NPASS Compound

Natural Product: NPC226713

Natural Product ID	NPC226713
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	HEXPWLIZWQZUCB-HXUWFJFHSA-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:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0003520] Pyranoflavonoids

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 56 59 0 0 0 0 0 0 0 0999 V2000 4.7702 2.6491 2.9463 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6882 1.6993 1.7924 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5279 1.2971 1.3269 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3050 0.3675 0.2026 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4819 -0.8212 0.6027 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0046 -1.8629 1.3290 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2532 -2.9566 1.7040 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9311 -2.9823 1.3239 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3856 -1.9407 0.5907 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9352 -1.9765 0.2169 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6766 -2.9360 0.5216 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4378 -0.8968 -0.5240 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8496 -0.9184 -0.9288 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.7050 -1.1375 0.2866 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7462 -1.9269 0.2032 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6045 -2.1587 1.3852 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0749 -2.5983 -1.0714 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2654 0.1854 -1.6645 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4521 1.2704 -2.0158 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9502 2.3363 -2.7485 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1215 3.4045 -3.0857 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7972 3.4368 -2.7074 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3191 2.3692 -1.9799 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1283 1.2940 -1.6330 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6311 0.1625 -0.8640 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6225 0.1391 -0.4778 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1375 -0.8486 0.2167 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0417 4.5352 -3.0832 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6486 4.4730 -3.8286 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1538 -4.0642 1.6847 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3462 -1.8561 1.7250 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9488 1.2238 1.1656 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7716 2.6998 3.4334 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0608 3.6556 2.6107 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5051 2.2521 3.6647 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6234 1.6846 1.8152 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7849 0.9155 -0.6029 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2934 0.0170 -0.2184 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7264 -3.7410 2.2749 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9608 -1.8376 -1.5782 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -0.6537 1.2056 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2269 -1.6483 2.2958 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7287 -3.2351 1.6275 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6068 -1.6765 1.1915 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3791 -3.4491 -1.2751 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1271 -3.0008 -1.0611 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9699 -1.8722 -1.8959 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9857 2.2979 -3.0369 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7033 2.3680 -1.6736 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1907 5.2676 -2.3984 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3001 5.1255 -3.4056 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2444 -4.9005 1.1059 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9094 -2.6218 1.3638 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8234 1.3137 0.0638 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1292 0.1902 1.5130 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8117 1.8873 1.4793 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 3 3 4 1 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 2 0 10 12 1 0 12 13 1 0 13 14 1 0 14 15 2 3 15 16 1 0 15 17 1 0 13 18 1 0 18 19 1 0 19 20 2 0 20 21 1 0 21 22 2 0 22 23 1 0 23 24 2 0 24 25 1 0 25 26 1 0 26 27 1 0 22 28 1 0 21 29 1 0 8 30 1 0 6 31 1 0 2 32 1 0 27 5 1 0 27 9 2 0 25 12 2 0 24 19 1 0 1 33 1 0 1 34 1 0 1 35 1 0 3 36 1 0 4 37 1 0 4 38 1 0 7 39 1 0 13 40 1 6 14 41 1 0 16 42 1 0 16 43 1 0 16 44 1 0 17 45 1 0 17 46 1 0 17 47 1 0 20 48 1 0 23 49 1 0 28 50 1 0 29 51 1 0 30 52 1 0 31 53 1 0 32 54 1 0 32 55 1 0 32 56 1 0 M END

Standard InCHIKey	HEXPWLIZWQZUCB-HXUWFJFHSA-N
Standard InCHI	InChI=1S/C25H24O7/c1-11(2)5-6-13-15(26)9-18(29)21-23(30)22-20(7-12(3)4)31-19-10-17(28)16(27)8-14(19)25(22)32-24(13)21/h5,7-10,20,26-29H,6H2,1-4H3/t20-/m1/s1
SMILES	CC(=CCc1c(cc(c2c(=O)c3[C@@H](C=C(C)C)Oc4cc(c(cc4-c3oc12)O)O)O)O)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	436.15	Volume:	441.897 ? Van der Waals volume.
Dense:	0.987	LogP:	4.164 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.363 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.816 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	3.0	Rigid Bonds:	24.0
TPSA:	120.36 ? Topological Polar Surface Area.	H-Bond Acceptor:	7.0
H-Bond Donor:	4.0	Rings:	4.0
Heavy Atoms:	7.0

MedChem Properties

QED Drug-Likeness Score:	0.329	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.932	Fsp³:	0.24
MCE-18:	82.742 ? 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:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	1	PAINS Alert:	1
Colloidal aggregators:	0.973	Fluc inhibitor:	0.593 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.991 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.647 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.279	Promiscuous compounds:	0.235

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.086	MDCK Permeability:	-4.755
Pgp-inhibitor:	0.004	Pgp-substrate:	0.22
PAMPA:	0.701 ? 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):	0.069
20% Bioavailability (F20%):	0.988	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.973
Plasma Protein Binding (PPB):	94.697%	Volume Distribution (VD):	0.079
Fu:	5.439% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.999
OATP1B3 inhibitor:	0.915	BCRP inhibitor:	0.833
BSEP inhibitor:	0.499

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	1.0
CYP2C19-inhibitor:	0.55	CYP2C19-substrate:	1.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.013
CYP2D6-inhibitor:	0.016	CYP2D6-substrate:	0.993
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	1.0 ? 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):

7.349

Half-life (T1/2):

1.725

ADMET: Toxicity

hERG Blockers:	0.027	hERG Blockers (10um):	0.579
Human Hepatotoxicity (H-HT):	0.682	Drug-induced Liver Injury (DILI):	0.947
AMES Toxicity:	0.805	Rat Oral Acute Toxicity:	0.906
Maximum Recommended Daily Dose:	0.925	Skin Sensitization:	0.988
Carcinogencity:	0.528	Eye Corrosion:	0.0
Eye Irritation:	0.404	Respiratory Toxicity:	0.975
Drug-induced Neurotoxicity:	0.039	Ototoxicity:	0.514
Hematotoxicity:	0.092	Drug-induced Nephrotoxicity:	0.167
Genotoxicity:	0.999	RPMI-8226 Immunitoxicity:	0.053
A549 Cytotoxicity:	0.852	Hek293 Cytotoxicity:	0.715
BCF:	1.784 ? 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:	4.863 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.686 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	6.063 ? 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
NPO28803	Artocarpus chama	Species	Moraceae	Eukaryota	n.a.	root	n.a.	PMID[15165133]
NPO28969	Solanum sarrachoides	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO29358	Senecio oxyodon	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO29519	Primula glaucescens	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO29409	Oenothera laciniata	Species	Onagraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO29462	Helinus ovatus	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO29156	Conyza incana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO29318	Cereus validus	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO28803	Artocarpus chama	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO29386	Agabus bipustulatus	Species	Dytiscidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO28969	Solanum sarrachoides	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28969	Solanum sarrachoides	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28969	Solanum sarrachoides	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29318	Cereus validus	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29156	Conyza incana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29409	Oenothera laciniata	Species	Onagraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29358	Senecio oxyodon	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28803	Artocarpus chama	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29462	Helinus ovatus	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29519	Primula glaucescens	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28969	Solanum sarrachoides	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29386	Agabus bipustulatus	Species	Dytiscidae	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 NPC226713 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	23165
0.1-0.2	23523
0.2-0.3	2880
0.3-0.4	226
0.4-0.5	55
0.5-0.6	7
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	Natural Product ID
0.7714	Intermediate Similarity	NPC469658
0.7	Intermediate Similarity	NPC608191
0.6375	Remote Similarity	NPC194427
0.557	Remote Similarity	NPC319752
0.5417	Remote Similarity	NPC63187
0.5135	Remote Similarity	NPC88804
0.5132	Remote Similarity	NPC96565
0.5132	Remote Similarity	NPC273538
0.5059	Remote Similarity	NPC189087
0.5059	Remote Similarity	NPC603859

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC226713 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4306
0.1-0.2	4814
0.2-0.3	28
0.3-0.4	1
0.4-0.5	0
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
0.5132	Remote Similarity	NPD4378	Phase 3

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