NPASS Compound

Natural Product: NPC482045

Natural Product ID	NPC482045
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	OOQZCQKEFKRXLR-UECATJJXSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	44587481
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001550] Sesquiterpenoids

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 60 60 0 0 0 0 0 0 0 0999 V2000 -7.6586 0.4683 1.6381 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0978 1.4141 0.6378 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1551 1.0075 -0.1872 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6520 -0.3822 -0.1244 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1606 -0.2988 0.1781 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5396 -1.6281 0.2660 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5759 -1.9693 -0.5404 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9704 -1.1693 -1.6032 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4794 -1.0259 -1.2481 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2064 -0.2333 -2.2670 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8053 0.8839 -1.9579 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9113 1.5259 -0.6506 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2682 1.6910 -0.2127 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0391 0.5723 -0.0617 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5804 -0.5572 -0.2963 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4378 0.7444 0.3898 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2240 -0.2904 0.5523 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6013 -0.2001 0.9905 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3491 -1.3898 1.1286 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6463 -1.2793 1.5434 C 0 0 0 0 0 0 0 0 0 0 0 0 9.2352 -0.0674 1.8252 C 0 0 0 0 0 0 0 0 0 0 0 0 8.4955 1.0793 1.6862 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1876 0.9999 1.2706 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0439 2.3454 1.9598 O 0 0 0 0 0 0 0 0 0 0 0 0 10.5508 0.0429 2.2458 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2147 -0.7252 -3.6919 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0208 -2.6169 1.3048 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6387 2.8058 0.6142 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.3688 0.9808 2.3310 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8012 0.1625 2.2998 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1110 -0.3951 1.1349 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7536 1.7172 -0.9172 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1938 -0.9136 0.6806 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8474 -0.9450 -1.0572 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1262 0.1146 1.2372 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6597 0.4419 -0.4276 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1620 -2.9870 -0.4090 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3474 -0.1670 -1.7611 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0339 -1.7830 -2.5413 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0124 -2.0547 -1.2830 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4521 -0.6617 -0.2273 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2984 1.4176 -2.7936 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3781 1.0931 0.1809 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4747 2.5639 -0.7833 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8189 1.7275 0.5883 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8208 -1.2741 0.3469 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8776 -2.3341 0.9050 H 0 0 0 0 0 0 0 0 0 0 0 0 9.2604 -2.1688 1.6638 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6535 1.9191 1.1776 H 0 0 0 0 0 0 0 0 0 0 0 0 9.2613 2.9448 1.1538 H 0 0 0 0 0 0 0 0 0 0 0 0 11.2492 0.3575 1.5764 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2138 -1.8320 -3.7303 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1696 -0.3985 -4.1842 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5987 -0.2767 -4.2832 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9675 -3.6344 0.9080 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0558 -2.3424 1.5877 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4172 -2.4904 2.2462 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1856 3.0291 1.5402 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.3702 2.8817 -0.2264 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8600 3.5597 0.4596 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 5 6 1 0 6 7 2 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 2 0 14 16 1 0 16 17 2 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 22 24 1 0 21 25 1 0 10 26 1 0 6 27 1 0 2 28 1 0 23 18 1 0 1 29 1 0 1 30 1 0 1 31 1 0 3 32 1 0 4 33 1 0 4 34 1 0 5 35 1 0 5 36 1 0 7 37 1 0 8 38 1 0 8 39 1 0 9 40 1 0 9 41 1 0 11 42 1 0 12 43 1 0 12 44 1 0 16 45 1 0 17 46 1 0 19 47 1 0 20 48 1 0 23 49 1 0 24 50 1 0 25 51 1 0 26 52 1 0 26 53 1 0 26 54 1 0 27 55 1 0 27 56 1 0 27 57 1 0 28 58 1 0 28 59 1 0 28 60 1 0 M END

Standard InCHIKey	OOQZCQKEFKRXLR-UECATJJXSA-N
Standard InCHI	InChI=1S/C24H32O4/c1-18(2)7-5-8-19(3)9-6-10-20(4)15-16-28-24(27)14-12-21-11-13-22(25)23(26)17-21/h7,9,11-15,17,25-26H,5-6,8,10,16H2,1-4H3/b14-12+,19-9-,20-15-
SMILES	CC(=CCC/C(=CCC/C(=CCOC(=O)/C=C/c1ccc(c(c1)O)O)/C)/C)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	384.23	Volume:	429.173 ? Van der Waals volume.
Dense:	0.895	LogP:	7.126 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.987 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.397 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	11.0	Rigid Bonds:	11.0
TPSA:	66.76 ? Topological Polar Surface Area.	H-Bond Acceptor:	4.0
H-Bond Donor:	2.0	Rings:	1.0
Heavy Atoms:	4.0

MedChem Properties

QED Drug-Likeness Score:	0.222	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.857	Fsp³:	0.375
MCE-18:	10.0 ? 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:	1	PAINS Alert:	1
Colloidal aggregators:	0.999	Fluc inhibitor:	0.996 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.246 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.514 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.683	Promiscuous compounds:	0.312

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.939	MDCK Permeability:	-4.719
Pgp-inhibitor:	0.792	Pgp-substrate:	0.013
PAMPA:	0.01 ? 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):	0.024
20% Bioavailability (F20%):	0.953	30% Bioavailability (F30%):	0.981
50% Bioavailability (F50%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.27	MRP1:	0.979
Plasma Protein Binding (PPB):	96.36%	Volume Distribution (VD):	-0.132
Fu:	4.046% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.961
OATP1B3 inhibitor:	0.956	BCRP inhibitor:	0.084
BSEP inhibitor:	0.935

ADMET: Metabolism

CYP1A2-inhibitor:	0.001	CYP1A2-substrate:	0.12
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.008
CYP2C9-inhibitor:	0.013	CYP2C9-substrate:	0.027
CYP2D6-inhibitor:	0.27	CYP2D6-substrate:	0.831
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.986 ? 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):

14.565

Half-life (T1/2):

1.156

ADMET: Toxicity

hERG Blockers:	0.12	hERG Blockers (10um):	0.717
Human Hepatotoxicity (H-HT):	0.376	Drug-induced Liver Injury (DILI):	0.039
AMES Toxicity:	0.147	Rat Oral Acute Toxicity:	0.025
Maximum Recommended Daily Dose:	0.281	Skin Sensitization:	1.0
Carcinogencity:	0.127	Eye Corrosion:	0.273
Eye Irritation:	0.987	Respiratory Toxicity:	0.278
Drug-induced Neurotoxicity:	0.203	Ototoxicity:	0.482
Hematotoxicity:	0.054	Drug-induced Nephrotoxicity:	0.146
Genotoxicity:	0.008	RPMI-8226 Immunitoxicity:	0.013
A549 Cytotoxicity:	0.224	Hek293 Cytotoxicity:	0.079
BCF:	1.643 ? 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:	5.146 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.869 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	6.423 ? 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
NPO40119	Eremophila longifolia	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28257200]
NPO40119	Eremophila longifolia	Species	Scrophulariaceae	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
Ratio EC50	1
EC50	2
IC50	2

Activity Type	# Activity
Cell line	4
Organism	1

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
NPT113	Cell line	RAW264.7	Mus musculus	Ratio EC50	=	10.3	n.a.	PMID[18667320]
NPT113	Cell line	RAW264.7	Mus musculus	EC50	=	2658.0	nM	PMID[18667320]
NPT113	Cell line	RAW264.7	Mus musculus	EC50	=	258.0	nM	PMID[18667320]
NPT171	Cell line	MRC5	Homo sapiens	IC50	=	13.3	ug.mL-1	PMID[28257200]
NPT471	Organism	Trypanosoma brucei brucei	Trypanosoma brucei brucei	IC50	=	0.23	ug.mL-1	PMID[28257200]

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 NPC482045 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	9995
0.1-0.2	34978
0.2-0.3	4195
0.3-0.4	569
0.4-0.5	98
0.5-0.6	15
0.6-0.7	5
0.7-0.8	0
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
0.8039	Intermediate Similarity	NPC482044
0.7551	Intermediate Similarity	NPC261453
0.6949	Remote Similarity	NPC482043
0.6923	Remote Similarity	NPC271641
0.6226	Remote Similarity	NPC33749
0.62	Remote Similarity	NPC95381
0.6	Remote Similarity	NPC328593
0.5926	Remote Similarity	NPC474967
0.5789	Remote Similarity	NPC203124
0.5789	Remote Similarity	NPC607366
0.5758	Remote Similarity	NPC30174
0.5556	Remote Similarity	NPC217472
0.5536	Remote Similarity	NPC147654
0.5424	Remote Similarity	NPC65791
0.5345	Remote Similarity	NPC263386
0.5345	Remote Similarity	NPC141791
0.5333	Remote Similarity	NPC204466
0.5294	Remote Similarity	NPC226250
0.52	Remote Similarity	NPC197467
0.5094	Remote Similarity	NPC304638
0.5088	Remote Similarity	NPC233669
0.5085	Remote Similarity	NPC18646

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC482045 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3672
0.1-0.2	5353
0.2-0.3	108
0.3-0.4	16
0.4-0.5	0
0.5-0.6	1
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
0.5192	Remote Similarity	NPD6927	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