarity	NPC126993
0.5357	Remote Similarity	NPC232112
0.5333	Remote Similarity	NPC185536
0.5254	Remote Similarity	NPC129829
0.5246	Remote Similarity	NPC144075
0.5246	Remote Similarity	NPC301226
0.5246	Remote Similarity	NPC600477
0.5246	Remote Similarity	NPC606605
0.5238	Remote Similarity	NPC119355
0.5152	Remote Similarity	NPC488508
0.5085	Remote Similarity	NPC142712
0.5079	Remote Similarity	NPC201725
0.5079	Remote Similarity	NPC93662

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC13554 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7684
0.1-0.2	1349
0.2-0.3	110
0.3-0.4	5
0.4-0.5	2
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