NPASS Compound

Natural Product: NPC117899

Natural Product ID	NPC117899
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Jaspic Acid
IUPAC Name	3-[[(1S,4aS,5R,8aS)-2,5,8a-trimethyl-5-(4-methylpent-3-enyl)-1,4,4a,6,7,8-hexahydronaphthalen-1-yl]methyl]-4-hydroxybenzoic acid
Synonyms	(-)-Jaspic Acid; Jaspic Acid
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL180947
PubChem CID	10179787
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids

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 68 70 0 0 0 0 0 0 0 0999 V2000 -6.2004 2.7489 1.0253 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5763 1.4226 1.0895 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9296 0.8363 0.0488 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3260 -0.4914 0.1735 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8515 -0.6368 0.1347 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1863 -0.2289 -1.0896 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.7807 -1.0325 -2.2501 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1397 1.2107 -1.4447 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4930 1.9239 -0.2682 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0531 1.4884 -0.0934 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1317 -0.0055 -0.0601 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7030 -0.6569 -1.1110 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5002 -2.1267 -1.2196 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7011 -2.5803 -0.5035 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7327 -1.7740 -0.1370 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5823 -0.3540 -0.5103 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5492 0.6001 0.0578 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9587 0.4204 -0.2972 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9042 0.0182 0.6069 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2279 -0.1105 0.2661 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6360 0.1695 -1.0192 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6880 0.5776 -1.9418 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3674 0.7036 -1.5942 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4287 1.1219 -2.5603 O 0 0 0 0 0 0 0 0 0 0 0 0 7.2063 -0.5471 1.2648 C 0 0 0 0 0 0 0 0 0 0 0 0 8.4169 -0.6688 0.9735 O 0 0 0 0 0 0 0 0 0 0 0 0 6.8288 -0.8398 2.5610 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8793 -2.3748 0.5780 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0098 -0.5630 1.3179 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6392 0.6603 2.3545 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1668 2.7652 0.4907 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5339 3.4637 0.4838 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3340 3.1530 2.0310 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9640 1.4569 -0.8457 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7647 -0.9459 1.1159 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8156 -1.1491 -0.6257 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6553 -1.7483 0.2789 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4800 -0.1025 1.0620 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0243 -1.3224 -3.0018 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5189 -0.4008 -2.8118 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2466 -1.9790 -1.8886 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0270 1.7172 -1.7392 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4223 1.3443 -2.3228 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1028 1.8440 0.6318 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4608 3.0028 -0.5403 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4808 1.8511 -1.0157 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3154 1.9999 0.8183 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3319 -0.2239 -2.0916 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3725 -2.7404 -0.9000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3422 -2.4562 -2.2956 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7737 -3.6237 -0.2496 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6026 -0.3515 -1.6466 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4495 0.5222 1.1877 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3104 1.6673 -0.1433 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6519 -0.2131 1.6531 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6822 0.0608 -1.2625 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0151 0.8012 -2.9684 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2091 2.1040 -2.6717 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4877 -0.9152 3.3312 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0747 -1.9515 1.5685 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6082 -3.4570 0.8017 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7857 -2.4956 -0.0697 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0138 -0.8108 1.7838 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3416 0.2846 1.9824 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5700 -1.4780 1.4237 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2454 -0.2571 2.3027 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0119 1.3152 3.1960 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5983 0.3574 2.6427 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 6 5 1 1 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 2 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 2 0 19 20 1 0 20 21 2 0 21 22 1 0 22 23 2 0 23 24 1 0 20 25 1 0 25 26 2 0 25 27 1 0 15 28 1 0 11 29 1 1 2 30 1 0 12 6 1 0 23 18 1 0 16 11 1 0 1 31 1 0 1 32 1 0 1 33 1 0 3 34 1 0 4 35 1 0 4 36 1 0 5 37 1 0 5 38 1 0 7 39 1 0 7 40 1 0 7 41 1 0 8 42 1 0 8 43 1 0 9 44 1 0 9 45 1 0 10 46 1 0 10 47 1 0 12 48 1 6 13 49 1 0 13 50 1 0 14 51 1 0 16 52 1 6 17 53 1 0 17 54 1 0 19 55 1 0 21 56 1 0 22 57 1 0 24 58 1 0 27 59 1 0 28 60 1 0 28 61 1 0 28 62 1 0 29 63 1 0 29 64 1 0 29 65 1 0 30 66 1 0 30 67 1 0 30 68 1 0 M END

Standard InCHIKey	IIMZFSAVKIVVHG-DAANFHMWSA-N
Standard InCHI	InChI=1S/C27H38O3/c1-18(2)8-6-13-26(4)14-7-15-27(5)22(19(3)9-12-24(26)27)17-21-16-20(25(29)30)10-11-23(21)28/h8-11,16,22,24,28H,6-7,12-15,17H2,1-5H3,(H,29,30)/t22-,24-,26-,27+/m0/s1
SMILES	CC(=CCC[C@@]1(C)CCC[C@]2([C@H]1CC=C([C@@H]2Cc1cc(ccc1O)C(=O)O)C)C)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	410.28	Volume:	460.431 ? Van der Waals volume.
Dense:	0.891	LogP:	5.763 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.833 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.655 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	6.0	Rigid Bonds:	19.0
TPSA:	57.53 ? Topological Polar Surface Area.	H-Bond Acceptor:	3.0
H-Bond Donor:	2.0	Rings:	3.0
Heavy Atoms:	3.0

MedChem Properties

QED Drug-Likeness Score:	0.489	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.137	Fsp³:	0.593
MCE-18:	77.558 ? 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:	0.586	Fluc inhibitor:	0.046 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.012 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.056 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.325	Promiscuous compounds:	0.113

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.706	MDCK Permeability:	-4.726
Pgp-inhibitor:	0.031	Pgp-substrate:	0.001
PAMPA:	0.944 ? 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):	0.001
20% Bioavailability (F20%):	0.053	30% Bioavailability (F30%):	0.052
50% Bioavailability (F50%):	0.961

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.004	MRP1:	0.952
Plasma Protein Binding (PPB):	96.37%	Volume Distribution (VD):	-0.409
Fu:	3.862% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	0.995	BCRP inhibitor:	0.03
BSEP inhibitor:	0.447

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.001
CYP2C19-inhibitor:	0.972	CYP2C19-substrate:	0.002
CYP2C9-inhibitor:	0.823	CYP2C9-substrate:	0.272
CYP2D6-inhibitor:	0.016	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.02	CYP3A4-substrate:	0.887
CYP2B6-substrate:	0.001	CYP2C8-inhibitor:	0.633
HLM stability:	0.015 ? 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):

2.609

Half-life (T1/2):

1.4

ADMET: Toxicity

hERG Blockers:	0.051	hERG Blockers (10um):	0.12
Human Hepatotoxicity (H-HT):	0.636	Drug-induced Liver Injury (DILI):	0.502
AMES Toxicity:	0.137	Rat Oral Acute Toxicity:	0.303
Maximum Recommended Daily Dose:	0.269	Skin Sensitization:	0.892
Carcinogencity:	0.17	Eye Corrosion:	0.227
Eye Irritation:	0.991	Respiratory Toxicity:	0.549
Drug-induced Neurotoxicity:	0.144	Ototoxicity:	0.513
Hematotoxicity:	0.342	Drug-induced Nephrotoxicity:	0.563
Genotoxicity:	0.109	RPMI-8226 Immunitoxicity:	0.034
A549 Cytotoxicity:	0.097	Hek293 Cytotoxicity:	0.056
BCF:	2.097 ? 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:	5.274 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.551 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.979 ? 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
NPO32440	Cacospongia sp.	Species	Thorectidae	Eukaryota	n.a.	n.a.	n.a.	PMID[11720537]
NPO32440	Cacospongia sp.	Species	Thorectidae	Eukaryota	n.a.	n.a.	n.a.	PMID[17346077]
NPO32440	Cacospongia sp.	Species	Thorectidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]

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	9
MIC	3
Ratio IC50	3

Activity Type	# Activity
Individual protein	6
Organism	3
Others	6

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT257	Individual protein	Arachidonate 15-lipoxygenase	Oryctolagus cuniculus	IC50	=	1400.0	nM	PMID[24950030]
NPT1119	Individual protein	Arachidonate 12-lipoxygenase	Homo sapiens	IC50	=	7600.0	nM	PMID[18841906]
NPT1119	Individual protein	Arachidonate 12-lipoxygenase	Homo sapiens	IC50	=	7900.0	nM	PMID[18345641]
NPT792	Individual protein	Arachidonate 15-lipoxygenase	Homo sapiens	IC50	=	1400.0	nM	PMID[25259627]
NPT792	Individual protein	Arachidonate 15-lipoxygenase	Homo sapiens	IC50	=	4700.0	nM	DOI[10.1271/bbb1961.55.3143]
NPT570	Individual protein	Arachidonate 5-lipoxygenase	Homo sapiens	IC50	=	14000.0	nM	PMID[9644059]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	MIC	>	400.0	ug.mL-1	PubChem BioAssay data set
NPT17	Organism	Staphylococcus epidermidis	Staphylococcus epidermidis	MIC	=	2.5	ug.mL-1	PMID[11908990]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	>	400.0	ug.mL-1	PMID[22981331]
NPT2	Others	Unspecified	n.a.	IC50	=	700.0	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Ratio IC50	=	0.5	n.a.	Open TG-GATES in vivo data: Biochemistry
NPT2	Others	Unspecified	n.a.	Ratio IC50	=	0.09	n.a.	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Ratio IC50	=	5.0	n.a.	PMID[17512094]
NPT2	Others	Unspecified	n.a.	IC50	=	300.0	nM	PMID[26327273]
NPT2	Others	Unspecified	n.a.	IC50	=	600.0	nM	PMID[18298075]

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 NPC117899 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	11651
0.1-0.2	35872
0.2-0.3	2262
0.3-0.4	53
0.4-0.5	14
0.5-0.6	4
0.6-0.7	1
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	Natural Product ID
0.7761	Intermediate Similarity	NPC18798
0.6338	Remote Similarity	NPC229894
0.5217	Remote Similarity	NPC474890
0.5217	Remote Similarity	NPC273282
0.52	Remote Similarity	NPC174991
0.52	Remote Similarity	NPC606673

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC117899 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4413
0.1-0.2	4661
0.2-0.3	76
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