NPASS Compound

Natural Product: NPC19879

Natural Product ID	NPC19879
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	KQUXIDHXURERGI-HNCPQSOCSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	5319026
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001549] Monoterpenoids [CHEMONTID:0001401] Menthane 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 29 28 0 0 0 0 0 0 0 0999 V2000 -2.7728 -1.3928 0.5331 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0947 -0.3380 0.0964 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8600 0.7715 -0.5198 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6428 -0.2740 0.2195 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.1468 0.9146 1.0119 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3224 0.7714 1.1506 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0211 0.0896 0.2856 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5182 -0.0345 0.4600 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4698 -0.6055 -0.9008 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0516 -0.1407 -1.1439 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0062 0.5360 -0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 -3.8512 -1.4667 0.4544 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2668 -2.2382 0.9945 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6725 0.3534 -1.1779 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3154 1.3734 0.2934 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1569 1.3670 -1.1427 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2421 -1.1804 0.7391 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3227 1.8710 0.4682 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6582 1.0114 1.9898 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8292 1.2467 1.9945 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0000 0.3328 -0.4812 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8722 0.5852 1.2976 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7976 -1.0846 0.6744 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4012 -1.6894 -0.6410 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1124 -0.4756 -1.7897 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4667 -0.7154 -1.9131 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0738 0.9480 -1.3977 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1538 -0.2659 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1476 -0.2701 -0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 2 4 1 0 4 5 1 0 5 6 1 0 6 7 2 0 7 8 1 0 7 9 1 0 9 10 1 0 10 4 1 0 1 12 1 0 1 13 1 0 3 14 1 0 3 15 1 0 3 16 1 0 4 17 1 1 5 18 1 0 5 19 1 0 6 20 1 0 8 21 1 0 8 22 1 0 8 23 1 0 9 24 1 0 9 25 1 0 10 26 1 0 10 27 1 0 11 28 1 0 11 29 1 0 M END

Standard InCHIKey	KQUXIDHXURERGI-HNCPQSOCSA-N
Standard InCHI	InChI=1S/C10H16.H2S/c1-8(2)10-6-4-9(3)5-7-10;/h4,10H,1,5-7H2,2-3H3;1H2/t10-;/m1./s1
SMILES	C=C(C)[C@@H]1CC=C(C)CC1.S

Calculated Properties

Physi-Chem Properties

Molecular Weight:	136.13	Volume:	167.687 ? Van der Waals volume.
Dense:	0.812	LogP:	4.244 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.133 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.742 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	1.0	Rigid Bonds:	7.0
TPSA:	0.0 ? Topological Polar Surface Area.	H-Bond Acceptor:	0.0
H-Bond Donor:	0.0	Rings:	1.0
Heavy Atoms:	0.0

MedChem Properties

QED Drug-Likeness Score:	0.485	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.165	Fsp³:	0.6
MCE-18:	15.0 ? 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:	Accepted	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.152	Fluc inhibitor:	0.186 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.005 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.0 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	1.0	Promiscuous compounds:	0.239

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.511	MDCK Permeability:	-4.501
Pgp-inhibitor:	0.676	Pgp-substrate:	0.137
PAMPA:	0.104 ? 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%):	0.023	30% Bioavailability (F30%):	0.034
50% Bioavailability (F50%):	0.113

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.844	MRP1:	0.906
Plasma Protein Binding (PPB):	91.772%	Volume Distribution (VD):	0.522
Fu:	8.748% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.275
OATP1B3 inhibitor:	0.158	BCRP inhibitor:	0.17
BSEP inhibitor:	0.723

ADMET: Metabolism

CYP1A2-inhibitor:	0.401	CYP1A2-substrate:	0.658
CYP2C19-inhibitor:	0.997	CYP2C19-substrate:	0.168
CYP2C9-inhibitor:	0.984	CYP2C9-substrate:	0.005
CYP2D6-inhibitor:	0.995	CYP2D6-substrate:	0.074
CYP3A4-inhibitor:	0.029	CYP3A4-substrate:	0.769
CYP2B6-substrate:	0.936	CYP2C8-inhibitor:	0.917
HLM stability:	0.838 ? 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):

12.315

Half-life (T1/2):

1.624

ADMET: Toxicity

hERG Blockers:	0.053	hERG Blockers (10um):	0.383
Human Hepatotoxicity (H-HT):	0.43	Drug-induced Liver Injury (DILI):	0.36
AMES Toxicity:	0.362	Rat Oral Acute Toxicity:	0.3
Maximum Recommended Daily Dose:	0.222	Skin Sensitization:	0.891
Carcinogencity:	0.679	Eye Corrosion:	0.982
Eye Irritation:	0.993	Respiratory Toxicity:	0.528
Drug-induced Neurotoxicity:	0.55	Ototoxicity:	0.216
Hematotoxicity:	0.393	Drug-induced Nephrotoxicity:	0.191
Genotoxicity:	0.059	RPMI-8226 Immunitoxicity:	0.055
A549 Cytotoxicity:	0.168	Hek293 Cytotoxicity:	0.091
BCF:	2.491 ? 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:	3.843 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.99 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.311 ? 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
NPO6473.1	Perilla frutescens var. acuta	Strain	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10757731]
NPO3392	Agastache rugosus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8789	Schizonepeta tenuifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO6473.1	Perilla frutescens var. acuta	Strain	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8650.1	Perilla frutescens var. arguta	Varieties	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8650.1	Perilla frutescens var. arguta	Varieties	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8789	Schizonepeta tenuifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3392	Agastache rugosus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6473.1	Perilla frutescens var. acuta	Strain	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8650.1	Perilla frutescens var. arguta	Varieties	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6473.1	Perilla frutescens var. acuta	Strain	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3392	Agastache rugosus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8789	Schizonepeta tenuifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8789	Schizonepeta tenuifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8789	Schizonepeta tenuifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO8650.1	Perilla frutescens var. arguta	Varieties	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8789	Schizonepeta tenuifolia	Species	Lamiaceae	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 NPC19879 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	33922
0.1-0.2	14740
0.2-0.3	1063
0.3-0.4	97
0.4-0.5	20
0.5-0.6	5
0.6-0.7	8
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC190810
1.0	High Similarity	NPC34764
1.0	High Similarity	NPC76145
0.75	Intermediate Similarity	NPC92224
0.6154	Remote Similarity	NPC297643
0.6154	Remote Similarity	NPC139717
0.6154	Remote Similarity	NPC229262
0.6	Remote Similarity	NPC100809
0.6	Remote Similarity	NPC209431
0.6	Remote Similarity	NPC148216
0.6	Remote Similarity	NPC130209
0.6	Remote Similarity	NPC148163
0.5909	Remote Similarity	NPC94901
0.52	Remote Similarity	NPC91962
0.52	Remote Similarity	NPC26906
0.52	Remote Similarity	NPC214584
0.5161	Remote Similarity	NPC244038

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC19879 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	8364
0.1-0.2	756
0.2-0.3	26
0.3-0.4	1
0.4-0.5	1
0.5-0.6	0
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	1

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD319	Phase 2
0.6	Remote Similarity	NPD342	Phase 1

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