NPASS Compound

Natural Product: NPC322915

Natural Product ID	NPC322915
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	OVFYFAUQNYAGFX-DHGKCCLASA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	22524485
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 41 42 0 0 0 0 0 0 0 0999 V2000 5.5770 -0.8641 -0.3942 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1190 -0.9060 -0.1130 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2833 -0.0302 -0.7419 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9336 -0.0794 -0.4715 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4333 -0.9958 0.4177 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2826 -1.8880 1.0581 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6381 -1.8548 0.8009 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1130 -1.0813 0.7154 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9672 -0.3347 0.2437 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8872 -1.2755 -0.4959 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3306 -0.9598 -0.1156 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4525 0.5507 -0.3055 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6331 1.1806 0.7987 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6202 0.3723 1.2402 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5091 1.7027 1.9152 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7192 2.4505 2.7912 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7749 0.9596 -0.2710 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4583 -1.2925 1.2428 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7143 -1.0863 -1.8641 O 0 0 0 0 0 0 0 0 0 0 0 0 3.7796 0.8828 -1.6273 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9943 1.8285 -2.3274 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8225 -0.4533 -1.3765 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1025 -0.3599 0.4525 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9873 -1.9161 -0.3845 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2626 0.6367 -0.9865 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8918 -2.6214 1.7652 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3159 -2.5398 1.2880 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6303 0.4293 -0.4810 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6353 -2.3079 -0.2570 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0313 -1.5068 -0.7467 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9589 0.7666 -1.2651 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1558 2.0849 0.3499 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0027 0.8958 2.4914 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2549 2.4051 1.4918 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0749 3.3577 2.9382 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9280 1.6116 -0.9711 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8685 -2.0782 1.3942 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2164 -1.7750 -2.3721 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6032 2.3055 -3.1049 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1928 1.2527 -2.8550 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4910 2.5329 -1.6368 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 3 4 1 0 4 5 2 0 5 6 1 0 6 7 2 0 5 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 13 15 1 0 15 16 1 0 12 17 1 0 11 18 1 0 10 19 1 0 3 20 1 0 20 21 1 0 7 2 1 0 14 9 1 0 1 22 1 0 1 23 1 0 1 24 1 0 4 25 1 0 6 26 1 0 7 27 1 0 9 28 1 0 10 29 1 0 11 30 1 0 12 31 1 0 13 32 1 0 15 33 1 0 15 34 1 0 16 35 1 0 17 36 1 0 18 37 1 0 19 38 1 0 21 39 1 0 21 40 1 0 21 41 1 0 M END

Standard InCHIKey	OVFYFAUQNYAGFX-DHGKCCLASA-N
Standard InCHI	InChI=1S/C14H20O7/c1-7-3-4-8(5-9(7)19-2)20-14-13(18)12(17)11(16)10(6-15)21-14/h3-5,10-18H,6H2,1-2H3/t10-,11-,12-,13-,14-/m1/s1
SMILES	CC1=C(C=C(C=C1)OC2C(C(C(C(O2)CO)O)O)O)OC

Calculated Properties

Physi-Chem Properties

Molecular Weight:	300.12	Volume:	287.21 ? Van der Waals volume.
Dense:	1.045	LogP:	0.044 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	0.338 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-1.344 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	4.0	Rigid Bonds:	12.0
TPSA:	108.61 ? Topological Polar Surface Area.	H-Bond Acceptor:	7.0
H-Bond Donor:	4.0	Rings:	2.0
Heavy Atoms:	7.0

MedChem Properties

QED Drug-Likeness Score:	0.575	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.346	Fsp³:	0.571
MCE-18:	48.364 ? 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:	0.057	Fluc inhibitor:	0.001 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.022 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.237 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.215	Promiscuous compounds:	0.113

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.806	MDCK Permeability:	-5.076
Pgp-inhibitor:	0.002	Pgp-substrate:	0.443
PAMPA:	0.881 ? 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):	0.834
20% Bioavailability (F20%):	0.332	30% Bioavailability (F30%):	0.805
50% Bioavailability (F50%):	0.909

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.066	MRP1:	0.912
Plasma Protein Binding (PPB):	73.233%	Volume Distribution (VD):	-0.182
Fu:	26.082% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.097
OATP1B3 inhibitor:	0.945	BCRP inhibitor:	0.246
BSEP inhibitor:	0.628

ADMET: Metabolism

CYP1A2-inhibitor:	0.025	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.566	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.958	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.344	CYP2D6-substrate:	0.002
CYP3A4-inhibitor:	0.699	CYP3A4-substrate:	0.084
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.008
HLM stability:	0.014 ? 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):

2.934

Half-life (T1/2):

2.417

ADMET: Toxicity

hERG Blockers:	0.093	hERG Blockers (10um):	0.419
Human Hepatotoxicity (H-HT):	0.544	Drug-induced Liver Injury (DILI):	0.455
AMES Toxicity:	0.614	Rat Oral Acute Toxicity:	0.197
Maximum Recommended Daily Dose:	0.105	Skin Sensitization:	0.223
Carcinogencity:	0.416	Eye Corrosion:	0.0
Eye Irritation:	0.439	Respiratory Toxicity:	0.122
Drug-induced Neurotoxicity:	0.418	Ototoxicity:	0.883
Hematotoxicity:	0.17	Drug-induced Nephrotoxicity:	0.206
Genotoxicity:	0.029	RPMI-8226 Immunitoxicity:	0.065
A549 Cytotoxicity:	0.043	Hek293 Cytotoxicity:	0.251
BCF:	0.328 ? 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:	2.482 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.037 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.005 ? 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
NPO10994	Sargentodoxa cuneata	Species	Lardizabalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10994	Sargentodoxa cuneata	Species	Lardizabalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10994	Sargentodoxa cuneata	Species	Lardizabalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10994	Sargentodoxa cuneata	Species	Lardizabalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO10994	Sargentodoxa cuneata	Species	Lardizabalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO10994	Sargentodoxa cuneata	Species	Lardizabalaceae	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 NPC322915 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	16825
0.1-0.2	28148
0.2-0.3	3802
0.3-0.4	685
0.4-0.5	284
0.5-0.6	78
0.6-0.7	19
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
0.7115	Intermediate Similarity	NPC218685
0.6735	Remote Similarity	NPC153149
0.6667	Remote Similarity	NPC276195
0.6667	Remote Similarity	NPC212729
0.6667	Remote Similarity	NPC604498
0.66	Remote Similarity	NPC25817
0.6531	Remote Similarity	NPC217854
0.6531	Remote Similarity	NPC269242
0.6471	Remote Similarity	NPC609376
0.64	Remote Similarity	NPC294470
0.6364	Remote Similarity	NPC479028
0.6364	Remote Similarity	NPC23084
0.6364	Remote Similarity	NPC479031
0.6226	Remote Similarity	NPC221090
0.619	Remote Similarity	NPC108674
0.6167	Remote Similarity	NPC479030
0.6154	Remote Similarity	NPC60589
0.6154	Remote Similarity	NPC469708
0.6078	Remote Similarity	NPC192810
0.6038	Remote Similarity	NPC200092
0.5926	Remote Similarity	NPC80098
0.5849	Remote Similarity	NPC299144
0.5833	Remote Similarity	NPC228907
0.5818	Remote Similarity	NPC166040
0.5806	Remote Similarity	NPC604892
0.5789	Remote Similarity	NPC604356
0.5789	Remote Similarity	NPC606892
0.5741	Remote Similarity	NPC226712
0.5741	Remote Similarity	NPC608788
0.5714	Remote Similarity	NPC210192
0.5686	Remote Similarity	NPC142319
0.566	Remote Similarity	NPC152722
0.5636	Remote Similarity	NPC69513
0.5636	Remote Similarity	NPC145900
0.5625	Remote Similarity	NPC99233
0.5593	Remote Similarity	NPC479029
0.5556	Remote Similarity	NPC146803
0.5538	Remote Similarity	NPC606849
0.5536	Remote Similarity	NPC48863
0.5536	Remote Similarity	NPC251981
0.5536	Remote Similarity	NPC13745
0.5522	Remote Similarity	NPC219163
0.5522	Remote Similarity	NPC486379
0.5517	Remote Similarity	NPC472024
0.5517	Remote Similarity	NPC251102
0.5517	Remote Similarity	NPC270849
0.5517	Remote Similarity	NPC210298
0.55	Remote Similarity	NPC290069
0.5484	Remote Similarity	NPC294166
0.5484	Remote Similarity	NPC115022
0.5455	Remote Similarity	NPC271479
0.5455	Remote Similarity	NPC12308
0.5455	Remote Similarity	NPC604833
0.5441	Remote Similarity	NPC472353
0.5439	Remote Similarity	NPC310661
0.5439	Remote Similarity	NPC215833
0.5424	Remote Similarity	NPC26653
0.5424	Remote Similarity	NPC26080
0.5424	Remote Similarity	NPC80600
0.5424	Remote Similarity	NPC165686
0.5424	Remote Similarity	NPC210478
0.541	Remote Similarity	NPC220560
0.541	Remote Similarity	NPC247146
0.5373	Remote Similarity	NPC76128
0.5352	Remote Similarity	NPC238140
0.5345	Remote Similarity	NPC49074
0.5333	Remote Similarity	NPC248355
0.5303	Remote Similarity	NPC30432
0.5303	Remote Similarity	NPC605700
0.5273	Remote Similarity	NPC604439
0.5263	Remote Similarity	NPC166168
0.5263	Remote Similarity	NPC214454
0.5263	Remote Similarity	NPC95292
0.5263	Remote Similarity	NPC610709
0.5254	Remote Similarity	NPC162093
0.5246	Remote Similarity	NPC55040
0.5246	Remote Similarity	NPC104167
0.5231	Remote Similarity	NPC175275
0.5217	Remote Similarity	NPC48640
0.5217	Remote Similarity	NPC206378
0.5217	Remote Similarity	NPC116922
0.5217	Remote Similarity	NPC106625
0.5172	Remote Similarity	NPC40377
0.5172	Remote Similarity	NPC9912
0.5167	Remote Similarity	NPC214910
0.5161	Remote Similarity	NPC302378
0.5161	Remote Similarity	NPC232673
0.5161	Remote Similarity	NPC34456
0.5156	Remote Similarity	NPC37468
0.5152	Remote Similarity	NPC178851
0.5152	Remote Similarity	NPC295970
0.5147	Remote Similarity	NPC199357
0.5139	Remote Similarity	NPC93924
0.5091	Remote Similarity	NPC9248
0.5082	Remote Similarity	NPC474491
0.5082	Remote Similarity	NPC473044
0.5079	Remote Similarity	NPC146540
0.507	Remote Similarity	NPC300537

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC322915 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3951
0.1-0.2	4969
0.2-0.3	202
0.3-0.4	25
0.4-0.5	2
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
0.5741	Remote Similarity	NPD1091	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