NPASS Compound

Natural Product: NPC34064

Natural Product ID	NPC34064
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	XEFLZEPEOLTAKR-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	622890
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000123] Benzopyrans [CHEMONTID:0003410] 1-benzopyrans [CHEMONTID:0002817] Dibenzopyrans [CHEMONTID:0000200] Xanthenes [CHEMONTID:0000204] Xanthones

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 30 33 0 0 0 0 0 0 0 0999 V2000 -1.2263 3.1451 -0.4342 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2183 2.1675 0.5874 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3383 0.8215 0.3873 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2151 0.0531 0.1911 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2719 -1.3124 -0.0164 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5318 -1.8896 -0.0191 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6890 -1.1277 0.1785 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5806 0.2314 0.3815 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8326 0.7917 0.5544 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7710 -0.2456 0.2463 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0328 -1.4389 0.2228 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8313 -2.0247 -0.2026 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0247 -1.4594 -0.1971 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1645 -2.2389 -0.3962 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3739 -1.6133 -0.3826 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5330 -0.2440 -0.1815 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3973 0.5239 0.0155 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1735 -0.0997 0.0032 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0183 0.6621 0.2006 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0964 1.8995 0.3868 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2768 3.5520 -0.4904 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8761 2.7632 -1.4035 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5886 4.0150 -0.1696 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6073 -2.9546 -0.1788 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5680 -0.2409 0.9985 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2339 -0.0630 -0.7600 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0521 -3.3084 -0.5541 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2766 -2.1879 -0.5336 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4939 0.2352 -0.1734 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4228 1.5880 0.1785 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 2 0 8 9 1 0 9 10 1 0 10 11 1 0 5 12 1 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 2 0 8 3 1 0 18 13 1 0 19 4 1 0 11 7 1 0 1 21 1 0 1 22 1 0 1 23 1 0 6 24 1 0 10 25 1 0 10 26 1 0 14 27 1 0 15 28 1 0 16 29 1 0 17 30 1 0 M END

Standard InCHIKey	XEFLZEPEOLTAKR-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C15H10O5/c1-17-15-12-10(6-11-14(15)19-7-18-11)20-9-5-3-2-4-8(9)13(12)16/h2-6H,7H2,1H3
SMILES	COc1c2c(cc3c1OCO3)oc1ccccc1c2=O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	270.05	Volume:	259.266 ? Van der Waals volume.
Dense:	1.042	LogP:	2.413 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.472 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.967 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	1.0	Rigid Bonds:	21.0
TPSA:	57.9 ? Topological Polar Surface Area.	H-Bond Acceptor:	5.0
H-Bond Donor:	0.0	Rings:	4.0
Heavy Atoms:	5.0

MedChem Properties

QED Drug-Likeness Score:	0.636	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.365	Fsp³:	0.133
MCE-18:	42.353 ? 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:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.119	Fluc inhibitor:	0.834 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.81 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.363 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.375	Promiscuous compounds:	0.263

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.851	MDCK Permeability:	-4.625
Pgp-inhibitor:	0.927	Pgp-substrate:	0.086
PAMPA:	0.103 ? 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):	0.031
20% Bioavailability (F20%):	0.098	30% Bioavailability (F30%):	0.157
50% Bioavailability (F50%):	0.578

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.214	MRP1:	0.625
Plasma Protein Binding (PPB):	95.575%	Volume Distribution (VD):	0.046
Fu:	4.674% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.712
OATP1B3 inhibitor:	0.932	BCRP inhibitor:	0.847
BSEP inhibitor:	0.993

ADMET: Metabolism

CYP1A2-inhibitor:	0.851	CYP1A2-substrate:	0.938
CYP2C19-inhibitor:	0.559	CYP2C19-substrate:	0.747
CYP2C9-inhibitor:	0.778	CYP2C9-substrate:	0.565
CYP2D6-inhibitor:	0.868	CYP2D6-substrate:	0.811
CYP3A4-inhibitor:	0.004	CYP3A4-substrate:	0.648
CYP2B6-substrate:	0.358	CYP2C8-inhibitor:	0.022
HLM stability:	0.279 ? 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):

3.272

Half-life (T1/2):

0.956

ADMET: Toxicity

hERG Blockers:	0.139	hERG Blockers (10um):	0.499
Human Hepatotoxicity (H-HT):	0.494	Drug-induced Liver Injury (DILI):	0.87
AMES Toxicity:	0.597	Rat Oral Acute Toxicity:	0.461
Maximum Recommended Daily Dose:	0.43	Skin Sensitization:	0.421
Carcinogencity:	0.897	Eye Corrosion:	0.465
Eye Irritation:	0.979	Respiratory Toxicity:	0.636
Drug-induced Neurotoxicity:	0.361	Ototoxicity:	0.134
Hematotoxicity:	0.344	Drug-induced Nephrotoxicity:	0.171
Genotoxicity:	0.467	RPMI-8226 Immunitoxicity:	0.067
A549 Cytotoxicity:	0.091	Hek293 Cytotoxicity:	0.295
BCF:	1.575 ? 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:	3.801 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.934 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.375 ? 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
NPO20441	Glaucium flavum	Species	Papaveraceae	Eukaryota	n.a.	root	n.a.	PMID[24317429]
NPO20441	Glaucium flavum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[38415909]
NPO4969	Sesbania bispinosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO20441	Glaucium flavum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO21068	Centaurea sulphurea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO19599	Pogostemon parviflorus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO4969	Sesbania bispinosa	Species	Fabaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO20441	Glaucium flavum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20441	Glaucium flavum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20441	Glaucium flavum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21068	Centaurea sulphurea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19599	Pogostemon parviflorus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20441	Glaucium flavum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4969	Sesbania bispinosa	Species	Fabaceae	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 NPC34064 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	30095
0.1-0.2	16938
0.2-0.3	2610
0.3-0.4	179
0.4-0.5	23
0.5-0.6	9
0.6-0.7	2
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
0.6346	Remote Similarity	NPC608827
0.614	Remote Similarity	NPC244371
0.5849	Remote Similarity	NPC231013
0.5614	Remote Similarity	NPC1608
0.5536	Remote Similarity	NPC63256
0.55	Remote Similarity	NPC195120
0.5345	Remote Similarity	NPC294502
0.5263	Remote Similarity	NPC200221
0.5167	Remote Similarity	NPC157983
0.5091	Remote Similarity	NPC605893
0.5082	Remote Similarity	NPC118154

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC34064 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4782
0.1-0.2	4170
0.2-0.3	193
0.3-0.4	5
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