NPASS Compound

Natural Product: NPC209944

Natural Product ID	NPC209944
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	(3Beta,24R)-Stigmasta-5,28-Diene-3,24-Diol
IUPAC Name	(3S,8S,9S,10R,13R,14S,17R)-17-[(2R,5R)-5-hydroxy-5-propan-2-ylhept-6-en-2-yl]-10,13-dimethyl-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-ol
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL524098
PubChem CID	14161396
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0002031] Stigmastanes and derivatives

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 79 82 0 0 0 0 0 0 0 0999 V2000 -7.0550 2.6185 -0.3765 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2754 2.0039 0.4510 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1197 1.1005 -0.1159 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.8629 -0.2296 -0.1087 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1142 -0.1333 -0.9866 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3609 -0.6059 1.2702 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0758 1.1393 0.9087 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7332 0.5930 0.8727 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3763 -0.8054 0.6084 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8966 -1.0802 0.8053 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6898 -2.5436 0.5091 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6536 -2.6351 -0.1956 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3049 -1.3897 0.3134 C 0 0 2 0 0 0 0 0 0 0 0 0 0.1475 -0.3555 0.1427 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0799 -0.0245 -1.2964 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6881 0.8600 0.8784 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0774 1.2491 0.5405 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0927 0.1770 0.4524 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5420 -0.9872 -0.3846 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4963 -2.1454 -0.3336 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9046 -1.7246 -0.1326 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3588 -0.4989 -0.0619 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3507 0.6205 -0.1977 C 0 0 1 0 0 0 0 0 0 0 0 0 4.1626 0.8282 -1.6806 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9752 1.8267 0.4643 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8195 1.4237 1.6579 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0816 0.7373 1.2520 C 0 0 1 0 0 0 0 0 0 0 0 0 6.8042 -0.2082 0.1341 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1081 1.6349 0.9479 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7318 -1.3124 -0.7942 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8609 1.6131 -1.3419 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.8685 3.2542 -0.0481 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9600 2.5506 -1.4683 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3578 2.0741 1.5056 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3174 -1.0754 -0.4906 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8217 0.2223 -1.9768 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.9494 0.3617 -0.4991 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4523 -1.2045 -1.1288 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9377 0.1928 1.7701 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5450 -0.9727 1.9401 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1076 -1.4518 1.1703 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0107 2.2822 1.2243 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5514 0.7865 1.9334 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2831 0.8155 1.9123 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1427 1.2936 0.1562 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8981 -1.4589 1.3081 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7529 -0.9631 1.9238 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5521 -3.1350 1.4654 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5030 -3.0436 -0.0079 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2544 -3.5043 0.1712 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5824 -2.7407 -1.2742 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4800 -1.4783 1.3839 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8198 0.5230 -1.5899 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9168 0.7211 -1.5003 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3369 -0.8558 -1.9898 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0570 1.7201 0.5798 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5983 0.6601 1.9617 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4111 1.9463 1.3682 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0908 1.9306 -0.3616 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3004 -0.2233 1.4459 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3953 -0.6760 -1.4404 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2610 -2.8377 0.5284 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4202 -2.7981 -1.2333 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6640 -2.5236 -0.0294 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2323 -0.1411 -2.2145 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2038 1.2837 -1.9415 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9544 1.4707 -2.1156 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2701 2.5805 0.8012 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6735 2.2857 -0.2596 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2390 0.7376 2.3077 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0669 2.3429 2.2173 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4502 0.1546 2.1362 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2822 0.1212 -0.8316 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3041 -1.1996 0.3382 H 0 0 0 0 0 0 0 0 0 0 0 0 8.2320 1.5938 -0.0383 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8247 -1.6002 -1.3675 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2327 -0.5528 -1.3987 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3484 -2.2265 -0.7760 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9359 1.0114 -2.1168 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 1 0 4 5 1 0 4 6 1 0 3 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 0 13 14 1 0 14 15 1 6 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 2 0 22 23 1 0 23 24 1 6 23 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 27 29 1 0 9 30 1 0 3 31 1 6 14 10 1 0 23 18 1 0 19 13 1 0 28 22 1 0 1 32 1 0 1 33 1 0 2 34 1 0 4 35 1 0 5 36 1 0 5 37 1 0 5 38 1 0 6 39 1 0 6 40 1 0 6 41 1 0 7 42 1 0 7 43 1 0 8 44 1 0 8 45 1 0 9 46 1 1 10 47 1 1 11 48 1 0 11 49 1 0 12 50 1 0 12 51 1 0 13 52 1 1 15 53 1 0 15 54 1 0 15 55 1 0 16 56 1 0 16 57 1 0 17 58 1 0 17 59 1 0 18 60 1 1 19 61 1 6 20 62 1 0 20 63 1 0 21 64 1 0 24 65 1 0 24 66 1 0 24 67 1 0 25 68 1 0 25 69 1 0 26 70 1 0 26 71 1 0 27 72 1 1 28 73 1 0 28 74 1 0 29 75 1 0 30 76 1 0 30 77 1 0 30 78 1 0 31 79 1 0 M END

Standard InCHIKey	OPGVEUGCNGNPSX-MEBFPAKGSA-N
Standard InCHI	InChI=1S/C29H48O2/c1-7-29(31,19(2)3)17-12-20(4)24-10-11-25-23-9-8-21-18-22(30)13-15-27(21,5)26(23)14-16-28(24,25)6/h7-8,19-20,22-26,30-31H,1,9-18H2,2-6H3/t20-,22+,23+,24-,25+,26+,27+,28-,29-/m1/s1
SMILES	C=C[C@](C(C)C)(CC[C@H]([C@H]1CC[C@@H]2[C@]1(C)CC[C@H]1[C@H]2CC=C2[C@]1(C)CC[C@@H](C2)O)C)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	428.37	Volume:	488.222 ? Van der Waals volume.
Dense:	0.877	LogP:	6.889 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.978 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-6.376 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	6.0	Rigid Bonds:	21.0
TPSA:	40.46 ? Topological Polar Surface Area.	H-Bond Acceptor:	2.0
H-Bond Donor:	2.0	Rings:	4.0
Heavy Atoms:	2.0

MedChem Properties

QED Drug-Likeness Score:	0.451	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.774	Fsp³:	0.862
MCE-18:	74.111 ? 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:	0.816	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:	0.579	Promiscuous compounds:	0.086

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.38	MDCK Permeability:	-4.975
Pgp-inhibitor:	0.002	Pgp-substrate:	0.08
PAMPA:	0.011 ? 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%):	0.011	30% Bioavailability (F30%):	0.602
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.007	MRP1:	0.076
Plasma Protein Binding (PPB):	82.297%	Volume Distribution (VD):	-0.089
Fu:	17.132% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.943
BSEP inhibitor:	0.023

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.053	CYP2C19-substrate:	0.007
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.372
CYP2D6-inhibitor:	0.019	CYP2D6-substrate:	0.025
CYP3A4-inhibitor:	0.999	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.645 ? 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):

15.811

Half-life (T1/2):

1.357

ADMET: Toxicity

hERG Blockers:	0.107	hERG Blockers (10um):	0.337
Human Hepatotoxicity (H-HT):	0.535	Drug-induced Liver Injury (DILI):	0.028
AMES Toxicity:	0.05	Rat Oral Acute Toxicity:	0.061
Maximum Recommended Daily Dose:	0.839	Skin Sensitization:	0.928
Carcinogencity:	0.804	Eye Corrosion:	0.131
Eye Irritation:	0.882	Respiratory Toxicity:	0.61
Drug-induced Neurotoxicity:	0.039	Ototoxicity:	0.413
Hematotoxicity:	0.131	Drug-induced Nephrotoxicity:	0.341
Genotoxicity:	0.034	RPMI-8226 Immunitoxicity:	0.058
A549 Cytotoxicity:	0.316	Hek293 Cytotoxicity:	0.657
BCF:	2.308 ? 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:	4.137 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.251 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.87 ? 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
NPO22431	Lessonia nigrescens	Species	Lessoniaceae	Eukaryota	Tubers	n.a.	n.a.	PMID[11720535]
NPO22674	Caulerpa racemosa	Species	Caulerpaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23548547]
NPO22674	Caulerpa racemosa	Species	Caulerpaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25497963]
NPO8725	Aristolochia indica	Species	Aristolochiaceae	Eukaryota	roots	n.a.	n.a.	PMID[6539809]
NPO11653	Sargassum ringoldianum	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10988	Crambe chelastra	Species	Esperiopsidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO847	Bignonia venusta	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO2751	Berchemia zeyheri	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8725	Aristolochia indica	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO22674	Caulerpa racemosa	Species	Caulerpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8725	Aristolochia indica	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8725	Aristolochia indica	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10988	Crambe chelastra	Species	Esperiopsidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22674	Caulerpa racemosa	Species	Caulerpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2751	Berchemia zeyheri	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22431	Lessonia nigrescens	Species	Lessoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11653	Sargassum ringoldianum	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO847	Bignonia venusta	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8725	Aristolochia indica	Species	Aristolochiaceae	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
Inhibition	5
IC50	3
MIC	1

Activity Type	# Activity
Individual protein	6
Cell line	1
Organism	1
Non-molecular	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1210	Individual protein	T-cell protein-tyrosine phosphatase	Homo sapiens	Inhibition	<	50.0	%	PMID[25497963]
NPT178	Individual protein	Protein-tyrosine phosphatase 1B	Homo sapiens	IC50	=	10340.0	nM	PMID[25497963]
NPT205	Individual protein	Protein-tyrosine phosphatase 1C	Homo sapiens	Inhibition	<	50.0	%	PMID[25497963]
NPT206	Individual protein	Protein-tyrosine phosphatase 2C	Homo sapiens	Inhibition	<	50.0	%	PMID[25497963]
NPT1870	Individual protein	Receptor-type tyrosine-protein phosphatase F (LAR)	Homo sapiens	Inhibition	<	50.0	%	PMID[25497963]
NPT911	Individual protein	Dual specificity phosphatase Cdc25B	Homo sapiens	Inhibition	<	50.0	%	PMID[25497963]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT81	Cell line	A549	Homo sapiens	IC50	>	100000.0	nM	PMID[25497963]
NPT88	Organism	Mycobacterium tuberculosis	Mycobacterium tuberculosis	MIC	=	0.125	ug.mL-1	PMID[11720535]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	IC50	>	100000.0	nM	PMID[25497963]

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 NPC209944 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	24613
0.1-0.2	21218
0.2-0.3	3643
0.3-0.4	240
0.4-0.5	78
0.5-0.6	25
0.6-0.7	16
0.7-0.8	2
0.8-0.85	5
0.85-0.9	0
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC241290
1.0	High Similarity	NPC164840
0.8431	Intermediate Similarity	NPC484739
0.8077	Intermediate Similarity	NPC155986
0.8	Intermediate Similarity	NPC162742
0.8	Intermediate Similarity	NPC304309
0.8	Intermediate Similarity	NPC470228
0.7885	Intermediate Similarity	NPC198968
0.7843	Intermediate Similarity	NPC22105
0.7843	Intermediate Similarity	NPC34019
0.7843	Intermediate Similarity	NPC107059
0.7692	Intermediate Similarity	NPC136188
0.7692	Intermediate Similarity	NPC28657
0.7692	Intermediate Similarity	NPC474216
0.7547	Intermediate Similarity	NPC230301
0.7547	Intermediate Similarity	NPC285893
0.7547	Intermediate Similarity	NPC134847
0.7407	Intermediate Similarity	NPC264245
0.7273	Intermediate Similarity	NPC321381
0.7143	Intermediate Similarity	NPC59453
0.7018	Intermediate Similarity	NPC603646
0.6897	Remote Similarity	NPC473943
0.6852	Remote Similarity	NPC600590
0.6842	Remote Similarity	NPC472265
0.678	Remote Similarity	NPC488870
0.6727	Remote Similarity	NPC154330
0.661	Remote Similarity	NPC240650
0.661	Remote Similarity	NPC155011
0.6607	Remote Similarity	NPC113733
0.6552	Remote Similarity	NPC318495
0.6545	Remote Similarity	NPC221758
0.65	Remote Similarity	NPC47761
0.6379	Remote Similarity	NPC328714
0.6271	Remote Similarity	NPC33913
0.6207	Remote Similarity	NPC51014
0.6066	Remote Similarity	NPC243985
0.6066	Remote Similarity	NPC280710
0.5968	Remote Similarity	NPC474164
0.5926	Remote Similarity	NPC96319
0.5902	Remote Similarity	NPC477522
0.5862	Remote Similarity	NPC328313
0.5833	Remote Similarity	NPC87604
0.5763	Remote Similarity	NPC76879
0.5738	Remote Similarity	NPC474634
0.5692	Remote Similarity	NPC601043
0.5692	Remote Similarity	NPC605412
0.5484	Remote Similarity	NPC1272
0.5484	Remote Similarity	NPC470614
0.5424	Remote Similarity	NPC151519
0.541	Remote Similarity	NPC317927
0.5333	Remote Similarity	NPC20688
0.5303	Remote Similarity	NPC474349
0.5303	Remote Similarity	NPC474189
0.5254	Remote Similarity	NPC81306
0.5156	Remote Similarity	NPC474752
0.5156	Remote Similarity	NPC474683
0.5143	Remote Similarity	NPC309493
0.5082	Remote Similarity	NPC109546
0.5082	Remote Similarity	NPC317458
0.5082	Remote Similarity	NPC47982
0.5079	Remote Similarity	NPC31564
0.5079	Remote Similarity	NPC145879

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC209944 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7821
0.1-0.2	1144
0.2-0.3	151
0.3-0.4	27
0.4-0.5	2
0.5-0.6	2
0.6-0.7	1
0.7-0.8	2
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
0.7692	Intermediate Similarity	NPD6942	Phase 4
0.7547	Intermediate Similarity	NPD7339	Approved
0.6545	Remote Similarity	NPD4786	Phase 1
0.5926	Remote Similarity	NPD3701	Pre-clinical
0.5424	Remote Similarity	NPD3667	Phase 4

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