NPASS Compound

Natural Product: NPC111451

Natural Product ID	NPC111451
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	YZNIFKFTGCAOST-UWVGGRQHSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001549] Monoterpenoids [CHEMONTID:0001564] Bicyclic monoterpenoids

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 25 26 0 0 0 0 0 0 0 0999 V2000 -2.0790 -1.2917 -0.4146 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5538 -0.2337 0.5165 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1842 1.0965 0.1670 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0748 -0.0938 0.5053 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8144 -1.2423 0.8740 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0693 -1.0147 0.1377 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0089 0.0441 -0.6320 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0533 0.5484 -1.4819 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9262 1.5754 -2.1976 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6756 0.6681 -0.5005 C 0 0 2 0 0 0 0 0 0 0 0 0 0.4414 1.3091 0.8544 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2493 -2.2437 0.1453 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4264 -1.5024 -1.2668 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0577 -0.9522 -0.8247 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8912 -0.4894 1.5420 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5450 1.6153 -0.5716 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2397 1.7650 1.0717 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2053 0.9710 -0.2510 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9579 -1.2463 1.9777 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3710 -2.1840 0.5090 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9261 -1.6983 0.2665 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0033 0.0416 -1.5281 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2416 1.1054 -1.4044 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2666 1.3041 1.6033 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2491 2.1484 0.9030 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 4 2 1 6 4 5 1 0 5 6 1 0 6 7 2 0 7 8 1 0 8 9 2 0 7 10 1 0 10 11 1 0 11 4 1 0 10 4 1 0 1 12 1 0 1 13 1 0 1 14 1 0 2 15 1 0 3 16 1 0 3 17 1 0 3 18 1 0 5 19 1 0 5 20 1 0 6 21 1 0 8 22 1 0 10 23 1 6 11 24 1 0 11 25 1 0 M END

Standard InCHIKey	YZNIFKFTGCAOST-UWVGGRQHSA-N
Standard InCHI	InChI=1S/C10H14O/c1-7(2)10-4-3-8(6-11)9(10)5-10/h3,6-7,9H,4-5H2,1-2H3/t9-,10-/m0/s1
SMILES	CC(C)[C@]12CC=C(C=O)[C@@H]2C1

Calculated Properties

Physi-Chem Properties

Molecular Weight:	150.1	Volume:	167.921 ? Van der Waals volume.
Dense:	0.894	LogP:	1.991 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.823 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.017 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	2.0	Rigid Bonds:	8.0
TPSA:	17.07 ? Topological Polar Surface Area.	H-Bond Acceptor:	1.0
H-Bond Donor:	0.0	Rings:	2.0
Heavy Atoms:	1.0

MedChem Properties

QED Drug-Likeness Score:	0.551	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.61	Fsp³:	0.7
MCE-18:	29.647 ? 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:	Rejected
Golden Triangle Rule:	Accepted	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.386	Fluc inhibitor:	0.286 ? 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:	0.002 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.852	Promiscuous compounds:	0.074

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.35	MDCK Permeability:	-4.334
Pgp-inhibitor:	0.771	Pgp-substrate:	0.651
PAMPA:	0.054 ? 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):	0.072
20% Bioavailability (F20%):	0.575	30% Bioavailability (F30%):	0.753
50% Bioavailability (F50%):	0.787

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.419	MRP1:	0.873
Plasma Protein Binding (PPB):	59.146%	Volume Distribution (VD):	0.313
Fu:	40.221% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.91
OATP1B3 inhibitor:	0.55	BCRP inhibitor:	0.394
BSEP inhibitor:	0.871

ADMET: Metabolism

CYP1A2-inhibitor:	0.112	CYP1A2-substrate:	0.702
CYP2C19-inhibitor:	0.794	CYP2C19-substrate:	0.798
CYP2C9-inhibitor:	0.071	CYP2C9-substrate:	0.1
CYP2D6-inhibitor:	0.126	CYP2D6-substrate:	0.189
CYP3A4-inhibitor:	0.371	CYP3A4-substrate:	0.714
CYP2B6-substrate:	0.099	CYP2C8-inhibitor:	0.951
HLM stability:	0.834 ? 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):

8.927

Half-life (T1/2):

1.313

ADMET: Toxicity

hERG Blockers:	0.087	hERG Blockers (10um):	0.433
Human Hepatotoxicity (H-HT):	0.444	Drug-induced Liver Injury (DILI):	0.269
AMES Toxicity:	0.642	Rat Oral Acute Toxicity:	0.613
Maximum Recommended Daily Dose:	0.604	Skin Sensitization:	0.622
Carcinogencity:	0.881	Eye Corrosion:	0.53
Eye Irritation:	0.936	Respiratory Toxicity:	0.769
Drug-induced Neurotoxicity:	0.49	Ototoxicity:	0.176
Hematotoxicity:	0.469	Drug-induced Nephrotoxicity:	0.347
Genotoxicity:	0.919	RPMI-8226 Immunitoxicity:	0.064
A549 Cytotoxicity:	0.133	Hek293 Cytotoxicity:	0.218
BCF:	1.746 ? 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:	4.182 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.538 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.087 ? 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
NPO15432	Sarcodon aspratus	Species	Thelephoraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15665489]
NPO4485	Lamellodysidea herbacea	Species	Dysideidae	Eukaryota	n.a.	Indonesian	n.a.	PMID[17311456]
NPO14752	Sinopodophyllum emodi	Species	Berberidaceae	Eukaryota	roots and rhizomes	n.a.	n.a.	PMID[21570846]
NPO4485	Lamellodysidea herbacea	Species	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	PMID[28841316]
NPO5517	Rhododendron tomentosum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32260539]
NPO9283	Trichia favoginea	Species	Trichiidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3860	Allium victorialis	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3200	Arthrophytum leptocladum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14661	Blepharis sindica	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8834	Cellulomonas biazotea	Species	Cellulomonadaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14035	Cladosporium tenuissimum	Species	Cladosporiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO6239	Corbicula fluminea	Species	Corbiculidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14156	Fragaria indica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO13289	Frullania brittoniae	Species	Frullaniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO4485	Lamellodysidea herbacea	Species	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11880	Latua pubiflora	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO238	Lobelia st	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15150	Phebalium gracile	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO27957.1	Pinus densiflora var. densiflora	Varieties	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO890	Remijia pedunculata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO5517	Rhododendron tomentosum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12622	Rudbeckia hirta	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15240	Saracha viscosa	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15432	Sarcodon aspratus	Species	Thelephoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14752	Sinopodophyllum emodi	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15616	Solanum toxicarum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14271	Spongia australis	Species	Spongiidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11098	Stelletta inconspicua	Species	Ancorinidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3860	Allium victorialis	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3860	Allium victorialis	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5517	Rhododendron tomentosum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3860	Allium victorialis	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11098	Stelletta inconspicua	Species	Ancorinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14035	Cladosporium tenuissimum	Species	Cladosporiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14156	Fragaria indica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5517	Rhododendron tomentosum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15616	Solanum toxicarum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8834	Cellulomonas biazotea	Species	Cellulomonadaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO11880	Latua pubiflora	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15240	Saracha viscosa	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3200	Arthrophytum leptocladum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO3860	Allium victorialis	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6239	Corbicula fluminea	Species	Corbiculidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14271	Spongia australis	Species	Spongiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14752	Sinopodophyllum emodi	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27957.1	Pinus densiflora var. densiflora	Varieties	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14661	Blepharis sindica	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9283	Trichia favoginea	Species	Trichiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15432	Sarcodon aspratus	Species	Thelephoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO890	Remijia pedunculata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO238	Lobelia st	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4485	Lamellodysidea herbacea	Species	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12622	Rudbeckia hirta	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13289	Frullania brittoniae	Species	Frullaniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15150	Phebalium gracile	Species	Rutaceae	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 NPC111451 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	23735
0.1-0.2	24728
0.2-0.3	1353
0.3-0.4	41
0.4-0.5	1
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	Natural Product ID
0.5357	Remote Similarity	NPC608603

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC111451 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7222
0.1-0.2	1885
0.2-0.3	42
0.3-0.4	1
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