NPASS Compound

Natural Product: NPC243950

Natural Product ID	NPC243950
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	XGTCGDUVXWLURC-DDQIWDDQSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
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 52 51 0 0 0 0 0 0 0 0999 V2000 6.6121 1.0681 2.0539 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8991 -0.2597 2.3299 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4813 -0.1415 1.9572 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9198 -0.9093 1.0377 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5486 -1.9583 0.2629 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6670 -1.8923 -1.1688 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3350 -0.9665 -2.0123 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7244 0.3287 -1.7458 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3765 0.4721 -2.4345 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4022 -0.5567 -1.9640 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0840 -0.4190 -2.6548 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0531 -0.1734 -2.0174 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2992 -0.0543 -2.7524 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4144 0.1949 -2.1325 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5028 0.3699 -0.7032 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6782 0.6305 -0.0980 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8177 0.8188 1.3622 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7579 -0.1867 1.9912 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1356 -0.0986 1.3978 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7315 1.2663 1.6036 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8417 1.7988 2.7332 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.1935 2.0042 0.5009 O 0 0 0 0 0 0 0 0 0 0 0 0 7.6681 0.8787 1.8745 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4642 1.7476 2.8999 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0852 1.5236 1.1856 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9279 -0.3918 3.4526 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4767 -1.0615 1.9070 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8924 0.6318 2.4874 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8211 -0.6945 0.9196 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5503 -2.2156 0.7382 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9663 -2.9294 0.5524 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1312 -2.8052 -1.6501 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5330 -1.1541 -3.1231 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3697 1.1044 -2.3265 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7114 0.5917 -0.7113 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9407 1.4806 -2.2689 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5297 0.4156 -3.5521 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7547 -1.5866 -2.1892 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2762 -0.4693 -0.8752 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0303 -0.5258 -3.7302 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9909 -0.0742 -0.9562 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2787 -0.1785 -3.8649 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3388 0.2778 -2.7217 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6747 0.3119 -0.0146 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5439 0.7023 -0.7276 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8238 0.7258 1.8250 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1769 1.8467 1.6172 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3807 -1.2088 1.8974 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8332 0.0817 3.0657 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2332 -0.4133 0.3636 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7758 -0.8049 1.9995 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.7028 2.8573 0.6787 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 4 5 1 0 5 6 1 0 6 7 2 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 2 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 2 0 20 22 1 0 1 23 1 0 1 24 1 0 1 25 1 0 2 26 1 0 2 27 1 0 3 28 1 0 4 29 1 0 5 30 1 0 5 31 1 0 6 32 1 0 7 33 1 0 8 34 1 0 8 35 1 0 9 36 1 0 9 37 1 0 10 38 1 0 10 39 1 0 11 40 1 0 12 41 1 0 13 42 1 0 14 43 1 0 15 44 1 0 16 45 1 0 17 46 1 0 17 47 1 0 18 48 1 0 18 49 1 0 19 50 1 0 19 51 1 0 22 52 1 0 M END

Standard InCHIKey	XGTCGDUVXWLURC-DDQIWDDQSA-N
Standard InCHI	InChI=1S/C20H30O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20(21)22/h3-4,6-7,11-16H,2,5,8-10,17-19H2,1H3,(H,21,22)/b4-3-,7-6-,12-11+,14-13-,16-15+
SMILES	CC/C=CC/C=CCCC/C=C/C=CC=CCCCC(=O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	302.22	Volume:	356.238 ? Van der Waals volume.
Dense:	0.848	LogP:	5.91 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.572 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.971 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	13.0	Rigid Bonds:	6.0
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:	0.258	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.047	Fsp³:	0.45
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:	0.212	Fluc inhibitor:	0.354 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.007 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.058 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.994	Promiscuous compounds:	0.376

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.156	MDCK Permeability:	-4.943
Pgp-inhibitor:	0.031	Pgp-substrate:	0.001
PAMPA:	0.051 ? 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):	0.008
20% Bioavailability (F20%):	0.18	30% Bioavailability (F30%):	0.662
50% Bioavailability (F50%):	0.778

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.992
Plasma Protein Binding (PPB):	96.758%	Volume Distribution (VD):	-0.726
Fu:	3.146% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.022
OATP1B3 inhibitor:	0.348	BCRP inhibitor:	0.026
BSEP inhibitor:	1.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.012	CYP1A2-substrate:	0.003
CYP2C19-inhibitor:	0.567	CYP2C19-substrate:	0.003
CYP2C9-inhibitor:	1.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.901	CYP2D6-substrate:	0.012
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.839
CYP2B6-substrate:	1.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.024 ? 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):

6.947

Half-life (T1/2):

0.371

ADMET: Toxicity

hERG Blockers:	0.142	hERG Blockers (10um):	0.194
Human Hepatotoxicity (H-HT):	0.236	Drug-induced Liver Injury (DILI):	0.0
AMES Toxicity:	0.924	Rat Oral Acute Toxicity:	0.063
Maximum Recommended Daily Dose:	0.13	Skin Sensitization:	1.0
Carcinogencity:	0.033	Eye Corrosion:	0.999
Eye Irritation:	0.999	Respiratory Toxicity:	0.978
Drug-induced Neurotoxicity:	0.023	Ototoxicity:	0.358
Hematotoxicity:	0.001	Drug-induced Nephrotoxicity:	0.477
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.023
A549 Cytotoxicity:	0.014	Hek293 Cytotoxicity:	0.015
BCF:	1.204 ? 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:	4.158 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.481 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.194 ? 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
NPO21178	Chloranthus serratus	Species	Chloranthaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19053511]
NPO21178	Chloranthus serratus	Species	Chloranthaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22372956]
NPO21178	Chloranthus serratus	Species	Chloranthaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27588583]
NPO2989	Atalantia monophylla	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28140592]
NPO21178	Chloranthus serratus	Species	Chloranthaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30724564]
NPO2989	Atalantia monophylla	Species	Rutaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[31390210]
NPO2989	Atalantia monophylla	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO21178	Chloranthus serratus	Species	Chloranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO21178	Chloranthus serratus	Species	Chloranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2989	Atalantia monophylla	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21178	Chloranthus serratus	Species	Chloranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2989	Atalantia monophylla	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21178	Chloranthus serratus	Species	Chloranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21178	Chloranthus serratus	Species	Chloranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2989	Atalantia monophylla	Species	Rutaceae	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 NPC243950 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	40298
0.1-0.2	8603
0.2-0.3	702
0.3-0.4	131
0.4-0.5	71
0.5-0.6	38
0.6-0.7	7
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
0.7812	Intermediate Similarity	NPC117572
0.7647	Intermediate Similarity	NPC70387
0.7429	Intermediate Similarity	NPC52955
0.7429	Intermediate Similarity	NPC88966
0.7429	Intermediate Similarity	NPC25417
0.7429	Intermediate Similarity	NPC1813
0.7353	Intermediate Similarity	NPC149821
0.7143	Intermediate Similarity	NPC91495
0.6944	Remote Similarity	NPC59051
0.6667	Remote Similarity	NPC321062
0.6486	Remote Similarity	NPC154245
0.6486	Remote Similarity	NPC85813
0.6486	Remote Similarity	NPC223697
0.6486	Remote Similarity	NPC6095
0.6216	Remote Similarity	NPC5413
0.5946	Remote Similarity	NPC95145
0.5946	Remote Similarity	NPC325642
0.5946	Remote Similarity	NPC207292
0.5946	Remote Similarity	NPC65174
0.587	Remote Similarity	NPC322461
0.5833	Remote Similarity	NPC281245
0.5789	Remote Similarity	NPC48162
0.5778	Remote Similarity	NPC325977
0.5778	Remote Similarity	NPC327112
0.5745	Remote Similarity	NPC605544
0.5745	Remote Similarity	NPC607260
0.5682	Remote Similarity	NPC323597
0.5682	Remote Similarity	NPC211752
0.5682	Remote Similarity	NPC323498
0.5676	Remote Similarity	NPC424
0.5676	Remote Similarity	NPC36061
0.5676	Remote Similarity	NPC69510
0.5676	Remote Similarity	NPC77272
0.5676	Remote Similarity	NPC290563
0.5676	Remote Similarity	NPC139029
0.5676	Remote Similarity	NPC281972
0.5676	Remote Similarity	NPC261831
0.5676	Remote Similarity	NPC87564
0.5652	Remote Similarity	NPC328311
0.5625	Remote Similarity	NPC329249
0.5476	Remote Similarity	NPC323436
0.5476	Remote Similarity	NPC327388
0.5435	Remote Similarity	NPC320642
0.5435	Remote Similarity	NPC329550
0.5319	Remote Similarity	NPC323045
0.5319	Remote Similarity	NPC317881
0.5306	Remote Similarity	NPC92558
0.5278	Remote Similarity	NPC270796
0.5263	Remote Similarity	NPC92114
0.5217	Remote Similarity	NPC320305
0.5217	Remote Similarity	NPC321838
0.5116	Remote Similarity	NPC322002
0.5116	Remote Similarity	NPC284212

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC243950 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7119
0.1-0.2	1857
0.2-0.3	131
0.3-0.4	25
0.4-0.5	9
0.5-0.6	4
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
0.7812	Intermediate Similarity	NPD4222	Phase 3
0.7429	Intermediate Similarity	NPD3172	Approved
0.6667	Remote Similarity	NPD39	Phase 4
0.6486	Remote Similarity	NPD4266	Phase 2
0.6216	Remote Similarity	NPD3173	Phase 4
0.5778	Remote Similarity	NPD4246	Phase 2
0.5676	Remote Similarity	NPD3195	Phase 2
0.5676	Remote Similarity	NPD3196	Approved
0.5278	Remote Similarity	NPD5326	Phase 3

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