NPASS Compound

Natural Product: NPC474268

Natural Product ID	NPC474268
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Acetylgaertneroside
IUPAC Name	methyl (1R,4aS,7R,7aS)-1-[(2S,3R,4S,5S,6R)-6-(acetyloxymethyl)-3,4,5-trihydroxyoxan-2-yl]oxy-4'-[hydroxy-(4-hydroxyphenyl)methyl]-5'-oxospiro[4a,7a-dihydro-1H-cyclopenta[c]pyran-7,2'-furan]-4-carboxylate
Synonyms	Acetylgaertneroside
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL464502
PubChem CID	44559437
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0004081] Iridoid 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 72 76 0 0 0 0 0 0 0 0999 V2000 2.7524 6.7038 -1.0817 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8284 5.6334 -1.1034 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0211 4.5125 -1.9304 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0636 4.5531 -2.6300 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0718 3.4136 -1.9492 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0070 3.4627 -1.1799 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9132 2.4561 -1.1616 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5793 1.1535 -1.5825 C 0 0 1 0 0 0 0 0 0 0 0 0 0.7303 0.9835 -2.2338 C 0 0 1 0 0 0 0 0 0 0 0 0 1.3149 2.2607 -2.8241 C 0 0 2 0 0 0 0 0 0 0 0 0 2.7526 1.9491 -2.9648 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0611 0.9492 -2.1716 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8638 0.4818 -1.4120 C 0 0 2 0 0 0 0 0 0 0 0 0 1.8729 -0.9279 -1.2802 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9880 -1.2427 0.0575 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0351 -2.4069 0.5835 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0494 0.0028 0.7977 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9761 0.9930 -0.0558 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1911 0.1076 2.3036 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4875 -0.5608 2.6654 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6689 0.0848 2.4131 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9011 -0.4825 2.7227 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9635 -1.7193 3.2955 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7739 -2.3792 3.5542 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5415 -1.8121 3.2448 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1647 -2.3518 3.6334 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1954 1.4381 2.7016 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8094 0.2199 -0.5758 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9080 -0.6091 -0.8288 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.9423 -0.3278 0.0790 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9990 -1.1942 -0.2620 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.3022 -0.7339 0.3342 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2990 -1.6562 -0.0614 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.6172 -1.4954 0.3341 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8479 -0.4728 1.0663 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.7072 -2.4381 -0.0553 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5714 -2.5424 0.2560 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5322 -3.0595 -0.7123 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.4511 -2.0216 -0.8300 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7941 -2.2392 -2.0683 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9737 -4.2629 -0.2851 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.6330 -3.4221 0.4047 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6174 6.4853 -1.7439 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1500 6.8647 -0.0455 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3012 7.6738 -1.3781 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1171 4.3448 -0.5505 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3742 0.9213 -2.3667 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6244 0.2866 -3.1135 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9064 2.4874 -3.8235 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4372 2.4956 -3.6487 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0393 0.5134 -2.0704 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0063 2.0404 0.2737 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3903 -0.4695 2.8052 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7081 1.0755 1.9577 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8431 0.0339 2.5230 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7693 -3.3709 4.0112 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6363 -2.3489 3.4579 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6811 -2.8911 2.9383 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8433 1.5509 3.4435 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3194 -0.3068 -1.8159 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0454 -1.2161 -1.3690 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5773 0.2682 0.0155 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1890 -0.7485 1.4530 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.3965 -1.9818 -0.7941 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.2327 -3.3677 -0.3896 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.2990 -2.7140 0.8651 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0359 -2.4042 1.2337 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0701 -3.1953 -1.6926 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7512 -2.1887 0.0195 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2266 -3.0514 -2.0093 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7737 -4.2383 0.6647 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9416 -3.5501 1.3155 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 3 5 1 0 5 6 2 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 2 0 12 13 1 0 13 14 1 1 14 15 1 0 15 16 2 0 15 17 1 0 17 18 2 0 17 19 1 0 19 20 1 0 20 21 2 0 21 22 1 0 22 23 2 0 23 24 1 0 24 25 2 0 23 26 1 0 19 27 1 0 8 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 31 32 1 0 32 33 1 0 33 34 1 0 34 35 2 0 34 36 1 0 31 37 1 0 37 38 1 0 38 39 1 0 39 40 1 0 38 41 1 0 37 42 1 0 10 5 1 0 18 13 1 0 25 20 1 0 39 29 1 0 13 9 1 0 1 43 1 0 1 44 1 0 1 45 1 0 6 46 1 0 8 47 1 6 9 48 1 6 10 49 1 6 11 50 1 0 12 51 1 0 18 52 1 0 19 53 1 0 21 54 1 0 22 55 1 0 24 56 1 0 25 57 1 0 26 58 1 0 27 59 1 0 29 60 1 6 31 61 1 6 32 62 1 0 32 63 1 0 36 64 1 0 36 65 1 0 36 66 1 0 37 67 1 1 38 68 1 6 39 69 1 1 40 70 1 0 41 71 1 0 42 72 1 0 M END

Standard InCHIKey	BDUPWFOFVQZENO-YNFGFELQSA-N
Standard InCHI	InChI=1S/C28H30O14/c1-12(29)38-11-18-21(32)22(33)23(34)27(40-18)41-26-19-15(17(10-39-26)24(35)37-2)7-8-28(19)9-16(25(36)42-28)20(31)13-3-5-14(30)6-4-13/h3-10,15,18-23,26-27,30-34H,11H2,1-2H3/t15-,18-,19-,20?,21-,22+,23-,26-,27+,28-/m1/s1
SMILES	COC(=O)C1=CO[C@@H]([C@H]2[C@@H]1C=C[C@@]12OC(=O)C(=C1)C(c1ccc(cc1)O)O)O[C@@H]1O[C@H](COC(=O)C)[C@H]([C@@H]([C@H]1O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	590.16	Volume:	549.397 ? Van der Waals volume.
Dense:	1.074	LogP:	0.648 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.172 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.93 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	9.0	Rigid Bonds:	30.0
TPSA:	207.74 ? Topological Polar Surface Area.	H-Bond Acceptor:	14.0
H-Bond Donor:	5.0	Rings:	5.0
Heavy Atoms:	14.0

MedChem Properties

QED Drug-Likeness Score:	0.15	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.641	Fsp³:	0.464
MCE-18:	150.927 ? 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:	0	PAINS Alert:	0
Colloidal aggregators:	0.565	Fluc inhibitor:	0.001 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.055 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.03 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.289	Promiscuous compounds:	0.083

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.931	MDCK Permeability:	-5.286
Pgp-inhibitor:	0.0	Pgp-substrate:	0.027
PAMPA:	0.983 ? 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):	0.004
20% Bioavailability (F20%):	0.718	30% Bioavailability (F30%):	0.999
50% Bioavailability (F50%):	0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.008	MRP1:	0.625
Plasma Protein Binding (PPB):	73.469%	Volume Distribution (VD):	-0.394
Fu:	28.382% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.999
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.0
BSEP inhibitor:	0.206

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.001	CYP2D6-substrate:	0.003
CYP3A4-inhibitor:	0.001	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.94
HLM stability:	0.077 ? 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):

1.804

Half-life (T1/2):

2.274

ADMET: Toxicity

hERG Blockers:	0.008	hERG Blockers (10um):	0.11
Human Hepatotoxicity (H-HT):	0.562	Drug-induced Liver Injury (DILI):	0.939
AMES Toxicity:	0.949	Rat Oral Acute Toxicity:	0.064
Maximum Recommended Daily Dose:	0.57	Skin Sensitization:	1.0
Carcinogencity:	0.699	Eye Corrosion:	0.0
Eye Irritation:	0.057	Respiratory Toxicity:	0.006
Drug-induced Neurotoxicity:	0.089	Ototoxicity:	0.932
Hematotoxicity:	0.268	Drug-induced Nephrotoxicity:	0.948
Genotoxicity:	0.995	RPMI-8226 Immunitoxicity:	0.134
A549 Cytotoxicity:	0.104	Hek293 Cytotoxicity:	0.297
BCF:	0.592 ? 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:	3.271 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.925 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.289 ? 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
NPO22304	Morinda morindoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12542353]
NPO22304	Morinda morindoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20149652]
NPO22304	Morinda morindoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7775983]
NPO22304	Morinda morindoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO22304	Morinda morindoides	Species	Rubiaceae	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

Activity Type	# Activity
IC50	2

Activity Type	# Activity
Organism	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
NPT992	Organism	Entamoeba histolytica	Entamoeba histolytica	IC50	=	5.4	ug.mL-1	PubChem BioAssay data set
NPT610	Others	Molecular identity unknown	n.a.	IC50	=	71000.0	nM	PMID[12542353]

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 NPC474268 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	10940
0.1-0.2	35334
0.2-0.3	3179
0.3-0.4	353
0.4-0.5	40
0.5-0.6	4
0.6-0.7	2
0.7-0.8	0
0.8-0.85	2
0.85-0.9	1
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC119773
0.8605	High Similarity	NPC469384
0.8148	Intermediate Similarity	NPC475539
0.8148	Intermediate Similarity	NPC143246
0.7	Intermediate Similarity	NPC286919
0.7	Intermediate Similarity	NPC475663
0.6591	Remote Similarity	NPC474620
0.6304	Remote Similarity	NPC475378
0.5816	Remote Similarity	NPC63304
0.567	Remote Similarity	NPC180586
0.5647	Remote Similarity	NPC254538
0.5567	Remote Similarity	NPC475528

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC474268 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4615
0.1-0.2	4466
0.2-0.3	68
0.3-0.4	1
0.4-0.5	0
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