NPASS Compound

Natural Product: NPC482048

Natural Product ID	NPC482048
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	VWQWXZAWFPZJDA-CGVGKPPMSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	16623
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0003569] Pregnane steroids [CHEMONTID:0001468] Gluco/mineralocorticoids, progestogins 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 67 70 0 0 0 0 0 0 0 0999 V2000 -3.5463 -1.7501 1.1142 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6733 -0.4380 0.4101 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.4574 0.4904 1.3144 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8632 -0.0931 1.5167 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5244 -0.0507 0.1922 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7089 0.3491 0.0928 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.7207 -0.4964 -0.9658 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4246 -0.6733 -0.8710 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6578 -1.1076 -2.0485 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2855 -1.5878 -1.7377 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5039 -0.8027 -0.7500 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.4772 0.0445 -1.4075 C 0 0 2 0 0 0 0 0 0 0 0 0 0.5669 -0.6393 -2.2068 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7104 0.3950 -2.2522 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2587 1.5295 -1.3901 C 0 0 2 0 0 0 0 0 0 0 0 0 2.2689 2.3724 -0.7876 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9651 3.5951 -0.7440 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5780 2.0540 -0.2255 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0356 0.7493 -0.3590 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2632 0.3575 0.1421 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9338 1.2615 0.7250 O 0 0 0 0 0 0 0 0 0 0 0 0 5.7798 -1.0112 0.0201 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1190 -1.0944 0.7075 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9811 -0.7745 2.1281 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8668 -0.5100 2.6338 O 0 0 0 0 0 0 0 0 0 0 0 0 8.1077 -0.7584 2.9585 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3625 0.7986 -0.3766 C 0 0 2 0 0 0 0 0 0 0 0 0 1.1856 -0.1005 0.4574 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5263 1.7218 0.3643 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6450 0.9440 1.0323 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.3928 0.1869 -0.0060 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.2252 0.2352 2.1229 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3516 2.3131 -2.1764 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6533 -2.3257 0.8779 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7248 -1.6337 2.2228 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4190 -2.3913 0.7919 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5951 1.4910 0.9055 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9788 0.4629 2.3156 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8199 -1.1250 1.8921 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3896 0.5245 2.2682 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2907 -0.6599 -1.8816 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6592 -0.2858 -2.8137 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2200 -1.9641 -2.5228 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3518 -2.6749 -1.4944 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7142 -1.5732 -2.7147 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0158 -1.4739 -0.0118 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9900 0.8357 -2.0048 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8597 -1.5647 -1.7101 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2023 -0.8962 -3.2103 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5910 -0.1447 -1.9120 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7756 0.7027 -3.3280 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3859 2.7526 -0.5960 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5597 2.2614 0.8780 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1096 -1.7612 0.5097 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8760 -1.3149 -1.0490 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7848 -0.3254 0.2328 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5994 -2.0779 0.5200 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0442 -0.3201 3.8869 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8195 0.5217 1.1194 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8534 -0.7671 -0.1195 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5732 -0.8157 1.0716 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9808 2.4327 -0.3473 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0168 2.3153 1.1408 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3533 1.7356 1.4190 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6584 0.9498 -0.8021 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5305 -0.6788 2.2100 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6255 2.2785 -3.1207 H 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 2 3 1 0 3 4 1 0 4 5 1 0 5 6 2 0 5 7 1 0 7 8 2 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 2 0 16 18 1 0 18 19 1 0 19 20 1 0 20 21 2 0 20 22 1 0 22 23 1 0 23 24 1 0 24 25 2 0 24 26 1 0 15 27 1 0 27 28 1 1 27 29 1 0 29 30 1 0 30 31 1 0 30 32 1 0 15 33 1 6 8 2 1 0 31 11 1 0 31 2 1 0 27 12 1 0 1 34 1 0 1 35 1 0 1 36 1 0 3 37 1 0 3 38 1 0 4 39 1 0 4 40 1 0 7 41 1 0 9 42 1 0 9 43 1 0 10 44 1 0 10 45 1 0 11 46 1 1 12 47 1 6 13 48 1 0 13 49 1 0 14 50 1 0 14 51 1 0 18 52 1 0 18 53 1 0 22 54 1 0 22 55 1 0 23 56 1 0 23 57 1 0 26 58 1 0 28 59 1 0 28 60 1 0 28 61 1 0 29 62 1 0 29 63 1 0 30 64 1 1 31 65 1 6 32 66 1 0 33 67 1 0 M END

Standard InCHIKey	VWQWXZAWFPZJDA-CGVGKPPMSA-N
Standard InCHI	InChI=1S/C25H34O8/c1-23-9-7-15(26)11-14(23)3-4-16-17-8-10-25(32,24(17,2)12-18(27)22(16)23)19(28)13-33-21(31)6-5-20(29)30/h11,16-18,22,27,32H,3-10,12-13H2,1-2H3,(H,29,30)/t16-,17-,18-,22+,23-,24-,25-/m0/s1
SMILES	C[C@]12CCC(=O)C=C1CC[C@H]1[C@@H]3CC[C@](C(=O)COC(=O)CCC(=O)O)([C@@]3(C)C[C@@H]([C@H]21)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	462.23	Volume:	463.87 ? Van der Waals volume.
Dense:	0.996	LogP:	1.858 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.048 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.847 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	7.0	Rigid Bonds:	24.0
TPSA:	138.2 ? Topological Polar Surface Area.	H-Bond Acceptor:	8.0
H-Bond Donor:	3.0	Rings:	4.0
Heavy Atoms:	8.0

MedChem Properties

QED Drug-Likeness Score:	0.511	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.342	Fsp³:	0.76
MCE-18:	79.091 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.391	Fluc inhibitor:	0.007 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.026 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.002 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.209	Promiscuous compounds:	0.989

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.144	MDCK Permeability:	-5.024
Pgp-inhibitor:	0.0	Pgp-substrate:	0.001
PAMPA:	0.974 ? 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):	0.051
20% Bioavailability (F20%):	0.964	30% Bioavailability (F30%):	0.952
50% Bioavailability (F50%):	0.775

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.831	MRP1:	0.428
Plasma Protein Binding (PPB):	96.717%	Volume Distribution (VD):	0.145
Fu:	3.946% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.999
OATP1B3 inhibitor:	0.998	BCRP inhibitor:	0.0
BSEP inhibitor:	0.86

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:	0.005	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.004
HLM stability:	0.001 ? 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):

4.952

Half-life (T1/2):

1.091

ADMET: Toxicity

hERG Blockers:	0.011	hERG Blockers (10um):	0.023
Human Hepatotoxicity (H-HT):	0.654	Drug-induced Liver Injury (DILI):	0.149
AMES Toxicity:	0.097	Rat Oral Acute Toxicity:	0.161
Maximum Recommended Daily Dose:	0.608	Skin Sensitization:	0.419
Carcinogencity:	0.791	Eye Corrosion:	0.0
Eye Irritation:	0.093	Respiratory Toxicity:	0.307
Drug-induced Neurotoxicity:	0.08	Ototoxicity:	0.824
Hematotoxicity:	0.551	Drug-induced Nephrotoxicity:	0.902
Genotoxicity:	0.971	RPMI-8226 Immunitoxicity:	0.078
A549 Cytotoxicity:	0.002	Hek293 Cytotoxicity:	0.03
BCF:	0.379 ? 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:	3.048 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.514 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.597 ? 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
NPO33460	Eremophila neglecta	Species	Scrophulariaceae	Eukaryota	n.a.	Australian desert	n.a.	PMID[17844993]
NPO33460	Eremophila neglecta	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26636180]

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
ID50	1
Inhibition	9
Kd	1
AC50	31
IC50	1

Activity Type	# Activity
Individual protein	35
Organism	7
Others	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1459	Individual protein	Glucocorticoid receptor	Mus musculus	Kd	=	190.0	nM	PMID[926113]
NPT1410	Individual protein	GABA receptor alpha-1 subunit	Rattus norvegicus	AC50	>	30000.0	nM	PMID[37468498]
NPT263	Individual protein	Muscarinic acetylcholine receptor M2	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT218	Individual protein	Adenosine A3 receptor	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT30	Individual protein	Cyclooxygenase-1	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT2761	Individual protein	Phosphodiesterase 4A	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT1788	Individual protein	Alpha-1a adrenergic receptor	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT222	Individual protein	Alpha-2a adrenergic receptor	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT1478	Individual protein	Vascular endothelial growth factor receptor 2	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT153	Individual protein	Androgen Receptor	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT108	Individual protein	Estrogen receptor alpha	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT204	Individual protein	Acetylcholinesterase	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT2769	Individual protein	Thromboxane A2 receptor	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT242	Individual protein	Dopamine D1 receptor	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT262	Individual protein	Muscarinic acetylcholine receptor M1	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT145	Individual protein	Mu opioid receptor	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT228	Individual protein	Norepinephrine transporter	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT261	Individual protein	Monoamine oxidase A	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT246	Individual protein	Dopamine transporter	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT291	Individual protein	Serotonin 2b (5-HT2b) receptor	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT295	Individual protein	Serotonin transporter	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT72	Individual protein	Solute carrier organic anion transporter family member 1B3	Homo sapiens	Inhibition	=	101.77	%	PMID[23571415]
NPT987	Individual protein	Histamine H3 receptor	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT73	Individual protein	Solute carrier organic anion transporter family member 1B1	Homo sapiens	Inhibition	=	93.98	%	PMID[23571415]
NPT98	Individual protein	HERG	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT542	Individual protein	Progesterone receptor	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT609	Individual protein	Human immunodeficiency virus type 1 protease	Human immunodeficiency virus 1	ID50	=	27.0	uM	PMID[8642563]
NPT92	Individual protein	Serotonin 1a (5-HT1a) receptor	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT5104	Individual protein	Phosphodiesterase 3A	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT670	Individual protein	Thrombin	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20	Organism	Candida albicans	Candida albicans	Inhibition	=	4.59	%	DOI[10.6019/CHEMBL4296181]
NPT173	Organism	Klebsiella pneumoniae	Klebsiella pneumoniae	Inhibition	=	-3.41	%	DOI[10.6019/CHEMBL4296181]
NPT85	Organism	Filobasidiella neoformans	Cryptococcus neoformans	Inhibition	=	6.86	%	DOI[10.6019/CHEMBL4296181]
NPT19	Organism	Escherichia coli	Escherichia coli	Inhibition	=	4.71	%	DOI[10.6019/CHEMBL4296181]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	Inhibition	=	18.29	%	DOI[10.6019/CHEMBL4296181]
NPT2922	Organism	Staphylococcus aureus subsp. aureus	Staphylococcus aureus subsp. aureus	Inhibition	=	-27.4	%	DOI[10.6019/CHEMBL4296181]
NPT2	Others	Unspecified	n.a.	IC50	>	100000.0	nM	PMID[17616582]
NPT747	Organism	Acinetobacter baumannii	Acinetobacter baumannii	Inhibition	=	6.01	%	DOI[10.6019/CHEMBL4296181]

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 NPC482048 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	15266
0.1-0.2	30573
0.2-0.3	3941
0.3-0.4	56
0.4-0.5	14
0.5-0.6	3
0.6-0.7	2
0.7-0.8	4
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8143	Intermediate Similarity	NPC488911
0.7429	Intermediate Similarity	NPC478926
0.6522	Remote Similarity	NPC18509
0.6522	Remote Similarity	NPC319582
0.5658	Remote Similarity	NPC44063
0.5211	Remote Similarity	NPC257176
0.5139	Remote Similarity	NPC328539

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC482048 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4798
0.1-0.2	4045
0.2-0.3	220
0.3-0.4	49
0.4-0.5	19
0.5-0.6	6
0.6-0.7	5
0.7-0.8	4
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD6373	Phase 4
0.8143	Intermediate Similarity	NPD6372	Approved
0.803	Intermediate Similarity	NPD5739	Phase 4
0.7429	Intermediate Similarity	NPD4768	Phase 4
0.7361	Intermediate Similarity	NPD7320	Phase 4
0.7286	Intermediate Similarity	NPD4767	Approved
0.7067	Intermediate Similarity	NPD6909	Phase 4
0.6974	Remote Similarity	NPD6908	Approved
0.6522	Remote Similarity	NPD4754	Approved
0.6522	Remote Similarity	NPD4755	Phase 4
0.6081	Remote Similarity	NPD5696	Phase 4
0.6049	Remote Similarity	NPD6650	Phase 4
0.5658	Remote Similarity	NPD5697	Phase 4
0.5513	Remote Similarity	NPD6899	Phase 4
0.525	Remote Similarity	NPD4730	Phase 4
0.5211	Remote Similarity	NPD3618	Phase 1
0.5125	Remote Similarity	NPD4729	Approved
0.5063	Remote Similarity	NPD5695	Phase 3

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