NPASS Compound

Natural Product: NPC145347

Natural Product ID	NPC145347
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	MNBSBRMQJLTPNQ-MBEZSMKLSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	101450424
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0002105] Glycosyl compounds [CHEMONTID:0004165] Phenolic glycosides

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 60 63 0 0 0 0 0 0 0 0999 V2000 -1.6564 -3.8004 -0.0861 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2110 -2.4913 -0.6633 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.6194 -2.3701 -0.1830 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.1992 -0.9929 -0.4156 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.1347 -0.2237 -1.2097 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.9004 -0.2079 -0.3321 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.3720 -1.4790 -0.2901 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0296 0.7235 -0.8622 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7770 1.7527 0.0400 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.2155 3.0804 -0.4537 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.2036 4.1669 -0.4642 C 0 0 1 0 0 0 0 0 0 0 0 0 1.1745 3.7734 -0.0381 C 0 0 1 0 0 0 0 0 0 0 0 0 2.0426 4.9580 0.2955 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5340 5.6835 1.3525 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0528 2.8936 1.0359 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6769 1.6597 0.4442 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9422 0.5852 1.2610 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7948 -0.4412 1.0344 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9176 -1.4448 2.0088 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7463 -2.5204 1.8804 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5032 -2.6287 0.7345 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3793 -3.7014 0.5228 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4522 -4.5610 1.4118 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1208 -3.7788 -0.6334 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9868 -2.7887 -1.5731 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1626 -1.7893 -1.3626 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4415 -1.6889 -0.2678 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5732 -0.6054 -0.0819 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8794 -3.5194 2.8320 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0936 4.7976 -1.7115 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4178 3.4950 0.1723 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5821 1.0966 -1.4071 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3528 -0.2946 0.7894 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3972 -3.2538 -0.9669 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3462 -4.6126 -0.3959 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6406 -3.6881 1.0340 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6277 -3.9851 -0.4134 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2322 -2.5878 -1.7767 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7239 -2.7119 0.8645 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1489 -0.9918 -0.9475 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9077 -0.7045 -2.1669 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2219 0.0558 0.7050 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3685 1.5310 0.9725 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5338 2.9327 -1.5306 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5781 4.9771 0.2291 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6496 3.2466 -0.9138 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0258 5.6246 -0.6035 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0885 4.6214 0.4487 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2186 5.8373 2.0724 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2702 1.5997 -0.4850 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3094 -1.3349 2.9029 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7879 -4.5941 -0.7962 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5790 -2.8503 -2.4970 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5214 0.1330 -0.8633 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0726 -3.9844 3.2271 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0351 5.7676 -1.6171 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1316 4.1516 0.8681 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5771 1.1094 -1.2922 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0351 0.4028 0.6195 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7030 -4.0295 -0.4578 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 6 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 12 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 2 0 19 20 1 0 20 21 2 0 21 22 1 0 22 23 2 0 22 24 1 0 24 25 2 0 25 26 1 0 26 27 1 0 27 28 2 0 20 29 1 0 11 30 1 0 10 31 1 0 5 32 1 0 4 33 1 0 3 34 1 0 7 2 1 0 16 9 1 0 28 18 1 0 27 21 1 0 1 35 1 0 1 36 1 0 1 37 1 0 2 38 1 6 3 39 1 1 4 40 1 6 5 41 1 6 6 42 1 1 9 43 1 1 10 44 1 6 11 45 1 1 12 46 1 6 13 47 1 0 13 48 1 0 14 49 1 0 16 50 1 6 19 51 1 0 24 52 1 0 25 53 1 0 28 54 1 0 29 55 1 0 30 56 1 0 31 57 1 0 32 58 1 0 33 59 1 0 34 60 1 0 M END

Standard InCHIKey	MNBSBRMQJLTPNQ-MBEZSMKLSA-N
Standard InCHI	InChI=1S/C21H26O13/c1-7-14(25)16(27)18(29)20(31-7)34-19-17(28)15(26)12(6-22)33-21(19)32-8-4-10(24)13-9(23)2-3-30-11(13)5-8/h2-5,7,12,14-22,24-29H,6H2,1H3/t7-,12+,14-,15+,16+,17-,18+,19+,20-,21+/m0/s1
SMILES	C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[C@@H]1[C@H]([C@@H]([C@@H](CO)O[C@H]1Oc1cc(c2c(=O)ccoc2c1)O)O)O)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	486.14	Volume:	438.637 ? Van der Waals volume.
Dense:	1.108	LogP:	-0.198 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	0.604 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-1.292 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	5.0	Rigid Bonds:	24.0
TPSA:	208.74 ? Topological Polar Surface Area.	H-Bond Acceptor:	13.0
H-Bond Donor:	7.0	Rings:	4.0
Heavy Atoms:	13.0

MedChem Properties

QED Drug-Likeness Score:	0.234	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.598	Fsp³:	0.571
MCE-18:	97.364 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.638	Fluc inhibitor:	0.128 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.264 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.165 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.261	Promiscuous compounds:	0.348

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.499	MDCK Permeability:	-5.171
Pgp-inhibitor:	0.0	Pgp-substrate:	0.861
PAMPA:	0.999 ? 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):	0.999
20% Bioavailability (F20%):	0.73	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.01	MRP1:	0.061
Plasma Protein Binding (PPB):	59.527%	Volume Distribution (VD):	-0.456
Fu:	41.169% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.176
BSEP inhibitor:	0.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.001
CYP2C9-inhibitor:	0.002	CYP2C9-substrate:	0.001
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.001
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.007
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.009
HLM stability:	0.07 ? 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):

1.51

Half-life (T1/2):

4.153

ADMET: Toxicity

hERG Blockers:	0.014	hERG Blockers (10um):	0.076
Human Hepatotoxicity (H-HT):	0.716	Drug-induced Liver Injury (DILI):	0.994
AMES Toxicity:	0.937	Rat Oral Acute Toxicity:	0.027
Maximum Recommended Daily Dose:	0.012	Skin Sensitization:	0.995
Carcinogencity:	0.171	Eye Corrosion:	0.0
Eye Irritation:	0.211	Respiratory Toxicity:	0.017
Drug-induced Neurotoxicity:	0.005	Ototoxicity:	0.975
Hematotoxicity:	0.369	Drug-induced Nephrotoxicity:	0.949
Genotoxicity:	0.929	RPMI-8226 Immunitoxicity:	0.276
A549 Cytotoxicity:	0.346	Hek293 Cytotoxicity:	0.241
BCF:	0.27 ? 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:	2.62 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.213 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.288 ? 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
NPO24093	Drynaria fortunei	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21377852]
NPO24093	Drynaria fortunei	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO24093	Drynaria fortunei	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24093	Drynaria fortunei	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24093	Drynaria fortunei	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24093	Drynaria fortunei	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO24093	Drynaria fortunei	Species	Polypodiaceae	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 NPC145347 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	22889
0.1-0.2	22647
0.2-0.3	3719
0.3-0.4	438
0.4-0.5	128
0.5-0.6	26
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	0

Similarity Score	Similarity Level	Natural Product ID
0.6941	Remote Similarity	NPC65003
0.686	Remote Similarity	NPC115674
0.6484	Remote Similarity	NPC195257
0.6395	Remote Similarity	NPC239549
0.6207	Remote Similarity	NPC8856
0.6087	Remote Similarity	NPC32641
0.6087	Remote Similarity	NPC256188
0.6044	Remote Similarity	NPC240306
0.5914	Remote Similarity	NPC35119
0.58	Remote Similarity	NPC311850
0.5625	Remote Similarity	NPC475382
0.5577	Remote Similarity	NPC198199
0.5481	Remote Similarity	NPC68592
0.5429	Remote Similarity	NPC298666
0.5376	Remote Similarity	NPC163242
0.5376	Remote Similarity	NPC272068
0.5354	Remote Similarity	NPC253685
0.5319	Remote Similarity	NPC155877
0.5278	Remote Similarity	NPC120952
0.5248	Remote Similarity	NPC25724
0.5248	Remote Similarity	NPC11468
0.5243	Remote Similarity	NPC480441
0.5243	Remote Similarity	NPC25523
0.5222	Remote Similarity	NPC80188
0.5195	Remote Similarity	NPC607702
0.5181	Remote Similarity	NPC134819
0.5149	Remote Similarity	NPC14187
0.5143	Remote Similarity	NPC255799
0.5104	Remote Similarity	NPC122809
0.5104	Remote Similarity	NPC470444
0.5096	Remote Similarity	NPC473644
0.506	Remote Similarity	NPC191154
0.5057	Remote Similarity	NPC160515
0.5045	Remote Similarity	NPC262222

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC145347 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5226
0.1-0.2	3833
0.2-0.3	82
0.3-0.4	5
0.4-0.5	4
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