NPASS Compound

Natural Product: NPC546126

Natural Product ID	NPC546126
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	DIDECYL PHTHALATE
IUPAC Name	didecyl benzene-1,2-dicarboxylate
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 78 78 0 0 0 0 0 0 0 0999 V2000 8.4119 -4.3490 0.2604 C 0 0 0 0 0 0 0 0 0 0 0 0 9.2249 -3.3571 -0.5585 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3801 -2.1748 -0.9337 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8503 -1.4426 0.2847 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0210 -0.2809 -0.2276 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4709 0.4793 0.9581 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6372 1.6476 0.4951 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4669 1.2500 -0.3444 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5069 0.3375 0.3672 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9224 0.9438 1.6021 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2007 2.1163 1.4158 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0417 2.2026 0.6061 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7130 1.1546 0.0737 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4040 3.4761 0.5068 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9436 4.5797 1.2140 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3826 5.8300 1.1663 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7422 6.0516 0.4155 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2651 4.9864 -0.2687 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7115 3.6877 -0.2403 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3617 2.6747 -1.0043 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4203 3.0607 -1.6602 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1024 1.3593 -1.1963 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8720 0.5015 -2.0030 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2982 0.3669 -1.5870 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4423 -0.1802 -0.1812 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8806 -0.3120 0.2274 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6504 -1.2427 -0.6814 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1133 -1.2929 -0.1551 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.9235 -2.1958 -1.0112 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.3662 -2.3405 -0.6976 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.7582 -2.8692 0.6284 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.3630 -2.0084 1.7850 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2361 -3.8989 1.2555 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4350 -4.4847 -0.2471 H 0 0 0 0 0 0 0 0 0 0 0 0 8.8940 -5.3378 0.2954 H 0 0 0 0 0 0 0 0 0 0 0 0 9.5522 -3.8415 -1.4981 H 0 0 0 0 0 0 0 0 0 0 0 0 10.1136 -3.0291 0.0171 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5142 -2.5045 -1.5248 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0201 -1.4519 -1.4894 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1666 -2.1388 0.8451 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6301 -1.1372 0.9844 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6935 0.3758 -0.8046 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2115 -0.7360 -0.8485 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3448 0.8852 1.5044 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8786 -0.1764 1.6011 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3034 2.2772 -0.1414 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3492 2.2783 1.3559 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9860 2.1765 -0.7117 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8363 0.7168 -1.2438 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1068 -0.5785 0.6438 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7046 0.0400 -0.3105 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3514 0.1532 2.1392 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7697 1.1929 2.2726 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8396 4.3743 1.8037 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8203 6.6464 1.7174 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2222 7.0319 0.3496 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1687 5.1965 -0.8624 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8572 0.8247 -3.0672 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4270 -0.5217 -2.0005 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9177 1.2712 -1.7415 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7504 -0.4122 -2.2601 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9615 0.5448 0.5110 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9877 -1.1867 -0.0905 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4038 0.6418 0.2926 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8804 -0.7666 1.2508 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2554 -2.2734 -0.6833 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7168 -0.8232 -1.7043 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4875 -0.2565 -0.1058 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9698 -1.6491 0.8891 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4384 -3.2121 -0.9806 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.8267 -1.8769 -2.1016 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.8086 -2.9700 -1.5237 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.8773 -1.3434 -0.8500 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.3764 -3.9122 0.7902 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.8874 -2.9538 0.6333 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.5402 -2.4788 2.3464 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.0977 -0.9884 1.4879 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.2058 -1.9696 2.5484 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 2 0 12 14 1 0 14 15 2 0 15 16 1 0 16 17 2 0 17 18 1 0 18 19 2 0 19 20 1 0 20 21 2 0 20 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 19 14 1 0 1 33 1 0 1 34 1 0 1 35 1 0 2 36 1 0 2 37 1 0 3 38 1 0 3 39 1 0 4 40 1 0 4 41 1 0 5 42 1 0 5 43 1 0 6 44 1 0 6 45 1 0 7 46 1 0 7 47 1 0 8 48 1 0 8 49 1 0 9 50 1 0 9 51 1 0 10 52 1 0 10 53 1 0 15 54 1 0 16 55 1 0 17 56 1 0 18 57 1 0 23 58 1 0 23 59 1 0 24 60 1 0 24 61 1 0 25 62 1 0 25 63 1 0 26 64 1 0 26 65 1 0 27 66 1 0 27 67 1 0 28 68 1 0 28 69 1 0 29 70 1 0 29 71 1 0 30 72 1 0 30 73 1 0 31 74 1 0 31 75 1 0 32 76 1 0 32 77 1 0 32 78 1 0 M END

Standard InCHIKey	PGIBJVOPLXHHGS-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C28H46O4/c1-3-5-7-9-11-13-15-19-23-31-27(29)25-21-17-18-22-26(25)28(30)32-24-20-16-14-12-10-8-6-4-2/h17-18,21-22H,3-16,19-20,23-24H2,1-2H3
SMILES	CCCCCCCCCCOC(=O)C1=CC=CC=C1C(=O)OCCCCCCCCCC

Calculated Properties

Physi-Chem Properties

Molecular Weight:	446.34	Volume:	506.266 ? Van der Waals volume.
Dense:	0.882	LogP:	8.513 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.495 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-7.614 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	22.0	Rigid Bonds:	8.0
TPSA:	52.6 ? 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:	0.149	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	1.986	Fsp³:	0.714
MCE-18:	7.0 ? 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:	0.643	Fluc inhibitor:	0.333 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.011 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.06 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.895	Promiscuous compounds:	0.139

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.089	MDCK Permeability:	-4.874
Pgp-inhibitor:	0.001	Pgp-substrate:	0.004
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):	0.289
20% Bioavailability (F20%):	0.963	30% Bioavailability (F30%):	0.987
50% Bioavailability (F50%):	0.693

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.019	MRP1:	0.998
Plasma Protein Binding (PPB):	100.83%	Volume Distribution (VD):	1.755
Fu:	0.531% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.433
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.238
BSEP inhibitor:	0.867

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	1.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.087
CYP2C9-inhibitor:	0.999	CYP2C9-substrate:	0.883
CYP2D6-inhibitor:	0.869	CYP2D6-substrate:	0.996
CYP3A4-inhibitor:	0.006	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.001	CYP2C8-inhibitor:	1.0
HLM stability:	0.544 ? 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):

5.019

Half-life (T1/2):

0.694

ADMET: Toxicity

hERG Blockers:	0.752	hERG Blockers (10um):	0.957
Human Hepatotoxicity (H-HT):	0.025	Drug-induced Liver Injury (DILI):	0.329
AMES Toxicity:	0.004	Rat Oral Acute Toxicity:	0.028
Maximum Recommended Daily Dose:	0.052	Skin Sensitization:	0.795
Carcinogencity:	0.673	Eye Corrosion:	0.492
Eye Irritation:	0.996	Respiratory Toxicity:	0.218
Drug-induced Neurotoxicity:	0.027	Ototoxicity:	0.044
Hematotoxicity:	0.001	Drug-induced Nephrotoxicity:	0.022
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.065
A549 Cytotoxicity:	0.325	Hek293 Cytotoxicity:	0.374
BCF:	-0.438 ? 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:	3.73 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.778 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	0.646 ? 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
NPO43258	Asystasia gangetica	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]

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
-	Rattus norvegicus	LD50	>	64.0	mL/kg	ToxVal
-	Rattus norvegicus	LD50	>	61824.0	mg/kg	ToxVal
-	Oryctolagus cuniculus	LD50	=	16228.8	mg/kg	ToxVal

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 NPC546126 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	20827
0.1-0.2	26991
0.2-0.3	1884
0.3-0.4	99
0.4-0.5	32
0.5-0.6	10
0.6-0.7	5
0.7-0.8	0
0.8-0.85	2
0.85-0.9	1
0.9-0.95	0
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC93084
1.0	High Similarity	NPC251854
1.0	High Similarity	NPC601045
0.871	High Similarity	NPC604461
0.8065	Intermediate Similarity	NPC10251
0.8	Intermediate Similarity	NPC603245
0.7714	Intermediate Similarity	NPC270699
0.7647	Intermediate Similarity	NPC78701
0.6341	Remote Similarity	NPC196246
0.6286	Remote Similarity	NPC608938
0.6098	Remote Similarity	NPC90522
0.6098	Remote Similarity	NPC604244
0.6	Remote Similarity	NPC607895
0.5938	Remote Similarity	NPC119271
0.5682	Remote Similarity	NPC295406
0.5682	Remote Similarity	NPC200422
0.5682	Remote Similarity	NPC289572
0.5682	Remote Similarity	NPC157478
0.561	Remote Similarity	NPC156892
0.55	Remote Similarity	NPC305912
0.55	Remote Similarity	NPC1082
0.5429	Remote Similarity	NPC214067
0.5278	Remote Similarity	NPC92754

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC546126 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	2945
0.1-0.2	5699
0.2-0.3	470
0.3-0.4	31
0.4-0.5	3
0.5-0.6	0
0.6-0.7	0
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8065	Intermediate Similarity	NPD2182	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