NPASS Compound

Natural Product: NPC104093

Natural Product ID	NPC104093
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	FLVQHDPEFVLJND-DEOSSOPVSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	10861829
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000050] Lactones [CHEMONTID:0001245] Gamma butyrolactones

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 75 75 0 0 0 0 0 0 0 0999 V2000 -9.6242 1.6470 -0.2302 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5518 1.9217 0.7427 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4641 0.9452 0.9512 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5575 0.7131 -0.2102 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1894 0.1679 -1.4265 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2577 -0.1290 -2.5457 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2643 -1.1838 -2.4894 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2071 -1.2280 -1.4419 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3192 -2.4025 -1.7909 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1799 -2.7160 -0.9395 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9927 -1.8526 -0.8044 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1706 -0.4663 -0.3424 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0467 0.3568 -0.0717 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9459 0.0569 1.0424 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6009 -1.2564 1.1314 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5673 -1.2549 2.3296 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6390 -0.2260 2.2204 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4601 -0.4612 0.9733 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5614 0.5339 0.7913 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5512 0.5373 1.9271 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6561 1.5185 1.7747 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5245 1.3657 0.5852 C 0 0 1 0 0 0 0 0 0 0 0 0 9.2397 0.0575 0.4895 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5069 -0.0777 -0.9945 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6489 0.9536 -1.6285 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5791 1.2063 -2.8563 O 0 0 0 0 0 0 0 0 0 0 0 0 7.9203 1.6110 -0.6464 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.7352 0.5946 -0.5436 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.6105 1.9147 0.2867 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.5613 2.3275 -1.1269 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.0275 2.1744 1.7516 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1065 2.9521 0.4795 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.9196 -0.0490 1.2688 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8605 1.2425 1.8598 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1616 1.7654 -0.5490 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5969 0.2516 0.1056 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.8884 -0.6848 -1.2207 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.8781 0.9953 -1.8175 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9086 -0.3517 -3.4731 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7927 0.8685 -2.8707 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6937 -1.1512 -3.4888 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7524 -2.2164 -2.5712 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6366 -1.5568 -0.4379 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7333 -0.2893 -1.2716 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9696 -2.3012 -2.8719 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9621 -3.3423 -1.8492 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5598 -2.9425 0.1166 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8047 -3.7478 -1.2839 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1883 -2.3726 -0.2805 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5573 -1.8272 -1.8993 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9127 -0.3406 0.4665 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6794 0.0614 -1.2538 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6231 0.3556 -1.0642 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2873 1.4364 0.0371 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3161 0.1478 2.0076 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6914 0.9032 1.2058 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8051 -1.9836 1.5235 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0177 -1.7006 0.2389 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9357 -1.0072 3.2135 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9727 -2.2536 2.4897 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3162 0.7998 2.3760 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3551 -0.4482 3.0719 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7930 -1.5029 0.9799 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7651 -0.3491 0.1129 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1234 1.5398 0.6376 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0889 0.2686 -0.1434 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9640 0.8573 2.8389 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9553 -0.4436 2.1622 H 0 0 0 0 0 0 0 0 0 0 0 0 8.2624 1.5016 2.6962 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2132 2.5519 1.7308 H 0 0 0 0 0 0 0 0 0 0 0 0 9.3361 2.1498 0.6829 H 0 0 0 0 0 0 0 0 0 0 0 0 10.2098 0.0963 0.9927 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6198 -0.8109 0.7801 H 0 0 0 0 0 0 0 0 0 0 0 0 9.1695 -1.0569 -1.3922 H 0 0 0 0 0 0 0 0 0 0 0 0 10.5813 0.0391 -1.2442 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 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 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 24 25 1 0 25 26 2 0 25 27 1 0 27 22 1 0 1 28 1 0 1 29 1 0 1 30 1 0 2 31 1 0 2 32 1 0 3 33 1 0 3 34 1 0 4 35 1 0 4 36 1 0 5 37 1 0 5 38 1 0 6 39 1 0 6 40 1 0 7 41 1 0 7 42 1 0 8 43 1 0 8 44 1 0 9 45 1 0 9 46 1 0 10 47 1 0 10 48 1 0 11 49 1 0 11 50 1 0 12 51 1 0 12 52 1 0 13 53 1 0 13 54 1 0 14 55 1 0 14 56 1 0 15 57 1 0 15 58 1 0 16 59 1 0 16 60 1 0 17 61 1 0 17 62 1 0 18 63 1 0 18 64 1 0 19 65 1 0 19 66 1 0 20 67 1 0 20 68 1 0 21 69 1 0 21 70 1 0 22 71 1 1 23 72 1 0 23 73 1 0 24 74 1 0 24 75 1 0 M END

Standard InCHIKey	FLVQHDPEFVLJND-DEOSSOPVSA-N
Standard InCHI	InChI=1S/C25H48O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-24-22-23-25(26)27-24/h24H,2-23H2,1H3/t24-/m0/s1
SMILES	CCCCCCCCCCCCCCCCCCCCC[C@H]1CCC(=O)O1

Calculated Properties

Physi-Chem Properties

Molecular Weight:	380.37	Volume:	447.344 ? Van der Waals volume.
Dense:	0.85	LogP:	6.849 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.133 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-6.514 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	20.0	Rigid Bonds:	6.0
TPSA:	26.3 ? Topological Polar Surface Area.	H-Bond Acceptor:	2.0
H-Bond Donor:	0.0	Rings:	1.0
Heavy Atoms:	2.0

MedChem Properties

QED Drug-Likeness Score:	0.156	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.684	Fsp³:	0.96
MCE-18:	10.612 ? 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:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.588	Fluc inhibitor:	0.322 ? 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:	0.001 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.991	Promiscuous compounds:	0.47

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.065	MDCK Permeability:	-4.921
Pgp-inhibitor:	0.012	Pgp-substrate:	0.053
PAMPA:	0.0 ? 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):	0.95
20% Bioavailability (F20%):	0.992	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.988
Plasma Protein Binding (PPB):	101.843%	Volume Distribution (VD):	1.936
Fu:	0.378% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.959
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.997
BSEP inhibitor:	0.941

ADMET: Metabolism

CYP1A2-inhibitor:	0.013	CYP1A2-substrate:	0.787
CYP2C19-inhibitor:	0.212	CYP2C19-substrate:	0.001
CYP2C9-inhibitor:	0.544	CYP2C9-substrate:	0.001
CYP2D6-inhibitor:	0.713	CYP2D6-substrate:	0.822
CYP3A4-inhibitor:	0.033	CYP3A4-substrate:	0.751
CYP2B6-substrate:	0.827	CYP2C8-inhibitor:	1.0
HLM stability:	0.529 ? 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):

4.16

Half-life (T1/2):

1.85

ADMET: Toxicity

hERG Blockers:	0.6	hERG Blockers (10um):	0.858
Human Hepatotoxicity (H-HT):	0.533	Drug-induced Liver Injury (DILI):	0.345
AMES Toxicity:	0.051	Rat Oral Acute Toxicity:	0.071
Maximum Recommended Daily Dose:	0.31	Skin Sensitization:	0.998
Carcinogencity:	0.302	Eye Corrosion:	0.993
Eye Irritation:	0.999	Respiratory Toxicity:	0.937
Drug-induced Neurotoxicity:	0.024	Ototoxicity:	0.084
Hematotoxicity:	0.125	Drug-induced Nephrotoxicity:	0.359
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.05
A549 Cytotoxicity:	0.867	Hek293 Cytotoxicity:	0.106
BCF:	0.028 ? 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:	4.113 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.127 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	2.394 ? 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
NPO28508	Flourensia cernua	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO28508	Flourensia cernua	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28508	Flourensia cernua	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28508	Flourensia cernua	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

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

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 NPC104093 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	23738
0.1-0.2	23033
0.2-0.3	2605
0.3-0.4	391
0.4-0.5	60
0.5-0.6	16
0.6-0.7	5
0.7-0.8	0
0.8-0.85	1
0.85-0.9	1
0.9-0.95	1
0.95-1	4

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC63182
1.0	High Similarity	NPC145045
1.0	High Similarity	NPC52700
0.95	High Similarity	NPC105329
0.9091	High Similarity	NPC603863
0.8571	High Similarity	NPC273545
0.8182	Intermediate Similarity	NPC326957
0.7619	Intermediate Similarity	NPC176500
0.7143	Intermediate Similarity	NPC94368
0.6667	Remote Similarity	NPC47363
0.6667	Remote Similarity	NPC287231
0.6667	Remote Similarity	NPC314084
0.6207	Remote Similarity	NPC489810
0.6	Remote Similarity	NPC478976
0.5517	Remote Similarity	NPC23155
0.5455	Remote Similarity	NPC321699
0.5333	Remote Similarity	NPC609089
0.5294	Remote Similarity	NPC481557
0.5294	Remote Similarity	NPC481560
0.5294	Remote Similarity	NPC481652
0.5294	Remote Similarity	NPC481651
0.52	Remote Similarity	NPC201622
0.52	Remote Similarity	NPC305660
0.52	Remote Similarity	NPC12156
0.52	Remote Similarity	NPC161097
0.52	Remote Similarity	NPC28598
0.52	Remote Similarity	NPC22903
0.52	Remote Similarity	NPC54980
0.5161	Remote Similarity	NPC55678
0.5143	Remote Similarity	NPC470436

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC104093 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6700
0.1-0.2	2260
0.2-0.3	175
0.3-0.4	10
0.4-0.5	3
0.5-0.6	1
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	Drug ID	Developmental Stage
0.6667	Remote Similarity	NPD2699	Pre-clinical
0.5161	Remote Similarity	NPD6125	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