NPASS Compound

Natural Product: NPC324579

Natural Product ID	NPC324579
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	GOZCEKPKECLKNO-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	539591
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 39 40 0 0 0 0 0 0 0 0999 V2000 6.2140 0.1716 0.3753 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3477 -0.1322 -0.7888 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8146 -0.4392 -1.8959 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8930 -0.0652 -0.6177 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0499 -0.3396 -1.6728 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6840 -0.2753 -1.5067 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1001 0.0572 -0.3109 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9757 0.3316 0.7460 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3447 0.2769 0.6152 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2471 0.1295 -0.1141 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2595 -0.1034 -1.0251 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0896 1.1428 -1.1988 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7661 1.5014 0.1056 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5028 0.2462 0.5724 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4408 -0.8041 0.7448 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0220 -1.1754 -0.5418 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9115 -1.9819 1.5515 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9831 -2.6313 0.9613 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3179 -0.1583 -0.4860 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5986 2.5802 -0.0155 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0134 1.0346 -2.2355 O 0 0 0 0 0 0 0 0 0 0 0 0 7.2550 -0.1671 0.1133 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8654 -0.3160 1.3058 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3157 1.2812 0.5301 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4598 -0.6112 -2.6528 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0760 -0.5044 -2.3827 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5443 0.6015 1.7188 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9950 0.4973 1.4615 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8863 -0.3773 -2.0159 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3990 1.9681 -1.4473 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9436 1.6471 0.8558 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0829 0.4403 1.4954 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5407 -0.3903 1.2546 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1127 -1.6317 2.5714 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0448 -2.6845 1.6268 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6112 -3.2791 0.3031 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0295 0.5256 -0.6610 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4836 3.1422 0.8032 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6484 0.4922 -2.9789 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 2 4 1 0 4 5 2 0 5 6 1 0 6 7 2 0 7 8 1 0 8 9 2 0 7 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 1 0 15 17 1 0 17 18 1 0 14 19 1 0 13 20 1 0 12 21 1 0 9 4 1 0 16 11 1 0 1 22 1 0 1 23 1 0 1 24 1 0 5 25 1 0 6 26 1 0 8 27 1 0 9 28 1 0 11 29 1 0 12 30 1 0 13 31 1 0 14 32 1 0 15 33 1 0 17 34 1 0 17 35 1 0 18 36 1 0 19 37 1 0 20 38 1 0 21 39 1 0 M END

Standard InCHIKey	GOZCEKPKECLKNO-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C14H18O7/c1-7(16)8-2-4-9(5-3-8)20-14-13(19)12(18)11(17)10(6-15)21-14/h2-5,10-15,17-19H,6H2,1H3
SMILES	CC(=O)C1=CC=C(C=C1)OC2C(C(C(C(O2)CO)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	298.11	Volume:	284.573 ? Van der Waals volume.
Dense:	1.048	LogP:	-0.762 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	-0.246 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-1.312 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	4.0	Rigid Bonds:	13.0
TPSA:	116.45 ? 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:	0.53	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.275	Fsp³:	0.5
MCE-18:	48.667 ? 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:	0.101	Fluc inhibitor:	0.009 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.031 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.053 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.318	Promiscuous compounds:	0.061

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.744	MDCK Permeability:	-4.827
Pgp-inhibitor:	0.0	Pgp-substrate:	0.478
PAMPA:	0.986 ? 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):	0.952
20% Bioavailability (F20%):	0.497	30% Bioavailability (F30%):	0.942
50% Bioavailability (F50%):	0.943

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.164	MRP1:	0.526
Plasma Protein Binding (PPB):	60.736%	Volume Distribution (VD):	-0.341
Fu:	38.997% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.015
OATP1B3 inhibitor:	0.936	BCRP inhibitor:	0.076
BSEP inhibitor:	0.046

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.004	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.006	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.013	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.004
HLM stability:	0.185 ? 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):

2.987

Half-life (T1/2):

2.088

ADMET: Toxicity

hERG Blockers:	0.075	hERG Blockers (10um):	0.361
Human Hepatotoxicity (H-HT):	0.563	Drug-induced Liver Injury (DILI):	0.527
AMES Toxicity:	0.7	Rat Oral Acute Toxicity:	0.189
Maximum Recommended Daily Dose:	0.087	Skin Sensitization:	0.182
Carcinogencity:	0.428	Eye Corrosion:	0.0
Eye Irritation:	0.51	Respiratory Toxicity:	0.138
Drug-induced Neurotoxicity:	0.369	Ototoxicity:	0.889
Hematotoxicity:	0.235	Drug-induced Nephrotoxicity:	0.184
Genotoxicity:	0.134	RPMI-8226 Immunitoxicity:	0.073
A549 Cytotoxicity:	0.037	Hek293 Cytotoxicity:	0.264
BCF:	0.15 ? 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:	2.345 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.074 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	2.948 ? 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
NPO30241	Picrorhiza scrophulariiflora	Species	Plantaginaceae	Eukaryota	n.a.	root	n.a.	PMID[15133218]
NPO30241	Picrorhiza scrophulariiflora	Species	Plantaginaceae	Eukaryota	n.a.	root	n.a.	PMID[15706916]
NPO16239	Rhodiola rosea	Species	Crassulaceae	Eukaryota	roots	n.a.	n.a.	PMID[19729316]
NPO30241	Picrorhiza scrophulariiflora	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24035096]
NPO16239	Rhodiola rosea	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14692	Salix babylonica	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO30241	Picrorhiza scrophulariiflora	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO30241	Picrorhiza scrophulariiflora	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14692	Salix babylonica	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14692	Salix babylonica	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16239	Rhodiola rosea	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO30241	Picrorhiza scrophulariiflora	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14692	Salix babylonica	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14692	Salix babylonica	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16239	Rhodiola rosea	Species	Crassulaceae	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 NPC324579 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	11181
0.1-0.2	33710
0.2-0.3	3725
0.3-0.4	781
0.4-0.5	340
0.5-0.6	82
0.6-0.7	13
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC294470
0.7674	Intermediate Similarity	NPC212729
0.7674	Intermediate Similarity	NPC604498
0.75	Intermediate Similarity	NPC269242
0.7391	Intermediate Similarity	NPC60589
0.7391	Intermediate Similarity	NPC469708
0.7234	Intermediate Similarity	NPC200092
0.7021	Intermediate Similarity	NPC609376
0.7	Intermediate Similarity	NPC218685
0.6735	Remote Similarity	NPC80098
0.6538	Remote Similarity	NPC251102
0.6538	Remote Similarity	NPC205054
0.6538	Remote Similarity	NPC210298
0.6522	Remote Similarity	NPC142319
0.6364	Remote Similarity	NPC228907
0.6275	Remote Similarity	NPC214454
0.6226	Remote Similarity	NPC23084
0.6226	Remote Similarity	NPC604356
0.6207	Remote Similarity	NPC474044
0.6111	Remote Similarity	NPC26080
0.6111	Remote Similarity	NPC165686
0.6	Remote Similarity	NPC604439
0.5926	Remote Similarity	NPC479028
0.5926	Remote Similarity	NPC479031
0.5918	Remote Similarity	NPC153149
0.5893	Remote Similarity	NPC79908
0.5882	Remote Similarity	NPC226712
0.5882	Remote Similarity	NPC608788
0.5849	Remote Similarity	NPC9912
0.5833	Remote Similarity	NPC276195
0.58	Remote Similarity	NPC25817
0.5714	Remote Similarity	NPC217854
0.566	Remote Similarity	NPC166040
0.5636	Remote Similarity	NPC270849
0.5636	Remote Similarity	NPC19470
0.5614	Remote Similarity	NPC222455
0.56	Remote Similarity	NPC192810
0.5577	Remote Similarity	NPC12308
0.5574	Remote Similarity	NPC248119
0.5574	Remote Similarity	NPC175275
0.5556	Remote Similarity	NPC310661
0.5536	Remote Similarity	NPC26653
0.5536	Remote Similarity	NPC481303
0.549	Remote Similarity	NPC9248
0.5484	Remote Similarity	NPC264381
0.5484	Remote Similarity	NPC259767
0.5484	Remote Similarity	NPC295970
0.5472	Remote Similarity	NPC221090
0.54	Remote Similarity	NPC484157
0.5397	Remote Similarity	NPC471029
0.5397	Remote Similarity	NPC601944
0.5385	Remote Similarity	NPC299144
0.5385	Remote Similarity	NPC198798
0.537	Remote Similarity	NPC48863
0.537	Remote Similarity	NPC166168
0.537	Remote Similarity	NPC251981
0.537	Remote Similarity	NPC13745
0.5357	Remote Similarity	NPC472024
0.5357	Remote Similarity	NPC606892
0.5345	Remote Similarity	NPC106025
0.5333	Remote Similarity	NPC294166
0.5333	Remote Similarity	NPC174377
0.5333	Remote Similarity	NPC115022
0.5283	Remote Similarity	NPC36434
0.5273	Remote Similarity	NPC40377
0.5263	Remote Similarity	NPC214910
0.5263	Remote Similarity	NPC210015
0.5263	Remote Similarity	NPC80600
0.5263	Remote Similarity	NPC164599
0.5254	Remote Similarity	NPC97326
0.5246	Remote Similarity	NPC479030
0.5246	Remote Similarity	NPC8497
0.5246	Remote Similarity	NPC479374
0.5238	Remote Similarity	NPC178851
0.5238	Remote Similarity	NPC177742
0.5238	Remote Similarity	NPC57587
0.5231	Remote Similarity	NPC170475
0.5192	Remote Similarity	NPC152722
0.5185	Remote Similarity	NPC69513
0.5185	Remote Similarity	NPC145900
0.5172	Remote Similarity	NPC248355
0.5172	Remote Similarity	NPC479029
0.5167	Remote Similarity	NPC199335
0.5167	Remote Similarity	NPC146540
0.5167	Remote Similarity	NPC477240
0.5161	Remote Similarity	NPC216752
0.5161	Remote Similarity	NPC121001
0.5156	Remote Similarity	NPC605700
0.5156	Remote Similarity	NPC606353
0.5152	Remote Similarity	NPC169761
0.5152	Remote Similarity	NPC26195
0.5091	Remote Similarity	NPC604209
0.5088	Remote Similarity	NPC485268
0.5088	Remote Similarity	NPC83975
0.5088	Remote Similarity	NPC479769
0.5085	Remote Similarity	NPC55040
0.5085	Remote Similarity	NPC599943
0.5082	Remote Similarity	NPC190217
0.5082	Remote Similarity	NPC611586
0.5079	Remote Similarity	NPC210192
0.5077	Remote Similarity	NPC186406
0.5077	Remote Similarity	NPC271479
0.5077	Remote Similarity	NPC108674
0.5075	Remote Similarity	NPC169968

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC324579 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	2646
0.1-0.2	6157
0.2-0.3	313
0.3-0.4	27
0.4-0.5	6
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
0.5882	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