NPASS Compound

Natural Product: NPC488364

Natural Product ID	NPC488364
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	SFYSEZGEYNZKDD-DUMLXZITSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	10031097
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003533] Flavonoid-7-O-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 71 74 0 0 0 0 0 0 0 0999 V2000 9.3211 -0.3390 0.2481 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8430 -0.4622 -0.0189 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3189 0.9548 -0.2342 C 0 0 0 0 0 0 0 0 0 0 0 0 8.0375 1.5718 -1.4169 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8451 0.9590 -0.4130 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1604 1.6209 0.4177 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2032 0.2895 -1.4205 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8091 0.2683 -1.6241 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1195 -0.3186 -0.4249 C 0 0 2 0 0 0 0 0 0 0 0 0 3.5410 -1.7612 -0.2532 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5005 -2.4558 0.5746 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6501 -1.5218 1.3981 C 0 0 2 0 0 0 0 0 0 0 0 0 1.0256 -0.4315 0.5355 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.2973 -0.6563 0.3554 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3687 0.1726 0.4107 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6299 -0.4656 0.2869 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8070 0.2374 0.3243 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7207 1.6023 0.4883 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9020 2.3013 0.5253 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8633 3.5461 0.6735 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0873 1.5882 0.3959 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1306 0.2266 0.2338 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3462 -0.5452 0.0963 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2227 -1.9256 -0.0627 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.2981 -2.7607 -0.2021 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5776 -2.2287 -0.1870 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.7358 -0.8853 -0.0337 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6137 -0.0559 0.1067 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.0186 -0.3437 -0.0176 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.6839 -3.0734 -0.3286 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9566 -0.3752 0.2080 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.2461 2.3497 0.4411 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5128 2.2453 0.6098 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3091 1.5279 0.5708 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1097 2.1964 0.6875 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5497 2.7786 -0.4326 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4318 3.6103 0.7737 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7473 -0.3163 -0.6740 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3552 -0.9842 2.4688 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7316 -3.3554 -0.1579 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8166 -1.8644 0.2981 O 0 0 0 0 0 0 0 0 0 0 0 0 9.7028 -1.3201 0.6098 H 0 0 0 0 0 0 0 0 0 0 0 0 9.5125 0.3823 1.0916 H 0 0 0 0 0 0 0 0 0 0 0 0 9.8949 -0.0560 -0.6443 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7009 -1.0948 -0.8975 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3607 -0.8342 0.8973 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6205 1.5282 0.6629 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4714 2.4381 -1.7978 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0230 1.9090 -1.0887 H 0 0 0 0 0 0 0 0 0 0 0 0 8.1744 0.7876 -2.1877 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4285 1.2755 -1.8418 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6264 -0.4318 -2.4859 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2763 0.2524 0.4920 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4981 -2.2175 -1.2807 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0670 -3.0873 1.3208 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8150 -2.1105 1.8222 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2333 0.5095 1.0661 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6887 -1.5435 0.1577 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2391 -2.3617 -0.0776 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.2199 -3.8307 -0.3261 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.8270 0.9708 0.2207 H 0 0 0 0 0 0 0 0 0 0 0 0 -11.2128 0.6164 -0.2724 H 0 0 0 0 0 0 0 0 0 0 0 0 -11.5284 -2.8844 0.2094 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3228 3.1268 1.1057 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6108 2.4345 -0.3782 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1391 2.3748 -1.3843 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5751 3.8730 -0.3913 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5973 4.1325 0.6007 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4077 -1.6390 3.2100 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3626 -4.0187 0.4853 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4295 -2.1023 -0.4421 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 3 5 1 0 5 6 2 0 5 7 1 0 7 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 14 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 2 0 19 21 1 0 21 22 2 0 22 23 1 0 23 24 2 0 24 25 1 0 25 26 2 0 26 27 1 0 27 28 2 0 27 29 1 0 26 30 1 0 22 31 1 0 21 32 1 0 18 33 1 0 33 34 2 0 34 35 1 0 35 36 1 0 33 37 1 0 13 38 1 0 12 39 1 0 11 40 1 0 10 41 1 0 38 9 1 0 34 15 1 0 31 17 1 0 28 23 1 0 1 42 1 0 1 43 1 0 1 44 1 0 2 45 1 0 2 46 1 0 3 47 1 0 4 48 1 0 4 49 1 0 4 50 1 0 8 51 1 0 8 52 1 0 9 53 1 1 10 54 1 6 11 55 1 1 12 56 1 1 13 57 1 1 16 58 1 0 24 59 1 0 25 60 1 0 28 61 1 0 29 62 1 0 30 63 1 0 32 64 1 0 36 65 1 0 36 66 1 0 36 67 1 0 37 68 1 0 39 69 1 0 40 70 1 0 41 71 1 0 M END

Standard InCHIKey	SFYSEZGEYNZKDD-DUMLXZITSA-N
Standard InCHI	InChI=1S/C27H30O14/c1-4-10(2)26(36)38-9-16-18(30)21(33)23(35)27(41-16)40-15-8-14-17(20(32)25(15)37-3)19(31)22(34)24(39-14)11-5-6-12(28)13(29)7-11/h5-8,10,16,18,21,23,27-30,32-35H,4,9H2,1-3H3/t10?,16-,18-,21+,23-,27-/m1/s1
SMILES	CCC(C)C(=O)OC[C@@H]1[C@H]([C@@H]([C@H]([C@H](Oc2cc3c(c(=O)c(c(c4ccc(c(c4)O)O)o3)O)c(c2OC)O)O1)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	578.16	Volume:	540.657 ? Van der Waals volume.
Dense:	1.069	LogP:	1.275 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.713 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.417 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	9.0	Rigid Bonds:	25.0
TPSA:	225.81 ? Topological Polar Surface Area.	H-Bond Acceptor:	14.0
H-Bond Donor:	7.0	Rings:	4.0
Heavy Atoms:	14.0

MedChem Properties

QED Drug-Likeness Score:	0.147	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.405	Fsp³:	0.407
MCE-18:	97.895 ? 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:	Accepted	BMS Rule:	0
Chelating Alert:	1	PAINS Alert:	1
Colloidal aggregators:	0.836	Fluc inhibitor:	0.302 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.902 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.9 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.053	Promiscuous compounds:	0.699

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.094	MDCK Permeability:	-5.441
Pgp-inhibitor:	0.009	Pgp-substrate:	0.017
PAMPA:	0.86 ? 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):	0.629
20% Bioavailability (F20%):	0.837	30% Bioavailability (F30%):	0.999
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.001	MRP1:	0.857
Plasma Protein Binding (PPB):	88.644%	Volume Distribution (VD):	-0.228
Fu:	7.667% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.995
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.772
BSEP inhibitor:	0.755

ADMET: Metabolism

CYP1A2-inhibitor:	0.001	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.005
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.004
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.537
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.992
HLM stability:	0.959 ? 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):

2.802

Half-life (T1/2):

2.867

ADMET: Toxicity

hERG Blockers:	0.027	hERG Blockers (10um):	0.4
Human Hepatotoxicity (H-HT):	0.388	Drug-induced Liver Injury (DILI):	0.936
AMES Toxicity:	0.55	Rat Oral Acute Toxicity:	0.105
Maximum Recommended Daily Dose:	0.128	Skin Sensitization:	0.985
Carcinogencity:	0.154	Eye Corrosion:	0.0
Eye Irritation:	0.698	Respiratory Toxicity:	0.058
Drug-induced Neurotoxicity:	0.005	Ototoxicity:	0.736
Hematotoxicity:	0.095	Drug-induced Nephrotoxicity:	0.195
Genotoxicity:	0.375	RPMI-8226 Immunitoxicity:	0.081
A549 Cytotoxicity:	0.724	Hek293 Cytotoxicity:	0.199
BCF:	0.597 ? 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:	3.382 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.74 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.217 ? 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
NPO40994	Inula britannica	Species	Asteraceae	Eukaryota	Flowers	n.a.	n.a.	PMID[10650074]

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
IC50	2

Activity Type	# Activity
Cell line	1
Others	1

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
NPT116	Cell line	HL-60	Homo sapiens	IC50	=	11.2	ug.mL-1	PMID[10650074]
NPT1	Others	Radical scavenging activity	n.a.	IC50	=	23.5	ug.mL-1	PMID[10650074]

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 NPC488364 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	8216
0.1-0.2	36724
0.2-0.3	3925
0.3-0.4	726
0.4-0.5	214
0.5-0.6	42
0.6-0.7	5
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9136	High Similarity	NPC233994
0.8588	High Similarity	NPC211532
0.7176	Intermediate Similarity	NPC117260
0.6703	Remote Similarity	NPC254540
0.6237	Remote Similarity	NPC211594
0.6064	Remote Similarity	NPC172807
0.6064	Remote Similarity	NPC477848
0.6042	Remote Similarity	NPC67105
0.5922	Remote Similarity	NPC603856
0.5766	Remote Similarity	NPC488078
0.5714	Remote Similarity	NPC238376
0.5699	Remote Similarity	NPC201292
0.5638	Remote Similarity	NPC488071
0.56	Remote Similarity	NPC204693
0.5591	Remote Similarity	NPC27640
0.5567	Remote Similarity	NPC116864
0.5567	Remote Similarity	NPC244776
0.549	Remote Similarity	NPC483415
0.5484	Remote Similarity	NPC277205
0.5484	Remote Similarity	NPC37919
0.5481	Remote Similarity	NPC80068
0.5463	Remote Similarity	NPC480796
0.5437	Remote Similarity	NPC483416
0.5437	Remote Similarity	NPC483707
0.5426	Remote Similarity	NPC245014
0.5421	Remote Similarity	NPC599948
0.54	Remote Similarity	NPC227508
0.534	Remote Similarity	NPC483414
0.5333	Remote Similarity	NPC473073
0.5263	Remote Similarity	NPC45638
0.5248	Remote Similarity	NPC275454
0.5243	Remote Similarity	NPC126784
0.5243	Remote Similarity	NPC241423
0.5234	Remote Similarity	NPC135358
0.5217	Remote Similarity	NPC488079
0.5192	Remote Similarity	NPC470443
0.5149	Remote Similarity	NPC187379
0.5143	Remote Similarity	NPC229409
0.514	Remote Similarity	NPC470445
0.5104	Remote Similarity	NPC105025
0.5096	Remote Similarity	NPC488073
0.5096	Remote Similarity	NPC153755
0.5096	Remote Similarity	NPC488074
0.5094	Remote Similarity	NPC486577
0.5093	Remote Similarity	NPC470446
0.5093	Remote Similarity	NPC470450
0.5053	Remote Similarity	NPC108831
0.5053	Remote Similarity	NPC182634
0.5051	Remote Similarity	NPC99957
0.5049	Remote Similarity	NPC210073

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC488364 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3399
0.1-0.2	5642
0.2-0.3	96
0.3-0.4	8
0.4-0.5	5
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