NPASS Compound

Natural Product: NPC544772

Natural Product ID	NPC544772
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	1,2-Isopropylidene-3-decanoylglycerol
IUPAC Name	[(4~{R})-2,2-dimethyl-1,3-dioxolan-4-yl]methyl decanoate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds]

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 50 50 0 0 0 0 0 0 0 0999 V2000 7.1498 1.1346 -0.0723 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0402 -0.1547 -0.7858 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8227 -0.4746 -1.5360 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5170 -0.6356 -0.8251 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0915 0.5446 -0.0754 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8329 0.5966 0.6665 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5115 0.4872 0.0797 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0740 -0.7421 -0.6279 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3910 -0.5793 -1.1093 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3005 -0.3313 0.0375 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3657 -1.0980 1.0274 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0969 0.7948 -0.0077 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0077 1.1521 0.9998 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0695 0.0836 1.1189 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1151 0.5941 2.0962 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0749 1.1518 1.2178 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0721 0.2618 0.1580 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8280 -1.0074 0.5512 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7396 0.8600 -1.0565 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7519 -0.0317 -0.1015 O 0 0 0 0 0 0 0 0 0 0 0 0 8.1975 1.5744 -0.2559 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1754 0.9909 1.0431 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4810 1.9387 -0.3630 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2596 -0.9991 -0.0750 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9014 -0.2052 -1.5292 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6867 0.1948 -2.4336 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0122 -1.4877 -2.0315 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7971 -0.9201 -1.6615 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6170 -1.5666 -0.1871 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9020 0.6955 0.7387 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1532 1.4445 -0.7626 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8560 -0.1002 1.5788 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8485 1.6124 1.2209 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2618 1.4192 -0.5393 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7608 0.6199 0.9394 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0794 -1.6135 0.0381 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6402 -0.8807 -1.5710 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6972 -1.5609 -1.5854 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4682 0.1761 -1.9038 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4910 1.2487 1.9867 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4876 2.1169 0.7334 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6563 -0.8867 1.3981 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7164 1.3742 2.7600 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5571 -0.2186 2.6992 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6265 -1.2148 -0.1773 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1078 -1.8578 0.5393 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2233 -0.8972 1.5948 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0842 0.0341 -1.6857 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0765 1.5603 -1.5746 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6643 1.3977 -0.6895 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 2 0 10 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 17 19 1 0 17 20 1 0 20 14 1 0 1 21 1 0 1 22 1 0 1 23 1 0 2 24 1 0 2 25 1 0 3 26 1 0 3 27 1 0 4 28 1 0 4 29 1 0 5 30 1 0 5 31 1 0 6 32 1 0 6 33 1 0 7 34 1 0 7 35 1 0 8 36 1 0 8 37 1 0 9 38 1 0 9 39 1 0 13 40 1 0 13 41 1 0 14 42 1 1 15 43 1 0 15 44 1 0 18 45 1 0 18 46 1 0 18 47 1 0 19 48 1 0 19 49 1 0 19 50 1 0 M END

Standard InCHIKey	KRBSCYNTGIRIAV-AWEZNQCLSA-N
Standard InCHI	InChI=1S/C16H30O4/c1-4-5-6-7-8-9-10-11-15(17)18-12-14-13-19-16(2,3)20-14/h14H,4-13H2,1-3H3/t14-/m0/s1
SMILES	CCCCCCCCCC(=O)OC[C@H]1COC(C)(C)O1

Calculated Properties

Physi-Chem Properties

Molecular Weight:	286.21	Volume:	309.26 ? Van der Waals volume.
Dense:	0.925	LogP:	4.934 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.92 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.156 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	11.0	Rigid Bonds:	6.0
TPSA:	44.76 ? Topological Polar Surface Area.	H-Bond Acceptor:	4.0
H-Bond Donor:	0.0	Rings:	1.0
Heavy Atoms:	4.0

MedChem Properties

QED Drug-Likeness Score:	0.452	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.719	Fsp³:	0.938
MCE-18:	17.548 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted	GSK Rule:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.002	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.005 ? 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:	0.988	Promiscuous compounds:	0.247

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.004	MDCK Permeability:	-4.675
Pgp-inhibitor:	0.036	Pgp-substrate:	0.39
PAMPA:	0.082 ? 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):	0.043
20% Bioavailability (F20%):	0.233	30% Bioavailability (F30%):	0.198
50% Bioavailability (F50%):	0.593

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.074	MRP1:	0.959
Plasma Protein Binding (PPB):	96.84%	Volume Distribution (VD):	0.196
Fu:	4.315% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.269
OATP1B3 inhibitor:	0.976	BCRP inhibitor:	0.403
BSEP inhibitor:	0.988

ADMET: Metabolism

CYP1A2-inhibitor:	0.007	CYP1A2-substrate:	0.999
CYP2C19-inhibitor:	0.003	CYP2C19-substrate:	0.079
CYP2C9-inhibitor:	0.624	CYP2C9-substrate:	0.148
CYP2D6-inhibitor:	0.009	CYP2D6-substrate:	0.782
CYP3A4-inhibitor:	0.001	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.001	CYP2C8-inhibitor:	0.986
HLM stability:	0.496 ? 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):

5.722

Half-life (T1/2):

0.419

ADMET: Toxicity

hERG Blockers:	0.066	hERG Blockers (10um):	0.599
Human Hepatotoxicity (H-HT):	0.861	Drug-induced Liver Injury (DILI):	0.862
AMES Toxicity:	0.773	Rat Oral Acute Toxicity:	0.489
Maximum Recommended Daily Dose:	0.053	Skin Sensitization:	0.986
Carcinogencity:	0.978	Eye Corrosion:	0.946
Eye Irritation:	0.996	Respiratory Toxicity:	0.38
Drug-induced Neurotoxicity:	0.036	Ototoxicity:	0.217
Hematotoxicity:	0.032	Drug-induced Nephrotoxicity:	0.125
Genotoxicity:	0.001	RPMI-8226 Immunitoxicity:	0.007
A549 Cytotoxicity:	0.048	Hek293 Cytotoxicity:	0.122
BCF:	1.509 ? 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:	4.226 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.542 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.266 ? 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
NPO2595	Aspergillus terreus	Species	Aspergillaceae	Eukaryota	n.a.	from the rhizosphere of Opuntia versicolor of the Sonoran Desert	n.a.	PMID[14695798]
NPO2595	Aspergillus terreus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16124769]
NPO2595	Aspergillus terreus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18271552]
NPO2595	Aspergillus terreus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22360613]
NPO2595	Aspergillus terreus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24534845]
NPO2595	Aspergillus terreus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25671343]
NPO2595	Aspergillus terreus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2921224]
NPO2595	Aspergillus terreus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30207465]
NPO2595	Aspergillus terreus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32163285]
NPO2595	Aspergillus terreus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32897070]
NPO2595	Aspergillus terreus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8984154]
NPO2595	Aspergillus terreus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO2595	Aspergillus terreus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2595	Aspergillus terreus	Species	Aspergillaceae	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 NPC544772 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	26804
0.1-0.2	21651
0.2-0.3	1219
0.3-0.4	125
0.4-0.5	42
0.5-0.6	14
0.6-0.7	1
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	Natural Product ID
0.6765	Remote Similarity	NPC55678
0.5625	Remote Similarity	NPC250028
0.5625	Remote Similarity	NPC236579
0.5625	Remote Similarity	NPC80234
0.5625	Remote Similarity	NPC203531
0.5625	Remote Similarity	NPC256163
0.5625	Remote Similarity	NPC40597
0.5366	Remote Similarity	NPC602940
0.5349	Remote Similarity	NPC54925
0.5143	Remote Similarity	NPC603612
0.5135	Remote Similarity	NPC488257
0.5135	Remote Similarity	NPC469937
0.5135	Remote Similarity	NPC94699
0.5135	Remote Similarity	NPC320588
0.5135	Remote Similarity	NPC53463

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC544772 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6970
0.1-0.2	2058
0.2-0.3	103
0.3-0.4	12
0.4-0.5	5
0.5-0.6	1
0.6-0.7	1
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
0.6765	Remote Similarity	NPD6125	Phase 4
0.525	Remote Similarity	NPD3730	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