NPASS Compound

Natural Product: NPC475849

Natural Product ID	NPC475849
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	(2S,3R,4S,5R,6R)-4,5-Dihydroxy-6-Methyl-2-((1Ar,4R,4As,7R,7As,7Bs)-1,1,4,7-Tetramethyldecahydro-1H-Cyclopropa[E]Azulen-4-Yloxy)Tetrahydro-2H-Pyran-3-Yl Isobutyrate
IUPAC Name	[(2S,3R,4S,5R,6R)-2-[[(1aR,4R,4aS,7R,7aS,7bS)-1,1,4,7-tetramethyl-2,3,4a,5,6,7,7a,7b-octahydro-1aH-cyclopropa[e]azulen-4-yl]oxy]-4,5-dihydroxy-6-methyloxan-3-yl] 2-methylpropanoate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL517303
PubChem CID	44567062
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides

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 73 76 0 0 0 0 0 0 0 0999 V2000 -5.2652 1.4495 0.5156 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5751 0.3307 1.1956 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0316 0.8613 2.5179 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8184 -0.0644 2.6976 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2195 0.0850 1.2801 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4275 -0.2913 0.4686 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3523 -0.2003 -0.9632 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8630 0.1790 -1.2800 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9783 0.7893 -1.9247 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0914 0.4908 -3.4309 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1490 2.2940 -1.7444 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2175 -1.1476 -1.4408 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0799 -1.7307 -0.0873 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0215 -0.8127 1.0858 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0952 -1.8185 2.2633 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0566 0.0015 1.1950 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3164 -0.4851 1.0949 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0035 0.2618 -0.0334 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2998 1.6436 0.5364 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4726 1.4603 1.4715 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3627 0.0816 2.0877 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0551 -0.2394 2.2479 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9386 0.2465 3.5074 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4831 2.4656 2.4429 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5107 2.5909 -0.4316 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1436 -0.3777 -0.4991 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2646 -0.7281 -1.8244 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3155 -0.4504 -2.5960 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4521 -1.4141 -2.3888 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6911 -0.5606 -2.1847 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2711 -1.7077 -3.8488 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5608 1.2702 -0.5146 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2358 1.6204 1.0765 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6941 2.3819 0.6991 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3757 -0.4093 1.5006 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6873 1.8881 2.3175 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7400 0.7581 3.3394 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1738 0.3833 3.4576 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2123 -1.0498 2.8906 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9908 1.1704 1.2803 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5124 -1.3887 0.7822 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7202 -1.1454 -1.4883 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3117 0.7875 -0.5543 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0861 -0.6111 -3.5879 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1925 0.9471 -3.8992 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9916 0.9231 -3.8672 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7951 2.5706 -0.7527 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5148 2.8127 -2.5009 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1910 2.5910 -1.9735 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8478 -1.8348 -2.0693 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2829 -1.0238 -2.0034 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1748 -2.3597 -0.0706 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9215 -2.4363 0.0844 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0995 -1.3245 3.2296 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2431 -2.5542 2.1592 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9926 -2.4320 2.0346 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4045 -1.5675 0.9022 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2910 0.3910 -0.8738 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4100 1.9367 1.1295 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3899 1.5061 0.8694 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0107 -0.6739 1.6285 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7586 -0.7213 4.0384 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4262 1.0342 4.0604 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0450 0.3593 3.4673 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3997 2.4212 2.8646 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6209 2.9735 -0.6851 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5896 -2.3614 -1.8389 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4492 -0.8803 -2.9118 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4379 0.5315 -2.2679 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0842 -0.8046 -1.1788 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6683 -0.8613 -4.4683 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8873 -2.5895 -4.1214 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2234 -1.9555 -4.1142 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 9 11 1 0 8 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 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 1 0 21 23 1 0 20 24 1 0 19 25 1 0 18 26 1 0 26 27 1 0 27 28 2 0 27 29 1 0 29 30 1 0 29 31 1 0 6 2 1 0 14 5 1 0 9 7 1 0 22 17 1 0 1 32 1 0 1 33 1 0 1 34 1 0 2 35 1 0 3 36 1 0 3 37 1 0 4 38 1 0 4 39 1 0 5 40 1 0 6 41 1 0 7 42 1 0 8 43 1 0 10 44 1 0 10 45 1 0 10 46 1 0 11 47 1 0 11 48 1 0 11 49 1 0 12 50 1 0 12 51 1 0 13 52 1 0 13 53 1 0 15 54 1 0 15 55 1 0 15 56 1 0 17 57 1 0 18 58 1 0 19 59 1 0 20 60 1 0 21 61 1 0 23 62 1 0 23 63 1 0 23 64 1 0 24 65 1 0 25 66 1 0 29 67 1 0 30 68 1 0 30 69 1 0 30 70 1 0 31 71 1 0 31 72 1 0 31 73 1 0 M END

Standard InCHIKey	KYBCKZPKDGOQLN-PHSVILLSSA-N
Standard InCHI	InChI=1S/C25H42O6/c1-12(2)22(28)30-21-20(27)19(26)14(4)29-23(21)31-25(7)11-10-16-18(24(16,5)6)17-13(3)8-9-15(17)25/h12-21,23,26-27H,8-11H2,1-7H3/t13-,14-,15+,16-,17-,18-,19+,20+,21-,23+,25-/m1/s1
SMILES	CC1CCC2C1C3C(C3(C)C)CCC2(C)OC4C(C(C(C(O4)C)O)O)OC(=O)C(C)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	438.3	Volume:	456.835 ? Van der Waals volume.
Dense:	0.959	LogP:	3.981 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.926 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.229 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	5.0	Rigid Bonds:	20.0
TPSA:	85.22 ? Topological Polar Surface Area.	H-Bond Acceptor:	6.0
H-Bond Donor:	2.0	Rings:	4.0
Heavy Atoms:	6.0

MedChem Properties

QED Drug-Likeness Score:	0.653	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.918	Fsp³:	0.96
MCE-18:	79.592 ? 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:	0.098	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.015 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.018 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.104	Promiscuous compounds:	0.006

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.591	MDCK Permeability:	-5.013
Pgp-inhibitor:	0.894	Pgp-substrate:	0.056
PAMPA:	0.135 ? 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):	0.019
20% Bioavailability (F20%):	0.322	30% Bioavailability (F30%):	0.774
50% Bioavailability (F50%):	0.986

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.183	MRP1:	1.0
Plasma Protein Binding (PPB):	87.568%	Volume Distribution (VD):	-0.026
Fu:	12.785% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.303
OATP1B3 inhibitor:	0.693	BCRP inhibitor:	0.02
BSEP inhibitor:	0.999

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.992	CYP2C19-substrate:	0.001
CYP2C9-inhibitor:	0.104	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.178	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.897	CYP2C8-inhibitor:	0.973
HLM stability:	0.39 ? 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):

12.131

Half-life (T1/2):

1.254

ADMET: Toxicity

hERG Blockers:	0.128	hERG Blockers (10um):	0.664
Human Hepatotoxicity (H-HT):	0.615	Drug-induced Liver Injury (DILI):	0.428
AMES Toxicity:	0.317	Rat Oral Acute Toxicity:	0.218
Maximum Recommended Daily Dose:	0.42	Skin Sensitization:	0.032
Carcinogencity:	0.28	Eye Corrosion:	0.0
Eye Irritation:	0.055	Respiratory Toxicity:	0.476
Drug-induced Neurotoxicity:	0.479	Ototoxicity:	0.94
Hematotoxicity:	0.11	Drug-induced Nephrotoxicity:	0.066
Genotoxicity:	0.004	RPMI-8226 Immunitoxicity:	0.067
A549 Cytotoxicity:	0.123	Hek293 Cytotoxicity:	0.473
BCF:	2.222 ? 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:	4.629 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.917 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.524 ? 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
NPO17716	Calendula arvensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1965654]
NPO17716	Calendula arvensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO17716	Calendula arvensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17716	Calendula arvensis	Species	Asteraceae	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
Activity	6
MIC50	1

Activity Type	# Activity
Organism	7

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
NPT2517	Organism	Human rhinovirus 1B	Human rhinovirus 1B	Activity	=	0.0	%	PMID[18710917]
NPT195	Organism	Vesicular stomatitis virus	Vesicular stomatitis virus	Activity	=	9.0	%	PMID[21495717]
NPT195	Organism	Vesicular stomatitis virus	Vesicular stomatitis virus	Activity	=	0.0	%	PMID[22683222]
NPT195	Organism	Vesicular stomatitis virus	Vesicular stomatitis virus	MIC50	>	20.0	ug.mL-1	PMID[21982797]

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 NPC475849 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	19704
0.1-0.2	27901
0.2-0.3	2230
0.3-0.4	7
0.4-0.5	1
0.5-0.6	6
0.6-0.7	4
0.7-0.8	0
0.8-0.85	1
0.85-0.9	2
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8947	High Similarity	NPC474266
0.8909	High Similarity	NPC216941
0.8033	Intermediate Similarity	NPC474182
0.7903	Intermediate Similarity	NPC130792
0.7377	Intermediate Similarity	NPC602042
0.6418	Remote Similarity	NPC610806
0.623	Remote Similarity	NPC188793
0.6	Remote Similarity	NPC604818
0.6	Remote Similarity	NPC611266
0.5753	Remote Similarity	NPC610208
0.5753	Remote Similarity	NPC610630
0.5417	Remote Similarity	NPC609800
0.5405	Remote Similarity	NPC606259
0.5278	Remote Similarity	NPC601777
0.5278	Remote Similarity	NPC609973

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC475849 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7062
0.1-0.2	2045
0.2-0.3	43
0.3-0.4	0
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