NPASS Compound

Natural Product: NPC162901

Natural Product ID	NPC162901
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	OBNDIDKDLXSSCB-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	53439977
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0000262] Fatty acids and conjugates [CHEMONTID:0002949] Long-chain fatty acids

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 54 53 0 0 0 0 0 0 0 0999 V2000 -4.8981 0.6905 1.8244 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7859 1.7488 0.7791 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2739 1.3581 -0.5676 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5471 0.1765 -1.1678 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0796 0.4581 -1.3232 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3461 -0.6932 -1.9233 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4565 -1.9316 -1.0735 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8960 -1.6706 0.3008 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4404 -1.2694 0.2395 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3673 -2.3678 -0.4009 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8483 -2.0084 -0.4578 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0184 -0.7671 -1.2653 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4510 -0.3435 -1.3626 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0833 0.1002 -0.1324 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5894 0.2714 1.0719 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3413 0.7315 2.2621 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7754 1.0670 2.0220 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9913 2.1954 1.0922 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9982 2.8287 0.6522 O 0 0 0 0 0 0 0 0 0 0 0 0 7.2674 2.5390 0.7204 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.6724 -0.3223 1.4965 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9360 0.6513 2.2664 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2377 0.9408 2.6866 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3801 2.6243 1.1138 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7293 2.1193 0.7157 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1230 2.2180 -1.2527 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3423 1.1218 -0.5628 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7930 -0.7683 -0.6683 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9566 0.0749 -2.2177 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0108 1.3215 -2.0497 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6036 0.8151 -0.3940 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7641 -0.9751 -2.9284 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2765 -0.4532 -2.1501 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9175 -2.7643 -1.5864 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5148 -2.2564 -1.0282 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0198 -2.6183 0.8931 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4327 -0.8401 0.8105 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4110 -0.3238 -0.3366 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0921 -1.1060 1.2945 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2743 -3.3191 0.1596 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0759 -2.5064 -1.4778 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3211 -2.8922 -0.9915 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1954 -1.9366 0.5596 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5906 -0.8677 -2.2845 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4768 0.1053 -0.7872 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4782 0.4356 -2.1731 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9988 -1.2133 -1.8362 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1760 0.3140 -0.2183 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5130 0.1066 1.2685 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3217 -0.0414 3.0770 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7644 1.5886 2.6858 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3682 0.1754 1.7499 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1950 1.4058 3.0139 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4562 3.0603 -0.1382 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 2 3 15 16 1 0 16 17 1 0 17 18 1 0 18 19 2 0 18 20 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 10 40 1 0 10 41 1 0 11 42 1 0 11 43 1 0 12 44 1 0 12 45 1 0 13 46 1 0 13 47 1 0 14 48 1 0 15 49 1 0 16 50 1 0 16 51 1 0 17 52 1 0 17 53 1 0 20 54 1 0 M END

Standard InCHIKey	OBNDIDKDLXSSCB-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h14-15H,2-13,16-17H2,1H3,(H,19,20)
SMILES	CCCCCCCCCCCCCC=CCCC(=O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	282.26	Volume:	332.192 ? Van der Waals volume.
Dense:	0.85	LogP:	7.051 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.751 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.957 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	15.0	Rigid Bonds:	2.0
TPSA:	37.3 ? Topological Polar Surface Area.	H-Bond Acceptor:	2.0
H-Bond Donor:	1.0	Rings:	0.0
Heavy Atoms:	2.0

MedChem Properties

QED Drug-Likeness Score:	0.291	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.07	Fsp³:	0.833
MCE-18:	0.0 ? 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:	0.24	Fluc inhibitor:	0.189 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.003 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.018 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.995	Promiscuous compounds:	0.885

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.07	MDCK Permeability:	-4.736
Pgp-inhibitor:	0.0	Pgp-substrate:	0.004
PAMPA:	0.045 ? 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):	0.245
20% Bioavailability (F20%):	0.295	30% Bioavailability (F30%):	0.597
50% Bioavailability (F50%):	0.26

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.01	MRP1:	0.99
Plasma Protein Binding (PPB):	98.138%	Volume Distribution (VD):	0.583
Fu:	1.321% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.543
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.1
BSEP inhibitor:	0.299

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.121
CYP2C19-inhibitor:	0.022	CYP2C19-substrate:	0.002
CYP2C9-inhibitor:	1.0	CYP2C9-substrate:	0.229
CYP2D6-inhibitor:	0.888	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.995
CYP2B6-substrate:	0.982	CYP2C8-inhibitor:	0.972
HLM stability:	0.004 ? 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):

4.274

Half-life (T1/2):

0.681

ADMET: Toxicity

hERG Blockers:	0.119	hERG Blockers (10um):	0.366
Human Hepatotoxicity (H-HT):	0.28	Drug-induced Liver Injury (DILI):	0.024
AMES Toxicity:	0.072	Rat Oral Acute Toxicity:	0.095
Maximum Recommended Daily Dose:	0.101	Skin Sensitization:	0.998
Carcinogencity:	0.198	Eye Corrosion:	0.997
Eye Irritation:	0.998	Respiratory Toxicity:	0.843
Drug-induced Neurotoxicity:	0.007	Ototoxicity:	0.168
Hematotoxicity:	0.082	Drug-induced Nephrotoxicity:	0.252
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.031
A549 Cytotoxicity:	0.227	Hek293 Cytotoxicity:	0.04
BCF:	0.829 ? 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:	3.989 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.563 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	1.93 ? 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
NPO14589	Teucrium divaricatum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11317	Tetradenia fruticosa	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO877	Cocculus leaeba	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14589	Teucrium divaricatum	Species	Lamiaceae	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 NPC162901 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	37563
0.1-0.2	10376
0.2-0.3	1483
0.3-0.4	274
0.4-0.5	92
0.5-0.6	34
0.6-0.7	11
0.7-0.8	2
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
0.7333	Intermediate Similarity	NPC424
0.7333	Intermediate Similarity	NPC36061
0.7333	Intermediate Similarity	NPC69510
0.7333	Intermediate Similarity	NPC77272
0.7333	Intermediate Similarity	NPC290563
0.7333	Intermediate Similarity	NPC139029
0.7333	Intermediate Similarity	NPC281972
0.7333	Intermediate Similarity	NPC92114
0.7333	Intermediate Similarity	NPC261831
0.7333	Intermediate Similarity	NPC87564
0.7	Intermediate Similarity	NPC281245
0.6667	Remote Similarity	NPC154245
0.6667	Remote Similarity	NPC85813
0.6667	Remote Similarity	NPC223697
0.6667	Remote Similarity	NPC59051
0.6667	Remote Similarity	NPC6095
0.6562	Remote Similarity	NPC95145
0.6562	Remote Similarity	NPC325642
0.6562	Remote Similarity	NPC65174
0.6364	Remote Similarity	NPC321062
0.6364	Remote Similarity	NPC91495
0.6364	Remote Similarity	NPC5413
0.5946	Remote Similarity	NPC52264
0.5806	Remote Similarity	NPC270796
0.5714	Remote Similarity	NPC52955
0.5714	Remote Similarity	NPC88966
0.5714	Remote Similarity	NPC25417
0.5714	Remote Similarity	NPC1813
0.5676	Remote Similarity	NPC137538
0.5641	Remote Similarity	NPC477201
0.5526	Remote Similarity	NPC487561
0.5429	Remote Similarity	NPC70387
0.5366	Remote Similarity	NPC243532
0.5333	Remote Similarity	NPC171736
0.5333	Remote Similarity	NPC301585
0.5333	Remote Similarity	NPC261080
0.5333	Remote Similarity	NPC132565
0.5333	Remote Similarity	NPC209970
0.5333	Remote Similarity	NPC216630
0.5333	Remote Similarity	NPC201844
0.5333	Remote Similarity	NPC301696
0.5333	Remote Similarity	NPC196924
0.5333	Remote Similarity	NPC307783
0.5333	Remote Similarity	NPC154186
0.5333	Remote Similarity	NPC149184
0.5333	Remote Similarity	NPC279026
0.5333	Remote Similarity	NPC113928
0.5333	Remote Similarity	NPC14227
0.525	Remote Similarity	NPC106851
0.525	Remote Similarity	NPC282788
0.525	Remote Similarity	NPC274927
0.5238	Remote Similarity	NPC68343
0.5238	Remote Similarity	NPC328089
0.5143	Remote Similarity	NPC149821
0.5128	Remote Similarity	NPC606120
0.5122	Remote Similarity	NPC179764

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC162901 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6698
0.1-0.2	2175
0.2-0.3	217
0.3-0.4	38
0.4-0.5	8
0.5-0.6	7
0.6-0.7	3
0.7-0.8	2
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
0.7333	Intermediate Similarity	NPD3195	Phase 2
0.7333	Intermediate Similarity	NPD3196	Approved
0.6842	Remote Similarity	NPD39	Phase 4
0.6667	Remote Similarity	NPD4266	Phase 2
0.6364	Remote Similarity	NPD3173	Phase 4
0.5946	Remote Similarity	NPD3194	Phase 4
0.5806	Remote Similarity	NPD5326	Phase 3
0.5714	Remote Similarity	NPD3172	Approved
0.5429	Remote Similarity	NPD3197	Phase 1
0.5333	Remote Similarity	NPD2270	Pre-clinical
0.5333	Remote Similarity	NPD633	Phase 3
0.5333	Remote Similarity	NPD9448	Phase 2

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