NPASS Compound

Natural Product: NPC604482

Natural Product ID	NPC604482
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	FIUFLISGGHNPSM-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1738950
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds]

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 25 0 0 0 0 0 0 0 0999 V2000 -4.0157 1.0690 0.8601 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2639 -0.0970 0.9973 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0208 -0.2759 0.4217 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4396 0.7186 -0.3417 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1963 0.5265 -0.9112 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5087 -0.6460 -0.7457 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8447 -0.9005 -1.3015 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9961 -0.7131 -0.3946 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1767 0.6309 0.1626 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1566 0.8137 0.9729 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3857 1.6991 -0.1126 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1016 -1.6430 0.0333 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3437 -1.4690 0.6103 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0158 1.4768 -0.1760 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7483 1.8844 1.5272 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0895 0.7959 1.0690 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9879 1.6466 -0.4779 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1819 1.3417 -1.5092 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9140 -1.9236 -1.7726 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0032 -0.2194 -2.1925 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9364 -1.4810 0.4399 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9518 -1.0264 -0.9285 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4678 2.6239 0.2527 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4695 -2.5599 0.1506 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7700 -2.2724 1.2044 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 2 0 9 11 1 0 6 12 1 0 12 13 2 0 13 3 1 0 1 14 1 0 1 15 1 0 1 16 1 0 4 17 1 0 5 18 1 0 7 19 1 0 7 20 1 0 8 21 1 0 8 22 1 0 11 23 1 0 12 24 1 0 13 25 1 0 M END

Standard InCHIKey	FIUFLISGGHNPSM-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C10H12O3/c1-13-9-5-2-8(3-6-9)4-7-10(11)12/h2-3,5-6H,4,7H2,1H3,(H,11,12)
SMILES	COc1ccc(CCC(=O)O)cc1

Calculated Properties

Physi-Chem Properties

Molecular Weight:	180.08	Volume:	188.785 ? Van der Waals volume.
Dense:	0.954	LogP:	1.829 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.64 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-1.877 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	4.0	Rigid Bonds:	7.0
TPSA:	46.53 ? Topological Polar Surface Area.	H-Bond Acceptor:	3.0
H-Bond Donor:	1.0	Rings:	1.0
Heavy Atoms:	3.0

MedChem Properties

QED Drug-Likeness Score:	0.767	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	1.344	Fsp³:	0.3
MCE-18:	6.0 ? 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:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.014	Fluc inhibitor:	0.003 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.197 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.177 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.979	Promiscuous compounds:	0.342

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.554	MDCK Permeability:	-4.746
Pgp-inhibitor:	0.09	Pgp-substrate:	0.042
PAMPA:	0.606 ? 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):	0.048
20% Bioavailability (F20%):	0.033	30% Bioavailability (F30%):	0.041
50% Bioavailability (F50%):	0.436

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.008	MRP1:	0.2
Plasma Protein Binding (PPB):	93.789%	Volume Distribution (VD):	-0.491
Fu:	6.648% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.983
OATP1B3 inhibitor:	0.975	BCRP inhibitor:	0.04
BSEP inhibitor:	0.948

ADMET: Metabolism

CYP1A2-inhibitor:	0.295	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.119	CYP2C19-substrate:	0.126
CYP2C9-inhibitor:	1.0	CYP2C9-substrate:	0.02
CYP2D6-inhibitor:	0.968	CYP2D6-substrate:	0.001
CYP3A4-inhibitor:	0.012	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.016	CYP2C8-inhibitor:	0.385
HLM stability:	0.044 ? 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):

4.884

Half-life (T1/2):

1.292

ADMET: Toxicity

hERG Blockers:	0.053	hERG Blockers (10um):	0.131
Human Hepatotoxicity (H-HT):	0.476	Drug-induced Liver Injury (DILI):	0.413
AMES Toxicity:	0.344	Rat Oral Acute Toxicity:	0.167
Maximum Recommended Daily Dose:	0.168	Skin Sensitization:	0.265
Carcinogencity:	0.474	Eye Corrosion:	0.795
Eye Irritation:	0.988	Respiratory Toxicity:	0.582
Drug-induced Neurotoxicity:	0.375	Ototoxicity:	0.564
Hematotoxicity:	0.55	Drug-induced Nephrotoxicity:	0.663
Genotoxicity:	0.102	RPMI-8226 Immunitoxicity:	0.037
A549 Cytotoxicity:	0.004	Hek293 Cytotoxicity:	0.029
BCF:	0.223 ? 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:	2.812 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	3.843 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.179 ? 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
NPO21995	Gelsemium elegans	Species	Gelsemiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16643063]
NPO21995	Gelsemium elegans	Species	Gelsemiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16989532]
NPO21995	Gelsemium elegans	Species	Gelsemiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24256496]
NPO21995	Gelsemium elegans	Species	Gelsemiaceae	Eukaryota	leaves and vine stems	Xishuangbanna Tropical Botanical Garden (XTBG), Chinese Academy of Science (CAS), Mengla County, Yunnan Province, China	2009-OCT	PMID[26103517]
NPO21995	Gelsemium elegans	Species	Gelsemiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26222693]
NPO21995	Gelsemium elegans	Species	Gelsemiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO21995	Gelsemium elegans	Species	Gelsemiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21995	Gelsemium elegans	Species	Gelsemiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21995	Gelsemium elegans	Species	Gelsemiaceae	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

Activity Type	# Activity
Inhibition	1
Potency	1

Activity Type	# Activity
Cell line	1
Single protein	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT22587	Single protein	Taste receptor type 2 member 39	Homo sapiens	Inhibition	=	40.0	%	EP-2323502-B1

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT65	Cell line	HepG2	Homo sapiens	Potency	n.a.	3162.3	nM	PubChem BioAssay data set

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 NPC604482 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	25834
0.1-0.2	21029
0.2-0.3	2774
0.3-0.4	182
0.4-0.5	24
0.5-0.6	6
0.6-0.7	4
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
0.7429	Intermediate Similarity	NPC205502
0.6571	Remote Similarity	NPC51345
0.6286	Remote Similarity	NPC173608
0.6061	Remote Similarity	NPC127343
0.6047	Remote Similarity	NPC601199
0.5814	Remote Similarity	NPC603304
0.5476	Remote Similarity	NPC194416
0.5429	Remote Similarity	NPC234639
0.5405	Remote Similarity	NPC245561
0.5135	Remote Similarity	NPC109241
0.5102	Remote Similarity	NPC602101

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC604482 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	2913
0.1-0.2	5326
0.2-0.3	839
0.3-0.4	64
0.4-0.5	7
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
0.5417	Remote Similarity	NPD2614	Pre-clinical

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