NPASS Compound

Natural Product: NPC320369

Natural Product ID	NPC320369
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	SHDCXMVFGZHYMZ-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	54305395
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000175] Glycerolipids [CHEMONTID:0003815] Triradylcglycerols [CHEMONTID:0001135] Triacylglycerols

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

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0 0 -21.5490 30.2260 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -24.1471 28.7260 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -24.8971 30.0250 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -22.2990 31.5250 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -23.0490 32.8240 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -25.6471 31.3240 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -26.3971 32.6231 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -23.7990 34.1231 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -24.5490 35.4221 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -27.1471 33.9221 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -27.8971 35.2211 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -25.2990 36.7211 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -26.0490 38.0202 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -28.6471 36.5202 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -28.8481 39.8683 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -29.3971 37.8192 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -26.7990 39.3192 0.0000 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 4 5 1 0 5 6 1 0 6 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 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 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 30 31 1 0 31 32 1 0 32 33 2 0 32 34 1 0 34 35 1 0 35 36 1 0 36 37 1 0 37 38 1 0 38 39 1 0 39 40 2 0 39 41 1 0 41 42 1 0 42 43 1 0 43 44 1 0 44 45 1 0 45 46 1 0 46 47 1 0 47 48 1 0 48 49 1 0 49 50 1 0 50 51 1 0 51 52 1 0 52 53 1 0 53 54 1 0 54 55 1 0 55 56 1 0 56 57 1 0 57 58 1 0 58 59 1 0 59 60 1 0 60 61 1 0 61 62 1 0 62 63 1 0 63 64 1 0 64 65 1 0 65 66 1 0 66 67 1 0 67 68 1 0 68 69 1 0 69 70 1 0 70 71 1 0 36 72 1 0 72 73 1 0 73 74 2 0 73 75 1 0 75 76 1 0 76 77 1 0 77 78 1 0 78 79 1 0 79 80 1 0 80 81 1 0 81 82 1 0 82 83 1 0 83 84 1 0 84 85 1 0 85 86 1 0 86 87 1 0 87 88 1 0 88 89 1 0 89 90 1 0 90 91 1 0 91 92 1 0 92 93 1 0 93 94 1 0 94 95 1 0 95 96 1 0 96 97 1 0 97 98 1 0 98 99 1 0 99100 1 0 100101 1 0 101102 1 0 102103 1 0 103104 1 0 104105 1 0 1106 1 0 1107 1 0 1108 1 0 2109 1 0 2110 1 0 3111 1 0 3112 1 0 4113 1 0 4114 1 0 5115 1 0 5116 1 0 6117 1 0 6118 1 0 7119 1 0 7120 1 0 8121 1 0 8122 1 0 9123 1 0 9124 1 0 10125 1 0 10126 1 0 11127 1 0 11128 1 0 12129 1 0 12130 1 0 13131 1 0 13132 1 0 14133 1 0 14134 1 0 15135 1 0 15136 1 0 16137 1 0 16138 1 0 17139 1 0 17140 1 0 18141 1 0 18142 1 0 19143 1 0 19144 1 0 20145 1 0 20146 1 0 21147 1 0 21148 1 0 22149 1 0 22150 1 0 23151 1 0 23152 1 0 24153 1 0 24154 1 0 25155 1 0 25156 1 0 26157 1 0 26158 1 0 27159 1 0 27160 1 0 28161 1 0 28162 1 0 29163 1 0 29164 1 0 30165 1 0 30166 1 0 31167 1 0 31168 1 0 35169 1 0 35170 1 0 36171 1 0 37172 1 0 37173 1 0 41174 1 0 41175 1 0 42176 1 0 42177 1 0 43178 1 0 43179 1 0 44180 1 0 44181 1 0 45182 1 0 45183 1 0 46184 1 0 46185 1 0 47186 1 0 47187 1 0 48188 1 0 48189 1 0 49190 1 0 49191 1 0 50192 1 0 50193 1 0 51194 1 0 51195 1 0 52196 1 0 52197 1 0 53198 1 0 53199 1 0 54200 1 0 54201 1 0 55202 1 0 55203 1 0 56204 1 0 56205 1 0 57206 1 0 57207 1 0 58208 1 0 58209 1 0 59210 1 0 59211 1 0 60212 1 0 60213 1 0 61214 1 0 61215 1 0 62216 1 0 62217 1 0 63218 1 0 63219 1 0 64220 1 0 64221 1 0 65222 1 0 65223 1 0 66224 1 0 66225 1 0 67226 1 0 67227 1 0 68228 1 0 68229 1 0 69230 1 0 69231 1 0 70232 1 0 70233 1 0 71234 1 0 71235 1 0 71236 1 0 75237 1 0 75238 1 0 76239 1 0 76240 1 0 77241 1 0 77242 1 0 78243 1 0 78244 1 0 79245 1 0 79246 1 0 80247 1 0 80248 1 0 81249 1 0 81250 1 0 82251 1 0 82252 1 0 83253 1 0 83254 1 0 84255 1 0 84256 1 0 85257 1 0 85258 1 0 86259 1 0 86260 1 0 87261 1 0 87262 1 0 88263 1 0 88264 1 0 89265 1 0 89266 1 0 90267 1 0 90268 1 0 91269 1 0 91270 1 0 92271 1 0 92272 1 0 93273 1 0 93274 1 0 94275 1 0 94276 1 0 95277 1 0 95278 1 0 96279 1 0 96280 1 0 97281 1 0 97282 1 0 98283 1 0 98284 1 0 99285 1 0 99286 1 0 100287 1 0 100288 1 0 101289 1 0 101290 1 0 102291 1 0 102292 1 0 103293 1 0 103294 1 0 104295 1 0 104296 1 0 105297 1 0 105298 1 0 105299 1 0 M END

Standard InCHIKey	SHDCXMVFGZHYMZ-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C99H194O6/c1-4-7-10-13-16-19-22-25-28-31-34-37-40-43-46-49-52-55-58-61-64-67-70-73-76-79-82-85-88-91-97(100)103-94-96(105-99(102)93-90-87-84-81-78-75-72-69-66-63-60-57-54-51-48-45-42-39-36-33-30-27-24-21-18-15-12-9-6-3)95-104-98(101)92-89-86-83-80-77-74-71-68-65-62-59-56-53-50-47-44-41-38-35-32-29-26-23-20-17-14-11-8-5-2/h96H,4-95H2,1-3H3
SMILES	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC(=O)OCC(COC(=O)CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC)OC(=O)CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC

Calculated Properties

Physi-Chem Properties

Molecular Weight:	1479.49	Volume:	1765.691 ? Van der Waals volume.
Dense:	0.838	LogP:	13.172 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	6.883 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-12.09 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	98.0	Rigid Bonds:	3.0
TPSA:	78.9 ? Topological Polar Surface Area.	H-Bond Acceptor:	6.0
H-Bond Donor:	0.0	Rings:	0.0
Heavy Atoms:	6.0

MedChem Properties

QED Drug-Likeness Score:	0.034	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.884	Fsp³:	0.97
MCE-18:	0.0 ? 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:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.665	Fluc inhibitor:	0.331 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.0 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.0 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.924	Promiscuous compounds:	0.331

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.302	MDCK Permeability:	-5.5
Pgp-inhibitor:	0.0	Pgp-substrate:	0.0
PAMPA:	0.0 ? 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):	1.0
20% Bioavailability (F20%):	1.0	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	1.0
Plasma Protein Binding (PPB):	121.627%	Volume Distribution (VD):	7.938
Fu:	0.0% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.02
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	1.0
BSEP inhibitor:	1.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	1.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	1.0
CYP2C9-inhibitor:	0.006	CYP2C9-substrate:	1.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	1.0
CYP3A4-inhibitor:	0.006	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.003 ? 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):

3.078

Half-life (T1/2):

20.225

ADMET: Toxicity

hERG Blockers:	1.0	hERG Blockers (10um):	1.0
Human Hepatotoxicity (H-HT):	0.59	Drug-induced Liver Injury (DILI):	0.121
AMES Toxicity:	0.0	Rat Oral Acute Toxicity:	0.002
Maximum Recommended Daily Dose:	0.489	Skin Sensitization:	1.0
Carcinogencity:	0.118	Eye Corrosion:	0.109
Eye Irritation:	0.73	Respiratory Toxicity:	1.0
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	0.032
Hematotoxicity:	0.005	Drug-induced Nephrotoxicity:	0.078
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.056
A549 Cytotoxicity:	1.0	Hek293 Cytotoxicity:	0.859
BCF:	-5.604 ? 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:	7.541 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	10.989 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.438 ? 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
NPO14406	Anser cygnoides	Species	Anatidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14406	Anser cygnoides	Species	Anatidae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO31199	Jnula britannica	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14406	Anser cygnoides	Species	Anatidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14406	Anser cygnoides	Species	Anatidae	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 NPC320369 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	25236
0.1-0.2	22159
0.2-0.3	2169
0.3-0.4	180
0.4-0.5	64
0.5-0.6	30
0.6-0.7	10
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	NPC55678
0.7647	Intermediate Similarity	NPC602940
0.75	Intermediate Similarity	NPC54925
0.6429	Remote Similarity	NPC224700
0.6429	Remote Similarity	NPC320663
0.6207	Remote Similarity	NPC47363
0.6207	Remote Similarity	NPC250028
0.6207	Remote Similarity	NPC236579
0.6207	Remote Similarity	NPC80234
0.6207	Remote Similarity	NPC287231
0.6207	Remote Similarity	NPC203531
0.6207	Remote Similarity	NPC256163
0.6207	Remote Similarity	NPC40597
0.587	Remote Similarity	NPC488690
0.5806	Remote Similarity	NPC603863
0.5625	Remote Similarity	NPC603612
0.561	Remote Similarity	NPC48218
0.561	Remote Similarity	NPC141481
0.561	Remote Similarity	NPC464342
0.5588	Remote Similarity	NPC488257
0.5588	Remote Similarity	NPC469937
0.5588	Remote Similarity	NPC94699
0.5588	Remote Similarity	NPC320588
0.5588	Remote Similarity	NPC53463
0.5517	Remote Similarity	NPC53541
0.551	Remote Similarity	NPC83839
0.5455	Remote Similarity	NPC149299
0.5455	Remote Similarity	NPC310746
0.5294	Remote Similarity	NPC26253
0.5294	Remote Similarity	NPC489083
0.5294	Remote Similarity	NPC23155
0.5227	Remote Similarity	NPC473559
0.5227	Remote Similarity	NPC324981
0.5192	Remote Similarity	NPC488693
0.5192	Remote Similarity	NPC488689
0.5161	Remote Similarity	NPC63182
0.5161	Remote Similarity	NPC145045
0.5161	Remote Similarity	NPC52700
0.5152	Remote Similarity	NPC80396
0.5152	Remote Similarity	NPC154642
0.5152	Remote Similarity	NPC600941
0.5143	Remote Similarity	NPC128061
0.5094	Remote Similarity	NPC331437

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC320369 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6706
0.1-0.2	2279
0.2-0.3	139
0.3-0.4	16
0.4-0.5	3
0.5-0.6	2
0.6-0.7	4
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	Drug ID	Developmental Stage
1.0	High Similarity	NPD6125	Phase 4
0.6571	Remote Similarity	NPD3730	Pre-clinical
0.6429	Remote Similarity	NPD8278	Phase 4
0.6207	Remote Similarity	NPD2699	Pre-clinical
0.6	Remote Similarity	NPD8277	Approved
0.575	Remote Similarity	NPD3728	Approved
0.551	Remote Similarity	NPD8304	Clinical (unspecified phase)

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