NPASS Compound

Natural Product: NPC203662

Natural Product ID	NPC203662
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	SMTKSCGLXONVGL-ZEIULZLQSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	131348
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene 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 68 70 0 0 0 0 0 0 0 0999 V2000 -1.0822 3.7869 0.4115 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6014 2.6692 -0.0858 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0582 1.2974 0.1978 C 0 0 1 0 0 0 0 0 0 0 0 0 0.1046 0.6174 0.9880 C 0 0 1 0 0 0 0 0 0 0 0 0 1.1186 0.1062 0.0705 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2375 -0.6576 0.6867 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2008 -1.1179 -0.2472 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9482 -0.2868 -1.0513 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8121 0.9608 -0.9969 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9354 -0.8100 -2.0063 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1333 -2.1696 -2.1241 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0569 -2.7003 -3.0108 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8037 -1.8575 -3.8017 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6145 -0.4952 -3.6929 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6905 0.0174 -2.8045 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3854 0.3235 -4.5067 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7308 -2.3707 -4.6928 O 0 0 0 0 0 0 0 0 0 0 0 0 6.2177 -4.0777 -3.0911 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4421 1.6404 1.9748 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5980 1.8677 2.8370 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7161 1.0657 2.5392 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2161 1.2142 1.1777 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.9510 0.0606 0.9050 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2902 0.3291 0.6258 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.6631 -0.0727 -0.7747 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1466 -1.5118 -0.8210 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.7113 -2.2376 0.4484 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.3759 -1.5189 1.5933 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.9602 -2.1227 2.9288 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2923 -3.4749 2.9344 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0439 -0.2130 1.6055 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0844 -3.5754 0.3560 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7673 -2.1831 -1.9655 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.5843 0.8201 -1.3051 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5961 2.4507 2.1576 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6020 2.3880 1.4450 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6667 3.4075 3.1965 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8087 4.2068 3.3729 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6760 4.7462 0.1391 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8976 3.7654 1.1067 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2418 2.8098 -0.7958 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2261 0.6767 -0.6989 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3838 -0.2782 1.4879 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5910 -0.6309 -0.6172 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5271 0.8571 -0.6462 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7692 -0.1205 1.4749 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8359 -1.6428 1.1301 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5610 -2.8363 -1.5155 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5880 1.0920 -2.7647 H 0 0 0 0 0 0 0 0 0 0 0 0 8.3874 0.1127 -4.5623 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7266 -2.1845 -4.5851 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1623 -4.6262 -2.2212 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5185 2.5711 3.6149 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9023 2.0563 1.0875 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4076 1.4452 0.6920 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7450 -0.0275 -1.3876 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2543 -1.4760 -0.7897 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6071 -2.1467 0.5339 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4932 -1.5925 1.4730 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8959 -1.9386 3.1397 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6070 -1.6506 3.7117 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1431 -3.6323 2.4890 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0037 -3.5951 0.0304 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4713 -1.6249 -2.7110 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4793 0.7558 -0.8949 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1992 4.5277 2.3680 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5242 5.1391 3.9001 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6351 3.6722 3.8708 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 2 0 8 10 1 0 10 11 2 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 2 0 14 16 1 0 13 17 1 0 12 18 1 0 4 19 1 0 19 20 2 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 28 29 1 0 29 30 1 0 28 31 1 0 27 32 1 0 26 33 1 0 25 34 1 0 19 35 1 0 35 36 2 0 35 37 1 0 37 38 1 0 22 3 1 0 31 24 1 0 15 10 1 0 1 39 1 0 1 40 1 0 2 41 1 0 3 42 1 6 4 43 1 1 5 44 1 0 5 45 1 0 6 46 1 0 6 47 1 0 11 48 1 0 15 49 1 0 16 50 1 0 17 51 1 0 18 52 1 0 20 53 1 0 22 54 1 1 24 55 1 6 25 56 1 6 26 57 1 1 27 58 1 1 28 59 1 6 29 60 1 0 29 61 1 0 30 62 1 0 32 63 1 0 33 64 1 0 34 65 1 0 38 66 1 0 38 67 1 0 38 68 1 0 M END

Standard InCHIKey	SMTKSCGLXONVGL-ZEIULZLQSA-N
Standard InCHI	InChI=1S/C24H30O14/c1-3-11-12(4-5-35-21(32)10-6-14(26)17(28)15(27)7-10)13(22(33)34-2)9-36-23(11)38-24-20(31)19(30)18(29)16(8-25)37-24/h3,6-7,9,11-12,16,18-20,23-31H,1,4-5,8H2,2H3/t11-,12+,16+,18+,19-,20+,23+,24-/m0/s1
SMILES	C=C[C@H]1[C@@H](CCOC(=O)c2cc(c(c(c2)O)O)O)C(=CO[C@@H]1O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)C(=O)OC

Calculated Properties

Physi-Chem Properties

Molecular Weight:	542.16	Volume:	502.599 ? Van der Waals volume.
Dense:	1.079	LogP:	0.622 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.12 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.161 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	11.0	Rigid Bonds:	21.0
TPSA:	221.9 ? Topological Polar Surface Area.	H-Bond Acceptor:	14.0
H-Bond Donor:	7.0	Rings:	3.0
Heavy Atoms:	14.0

MedChem Properties

QED Drug-Likeness Score:	0.113	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.742	Fsp³:	0.5
MCE-18:	82.667 ? 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:	0.465	Fluc inhibitor:	0.063 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.064 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.345 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.137	Promiscuous compounds:	0.478

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.209	MDCK Permeability:	-5.383
Pgp-inhibitor:	0.0	Pgp-substrate:	0.004
PAMPA:	0.93 ? 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):	0.01
20% Bioavailability (F20%):	0.938	30% Bioavailability (F30%):	0.998
50% Bioavailability (F50%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.001	MRP1:	1.0
Plasma Protein Binding (PPB):	66.879%	Volume Distribution (VD):	-0.471
Fu:	30.708% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.984
OATP1B3 inhibitor:	0.999	BCRP inhibitor:	0.358
BSEP inhibitor:	0.004

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.018
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.951
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.074
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.386 ? 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):

3.101

Half-life (T1/2):

2.677

ADMET: Toxicity

hERG Blockers:	0.016	hERG Blockers (10um):	0.384
Human Hepatotoxicity (H-HT):	0.115	Drug-induced Liver Injury (DILI):	0.988
AMES Toxicity:	0.823	Rat Oral Acute Toxicity:	0.011
Maximum Recommended Daily Dose:	0.037	Skin Sensitization:	1.0
Carcinogencity:	0.314	Eye Corrosion:	0.0
Eye Irritation:	0.181	Respiratory Toxicity:	0.002
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	0.993
Hematotoxicity:	0.02	Drug-induced Nephrotoxicity:	0.088
Genotoxicity:	0.57	RPMI-8226 Immunitoxicity:	0.02
A549 Cytotoxicity:	0.964	Hek293 Cytotoxicity:	0.342
BCF:	0.57 ? 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:	3.331 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.991 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.31 ? 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
NPO12588	Cornus officinalis	Species	Cornaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[29140705]
NPO12588	Cornus officinalis	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12588	Cornus officinalis	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12588	Cornus officinalis	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12588	Cornus officinalis	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12588	Cornus officinalis	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO12588	Cornus officinalis	Species	Cornaceae	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 NPC203662 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	9252
0.1-0.2	35856
0.2-0.3	4174
0.3-0.4	420
0.4-0.5	122
0.5-0.6	23
0.6-0.7	3
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	NPC46641
0.6667	Remote Similarity	NPC307699
0.6471	Remote Similarity	NPC601841
0.6301	Remote Similarity	NPC117596
0.5657	Remote Similarity	NPC472131
0.5532	Remote Similarity	NPC212808
0.5443	Remote Similarity	NPC27687
0.5443	Remote Similarity	NPC61201
0.5347	Remote Similarity	NPC472130
0.5256	Remote Similarity	NPC474730
0.525	Remote Similarity	NPC37240
0.519	Remote Similarity	NPC35185
0.519	Remote Similarity	NPC4899
0.519	Remote Similarity	NPC255677
0.519	Remote Similarity	NPC177013
0.519	Remote Similarity	NPC22149
0.519	Remote Similarity	NPC306344
0.5122	Remote Similarity	NPC609500
0.5106	Remote Similarity	NPC202391
0.5106	Remote Similarity	NPC296659
0.5062	Remote Similarity	NPC106668
0.506	Remote Similarity	NPC488472
0.506	Remote Similarity	NPC222062
0.506	Remote Similarity	NPC257424
0.5054	Remote Similarity	NPC319995
0.5054	Remote Similarity	NPC289415
0.5049	Remote Similarity	NPC474905

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC203662 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4447
0.1-0.2	4622
0.2-0.3	79
0.3-0.4	2
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