NPASS Compound

Natural Product: NPC507044

Natural Product ID	NPC507044
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	DTXSID401032165
IUPAC Name	methyl 2,6,11,15-tetramethyl-17-(2,6,6-trimethylcyclohexen-1-yl)heptadeca-2,4,6,8,10,12,14,16-octaenoate
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 75 75 0 0 0 0 0 0 0 0999 V2000 14.0344 0.3626 0.8684 C 0 0 0 0 0 0 0 0 0 0 0 0 12.9556 0.2820 -0.0527 O 0 0 0 0 0 0 0 0 0 0 0 0 11.6394 0.2617 0.3103 C 0 0 0 0 0 0 0 0 0 0 0 0 11.3194 0.3156 1.5158 O 0 0 0 0 0 0 0 0 0 0 0 0 10.5998 0.1776 -0.6939 C 0 0 0 0 0 0 0 0 0 0 0 0 10.9229 0.1114 -2.1263 C 0 0 0 0 0 0 0 0 0 0 0 0 9.2992 0.1575 -0.3449 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2795 0.0750 -1.3291 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9897 0.0404 -1.2528 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1587 0.0766 -0.0979 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7045 0.1663 1.3064 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8248 0.0302 -0.2226 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0993 -0.0558 -1.4424 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7661 -0.0989 -1.5144 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9530 -0.0609 -0.3466 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6131 -0.1015 -0.3317 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1006 -0.1936 -1.6040 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0884 -0.0554 0.9297 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3380 -0.0733 1.2472 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5140 -0.1444 0.4894 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8251 -0.1699 0.9185 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9753 -0.1194 2.3693 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8064 -0.2557 -0.1223 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9953 -0.3006 -0.4998 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3712 -0.2960 -0.1537 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.2881 -0.3989 -1.1780 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8271 -0.5059 -2.5711 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.7507 -0.4254 -0.9422 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.1687 -1.2183 0.2619 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.0448 -1.3325 1.2583 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.0868 -0.1448 1.1219 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.9038 1.1605 1.0956 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3072 -0.1229 2.3788 C 0 0 0 0 0 0 0 0 0 0 0 0 14.2793 -0.6538 1.2645 H 0 0 0 0 0 0 0 0 0 0 0 0 14.9110 0.7661 0.3496 H 0 0 0 0 0 0 0 0 0 0 0 0 13.7899 0.9951 1.7389 H 0 0 0 0 0 0 0 0 0 0 0 0 10.5248 0.9753 -2.6943 H 0 0 0 0 0 0 0 0 0 0 0 0 10.5345 -0.8064 -2.6251 H 0 0 0 0 0 0 0 0 0 0 0 0 12.0355 0.0614 -2.2478 H 0 0 0 0 0 0 0 0 0 0 0 0 9.1216 0.2077 0.7022 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6897 0.0312 -2.3988 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4508 -0.0279 -2.2285 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2583 -0.7500 1.5594 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2090 1.1035 1.5107 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8046 0.1266 2.0124 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2957 0.0648 0.7361 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6254 -0.0916 -2.4083 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3787 -0.1622 -2.5281 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3961 0.0079 0.6631 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5582 -0.3187 -2.5070 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6981 0.7191 -1.7298 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6843 -1.1521 -1.6053 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6184 0.0094 1.8186 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5011 0.0049 2.3721 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4234 -0.1836 -0.6130 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3106 0.8260 2.7941 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6689 -0.9546 2.7003 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0319 -0.4064 2.9292 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1265 -0.3152 -1.1550 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9501 -0.3836 -1.7180 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2151 -1.4067 -2.7862 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.7051 -0.5526 -3.2739 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2711 0.3917 -2.9131 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.1874 -1.0173 -1.8215 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.2203 0.5595 -1.0565 H 0 0 0 0 0 0 0 0 0 0 0 0 -11.0523 -0.7235 0.7092 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.4802 -2.2554 0.0206 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.4711 -1.2951 2.2758 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.4621 -2.2419 1.1456 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.6705 1.7587 0.2166 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.9639 0.9021 1.2443 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.6289 1.7391 2.0243 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.0746 0.1184 3.2139 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5970 0.6989 2.4663 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8551 -1.0908 2.5974 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 3 5 1 0 5 6 1 0 5 7 2 3 7 8 1 0 8 9 2 3 9 10 1 0 10 11 1 0 10 12 2 3 12 13 1 0 13 14 2 3 14 15 1 0 15 16 2 3 16 17 1 0 16 18 1 0 18 19 2 3 19 20 1 0 20 21 2 3 21 22 1 0 21 23 1 0 23 24 2 3 24 25 1 0 25 26 2 0 26 27 1 0 26 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 31 32 1 0 31 33 1 0 31 25 1 0 1 34 1 0 1 35 1 0 1 36 1 0 6 37 1 0 6 38 1 0 6 39 1 0 7 40 1 0 8 41 1 0 9 42 1 0 11 43 1 0 11 44 1 0 11 45 1 0 12 46 1 0 13 47 1 0 14 48 1 0 15 49 1 0 17 50 1 0 17 51 1 0 17 52 1 0 18 53 1 0 19 54 1 0 20 55 1 0 22 56 1 0 22 57 1 0 22 58 1 0 23 59 1 0 24 60 1 0 27 61 1 0 27 62 1 0 27 63 1 0 28 64 1 0 28 65 1 0 29 66 1 0 29 67 1 0 30 68 1 0 30 69 1 0 32 70 1 0 32 71 1 0 32 72 1 0 33 73 1 0 33 74 1 0 33 75 1 0 M END

Standard InCHIKey	WWGLUXSMFKKERG-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C31H42O2/c1-24(14-9-10-15-25(2)18-12-19-28(5)30(32)33-8)16-11-17-26(3)21-22-29-27(4)20-13-23-31(29,6)7/h9-12,14-19,21-22H,13,20,23H2,1-8H3
SMILES	COC(=O)C(C)=CC=CC(C)=CC=CC=C(C)C=CC=C(C)C=CC1=C(C)CCCC1(C)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	446.32	Volume:	527.391 ? Van der Waals volume.
Dense:	0.846	LogP:	9.577 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	5.986 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-8.985 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	10.0	Rigid Bonds:	15.0
TPSA:	26.3 ? Topological Polar Surface Area.	H-Bond Acceptor:	2.0
H-Bond Donor:	0.0	Rings:	1.0
Heavy Atoms:	2.0

MedChem Properties

QED Drug-Likeness Score:	0.201	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.607	Fsp³:	0.387
MCE-18:	15.419 ? 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:	Accepted	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.999	Fluc inhibitor:	0.665 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.027 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.079 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.685	Promiscuous compounds:	0.085

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.887	MDCK Permeability:	-4.76
Pgp-inhibitor:	0.608	Pgp-substrate:	0.185
PAMPA:	0.055 ? 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):	0.0
20% Bioavailability (F20%):	0.01	30% Bioavailability (F30%):	0.157
50% Bioavailability (F50%):	0.898

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.987	MRP1:	0.999
Plasma Protein Binding (PPB):	95.99%	Volume Distribution (VD):	0.606
Fu:	3.658% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.91
OATP1B3 inhibitor:	0.255	BCRP inhibitor:	0.035
BSEP inhibitor:	1.0

ADMET: Metabolism

CYP1A2-inhibitor:	1.0	CYP1A2-substrate:	1.0
CYP2C19-inhibitor:	1.0	CYP2C19-substrate:	0.692
CYP2C9-inhibitor:	1.0	CYP2C9-substrate:	0.017
CYP2D6-inhibitor:	0.94	CYP2D6-substrate:	0.999
CYP3A4-inhibitor:	1.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	1.0	CYP2C8-inhibitor:	1.0
HLM stability:	1.0 ? 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):

8.601

Half-life (T1/2):

0.166

ADMET: Toxicity

hERG Blockers:	0.253	hERG Blockers (10um):	0.645
Human Hepatotoxicity (H-HT):	0.412	Drug-induced Liver Injury (DILI):	0.236
AMES Toxicity:	0.818	Rat Oral Acute Toxicity:	0.825
Maximum Recommended Daily Dose:	0.954	Skin Sensitization:	0.989
Carcinogencity:	0.831	Eye Corrosion:	0.01
Eye Irritation:	0.504	Respiratory Toxicity:	0.892
Drug-induced Neurotoxicity:	0.636	Ototoxicity:	0.339
Hematotoxicity:	0.261	Drug-induced Nephrotoxicity:	0.789
Genotoxicity:	0.768	RPMI-8226 Immunitoxicity:	0.159
A549 Cytotoxicity:	0.244	Hek293 Cytotoxicity:	0.529
BCF:	2.886 ? 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:	4.68 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.528 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.524 ? 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
NPO12507	Bixa orellana	Species	Bixaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12507	Bixa orellana	Species	Bixaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12507	Bixa orellana	Species	Bixaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12507	Bixa orellana	Species	Bixaceae	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 NPC507044 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	25348
0.1-0.2	23694
0.2-0.3	765
0.3-0.4	26
0.4-0.5	10
0.5-0.6	10
0.6-0.7	4
0.7-0.8	1
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
0.7105	Intermediate Similarity	NPC17810
0.7105	Intermediate Similarity	NPC606095
0.6667	Remote Similarity	NPC22019
0.6667	Remote Similarity	NPC281986
0.6667	Remote Similarity	NPC321568
0.6383	Remote Similarity	NPC226066
0.5778	Remote Similarity	NPC55412
0.5778	Remote Similarity	NPC249645
0.566	Remote Similarity	NPC228978
0.566	Remote Similarity	NPC600770
0.56	Remote Similarity	NPC254886
0.5306	Remote Similarity	NPC329416
0.5306	Remote Similarity	NPC317025
0.5306	Remote Similarity	NPC326645
0.5306	Remote Similarity	NPC317177
0.5098	Remote Similarity	NPC276336

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC507044 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7663
0.1-0.2	1462
0.2-0.3	12
0.3-0.4	2
0.4-0.5	3
0.5-0.6	6
0.6-0.7	1
0.7-0.8	1
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
0.7105	Intermediate Similarity	NPD8262	Phase 4
0.6383	Remote Similarity	NPD5325	Clinical (unspecified phase)
0.5778	Remote Similarity	NPD4219	Phase 4
0.566	Remote Similarity	NPD8039	Phase 4
0.5306	Remote Similarity	NPD4191	Approved
0.5306	Remote Similarity	NPD4192	Phase 4
0.5306	Remote Similarity	NPD4193	Phase 4
0.5306	Remote Similarity	NPD4194	Phase 4

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