NPASS Compound

Natural Product: NPC76938

Natural Product ID	NPC76938
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	3-(10-Phenyldecyl)Phenol
IUPAC Name	3-(10-phenyldecyl)phenol
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL477541
PubChem CID	44575633
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000134] Phenols [CHEMONTID:0004647] 1-hydroxy-4-unsubstituted benzenoids

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 53 54 0 0 0 0 0 0 0 0999 V2000 6.4489 0.8683 -3.2938 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5469 1.0940 -2.2597 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5109 1.9694 -2.4493 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6302 2.1853 -1.4296 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7864 1.5235 -0.2171 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8342 0.6327 -0.0136 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7012 0.4440 -1.0703 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0328 -0.0906 1.2644 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3095 -1.4187 1.2895 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8234 -1.1529 1.1035 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0388 -2.4218 1.1171 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5761 -2.1382 0.9229 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0482 -1.2612 2.0098 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4292 -0.9665 1.8402 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7299 -0.2678 0.5442 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2292 -0.0328 0.4989 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6413 0.6716 -0.7775 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1298 0.8414 -0.6969 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6983 1.9640 -0.1312 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0612 2.1411 -0.0465 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8731 1.1483 -0.5514 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3626 0.0074 -1.1265 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9913 -0.1212 -1.1867 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4221 1.1029 -3.2293 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3939 2.4811 -3.3932 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7974 2.8708 -1.5413 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0963 1.6920 0.5834 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5257 -0.2495 -0.9268 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6910 0.5516 2.1031 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1232 -0.2296 1.3972 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4938 -1.8748 2.2757 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7375 -2.0457 0.5069 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5328 -0.5111 1.9653 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6409 -0.6280 0.1620 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1372 -2.9683 2.0852 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3544 -3.0921 0.2916 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0267 -3.1175 0.9758 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3786 -1.6711 -0.0810 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1429 -1.8183 2.9700 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5429 -0.2971 2.1261 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0636 -1.8536 1.9164 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7077 -0.2771 2.6628 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5084 -0.9389 -0.3317 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1609 0.6506 0.3886 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4574 0.6694 1.3349 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7239 -1.0039 0.5917 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3611 0.0146 -1.6260 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1188 1.6298 -0.9107 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0109 2.7260 0.2566 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4797 3.0369 0.4051 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.9418 1.2556 -0.5009 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.0650 -0.7232 -1.4985 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5796 -1.0006 -1.6299 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 3 4 1 0 4 5 2 0 5 6 1 0 6 7 2 0 6 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 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 2 0 19 20 1 0 20 21 2 0 21 22 1 0 22 23 2 0 7 2 1 0 23 18 1 0 1 24 1 0 3 25 1 0 4 26 1 0 5 27 1 0 7 28 1 0 8 29 1 0 8 30 1 0 9 31 1 0 9 32 1 0 10 33 1 0 10 34 1 0 11 35 1 0 11 36 1 0 12 37 1 0 12 38 1 0 13 39 1 0 13 40 1 0 14 41 1 0 14 42 1 0 15 43 1 0 15 44 1 0 16 45 1 0 16 46 1 0 17 47 1 0 17 48 1 0 19 49 1 0 20 50 1 0 21 51 1 0 22 52 1 0 23 53 1 0 M END

Standard InCHIKey	RZNASAROZKRKEJ-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C22H30O/c23-22-18-12-17-21(19-22)16-9-6-4-2-1-3-5-8-13-20-14-10-7-11-15-20/h7,10-12,14-15,17-19,23H,1-6,8-9,13,16H2
SMILES	Oc1cccc(c1)CCCCCCCCCCc1ccccc1

Calculated Properties

Physi-Chem Properties

Molecular Weight:	310.23	Volume:	364.927 ? Van der Waals volume.
Dense:	0.85	LogP:	6.093 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.9 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.446 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	11.0	Rigid Bonds:	12.0
TPSA:	20.23 ? Topological Polar Surface Area.	H-Bond Acceptor:	1.0
H-Bond Donor:	1.0	Rings:	2.0
Heavy Atoms:	1.0

MedChem Properties

QED Drug-Likeness Score:	0.483	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	1.723	Fsp³:	0.455
MCE-18:	9.0 ? 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:	0.856	Fluc inhibitor:	0.344 ? 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:	0.162 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.868	Promiscuous compounds:	0.092

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.087	MDCK Permeability:	-4.767
Pgp-inhibitor:	0.969	Pgp-substrate:	0.026
PAMPA:	0.01 ? 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):	0.074
20% Bioavailability (F20%):	0.795	30% Bioavailability (F30%):	0.987
50% Bioavailability (F50%):	0.975

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.213	MRP1:	0.274
Plasma Protein Binding (PPB):	100.5%	Volume Distribution (VD):	1.111
Fu:	0.103% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.964
OATP1B3 inhibitor:	0.99	BCRP inhibitor:	0.768
BSEP inhibitor:	0.999

ADMET: Metabolism

CYP1A2-inhibitor:	0.342	CYP1A2-substrate:	0.987
CYP2C19-inhibitor:	0.168	CYP2C19-substrate:	0.775
CYP2C9-inhibitor:	0.919	CYP2C9-substrate:	0.911
CYP2D6-inhibitor:	0.84	CYP2D6-substrate:	0.343
CYP3A4-inhibitor:	0.275	CYP3A4-substrate:	0.998
CYP2B6-substrate:	0.783	CYP2C8-inhibitor:	0.98
HLM stability:	0.91 ? 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):

4.771

Half-life (T1/2):

0.338

ADMET: Toxicity

hERG Blockers:	0.822	hERG Blockers (10um):	0.933
Human Hepatotoxicity (H-HT):	0.565	Drug-induced Liver Injury (DILI):	0.129
AMES Toxicity:	0.161	Rat Oral Acute Toxicity:	0.17
Maximum Recommended Daily Dose:	0.366	Skin Sensitization:	0.973
Carcinogencity:	0.14	Eye Corrosion:	0.747
Eye Irritation:	0.993	Respiratory Toxicity:	0.79
Drug-induced Neurotoxicity:	0.3	Ototoxicity:	0.173
Hematotoxicity:	0.101	Drug-induced Nephrotoxicity:	0.31
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.051
A549 Cytotoxicity:	0.807	Hek293 Cytotoxicity:	0.725
BCF:	1.743 ? 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:	5.405 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.289 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	6.441 ? 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
NPO11253	Knema glomerata	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8201311]
NPO11253	Knema glomerata	Species	Myristicaceae	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

Activity Type	# Activity
T/C	1
ED50	3

Activity Type	# Activity
Cell line	3
Organism	1

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
NPT81	Cell line	A549	Homo sapiens	ED50	=	35.01	ug ml-1	PMID[25630222]
NPT83	Cell line	MCF7	Homo sapiens	ED50	=	7.76	ug ml-1	PMID[20843939]
NPT139	Cell line	HT-29	Homo sapiens	ED50	=	28.59	ug ml-1	PMID[18157122]
NPT141	Organism	Agrobacterium tumefaciens	Agrobacterium tumefaciens	T/C	=	54.0	%	PMID[8201311]

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
-	Artemia	LC50	=	0.45	ug.mL-1	PMID[26465972]

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 NPC76938 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	29421
0.1-0.2	17558
0.2-0.3	2488
0.3-0.4	271
0.4-0.5	72
0.5-0.6	20
0.6-0.7	9
0.7-0.8	0
0.8-0.85	3
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC32714
0.8182	Intermediate Similarity	NPC3358
0.8182	Intermediate Similarity	NPC306884
0.8182	Intermediate Similarity	NPC603092
0.7647	Intermediate Similarity	NPC241891
0.7647	Intermediate Similarity	NPC134829
0.725	Intermediate Similarity	NPC294741
0.7105	Intermediate Similarity	NPC483454
0.7105	Intermediate Similarity	NPC162314
0.697	Remote Similarity	NPC610566
0.6923	Remote Similarity	NPC94139
0.6923	Remote Similarity	NPC147284
0.6429	Remote Similarity	NPC210497
0.6429	Remote Similarity	NPC192
0.641	Remote Similarity	NPC487734
0.6364	Remote Similarity	NPC606762
0.625	Remote Similarity	NPC487735
0.6061	Remote Similarity	NPC210849
0.5882	Remote Similarity	NPC246056
0.5882	Remote Similarity	NPC609251
0.5833	Remote Similarity	NPC123273
0.5833	Remote Similarity	NPC318325
0.5778	Remote Similarity	NPC259942
0.5778	Remote Similarity	NPC92624
0.5625	Remote Similarity	NPC27974
0.5556	Remote Similarity	NPC606008
0.55	Remote Similarity	NPC474839
0.5455	Remote Similarity	NPC188814
0.5455	Remote Similarity	NPC599916
0.5455	Remote Similarity	NPC608141
0.5405	Remote Similarity	NPC294186
0.5405	Remote Similarity	NPC147310
0.5405	Remote Similarity	NPC137415
0.5405	Remote Similarity	NPC166313
0.5405	Remote Similarity	NPC192032
0.5405	Remote Similarity	NPC24407
0.5405	Remote Similarity	NPC11280
0.5278	Remote Similarity	NPC242240

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC76938 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5056
0.1-0.2	3674
0.2-0.3	381
0.3-0.4	35
0.4-0.5	4
0.5-0.6	0
0.6-0.7	0
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
		NPD

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