NPASS Compound

Natural Product: NPC55903

Natural Product ID	NPC55903
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	3-Tert-Butylphenol
IUPAC Name	3-tert-butylphenol
Synonyms	3-Tert-Butylphenol
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL224899
PubChem CID	11450
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0002279] Benzene and substituted derivatives [CHEMONTID:0002811] Phenylpropanes

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 25 25 0 0 0 0 0 0 0 0999 V2000 -1.6924 1.1733 0.7323 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2382 -0.0300 -0.0624 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8343 -1.2796 0.5561 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7070 0.1738 -1.4875 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2441 -0.1600 -0.0529 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8149 -1.2126 -0.7366 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1855 -1.3072 -0.7104 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9650 -0.3886 -0.0288 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3917 0.6640 0.6547 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0073 0.7576 0.6268 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1616 1.6015 1.3485 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4242 1.0799 1.8004 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2435 2.0938 0.3180 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8039 1.1843 0.6873 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8638 -1.4887 0.1510 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1815 -2.1706 0.4148 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9690 -1.0657 1.6523 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7030 -0.7695 -2.0692 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7548 0.5471 -1.5204 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0371 0.9455 -1.9415 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1773 -1.9159 -1.2611 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6533 -2.1276 -1.2417 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0449 -0.4516 -0.0002 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5888 1.5986 1.1755 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2182 2.5481 0.9950 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 4 1 0 2 5 1 0 5 6 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 2 0 9 11 1 0 10 5 1 0 1 12 1 0 1 13 1 0 1 14 1 0 3 15 1 0 3 16 1 0 3 17 1 0 4 18 1 0 4 19 1 0 4 20 1 0 6 21 1 0 7 22 1 0 8 23 1 0 10 24 1 0 11 25 1 0 M END

Standard InCHIKey	CYEKUDPFXBLGHH-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C10H14O/c1-10(2,3)8-5-4-6-9(11)7-8/h4-7,11H,1-3H3
SMILES	CC(C)(C)c1cccc(c1)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	150.1	Volume:	173.841 ? Van der Waals volume.
Dense:	0.863	LogP:	3.282 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.022 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.361 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	1.0	Rigid Bonds:	6.0
TPSA:	20.23 ? Topological Polar Surface Area.	H-Bond Acceptor:	1.0
H-Bond Donor:	1.0	Rings:	1.0
Heavy Atoms:	1.0

MedChem Properties

QED Drug-Likeness Score:	0.603	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	1.736	Fsp³:	0.4
MCE-18:	8.0 ? 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:	Rejected
Golden Triangle Rule:	Accepted	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.042	Fluc inhibitor:	0.187 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.002 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.0 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.997	Promiscuous compounds:	0.12

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.731	MDCK Permeability:	-4.67
Pgp-inhibitor:	0.268	Pgp-substrate:	0.499
PAMPA:	0.278 ? 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):	0.389
20% Bioavailability (F20%):	0.85	30% Bioavailability (F30%):	0.952
50% Bioavailability (F50%):	0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.016	MRP1:	0.289
Plasma Protein Binding (PPB):	74.567%	Volume Distribution (VD):	0.319
Fu:	26.619% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.979
OATP1B3 inhibitor:	0.975	BCRP inhibitor:	0.114
BSEP inhibitor:	0.515

ADMET: Metabolism

CYP1A2-inhibitor:	0.001	CYP1A2-substrate:	0.587
CYP2C19-inhibitor:	0.018	CYP2C19-substrate:	0.083
CYP2C9-inhibitor:	0.132	CYP2C9-substrate:	0.148
CYP2D6-inhibitor:	0.611	CYP2D6-substrate:	0.019
CYP3A4-inhibitor:	0.447	CYP3A4-substrate:	0.875
CYP2B6-substrate:	0.004	CYP2C8-inhibitor:	0.992
HLM stability:	0.978 ? 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):

10.116

Half-life (T1/2):

0.669

ADMET: Toxicity

hERG Blockers:	0.177	hERG Blockers (10um):	0.764
Human Hepatotoxicity (H-HT):	0.357	Drug-induced Liver Injury (DILI):	0.145
AMES Toxicity:	0.22	Rat Oral Acute Toxicity:	0.337
Maximum Recommended Daily Dose:	0.51	Skin Sensitization:	0.707
Carcinogencity:	0.442	Eye Corrosion:	0.968
Eye Irritation:	0.997	Respiratory Toxicity:	0.643
Drug-induced Neurotoxicity:	0.646	Ototoxicity:	0.286
Hematotoxicity:	0.178	Drug-induced Nephrotoxicity:	0.162
Genotoxicity:	0.057	RPMI-8226 Immunitoxicity:	0.039
A549 Cytotoxicity:	0.34	Hek293 Cytotoxicity:	0.417
BCF:	1.733 ? 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:	3.769 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.76 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.397 ? 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
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	Flowers	n.a.	n.a.	DOI[10.1016/j.foodchem.2009.03.042]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	Flowers	n.a.	n.a.	DOI[10.3136/fstr.15.499]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	Flowers	n.a.	n.a.	DOI[10.5897/AJB10.140]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	Flowers	n.a.	n.a.	DOI[10.5897/AJB2010.000-3252]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	Flowers	Tongxiang, China	n.a.	PMID[24621197]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	Flowers	n.a.	n.a.	PMID[28248102]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	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
Potency	5
log(1/ID50)	1
Activity	1

Activity Type	# Activity
Cell line	2
Others	5

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
NPT137	Cell line	L1210	Mus musculus	log(1/ID50)	=	3.88	n.a.	PMID[16279782]
NPT137	Cell line	L1210	Mus musculus	Activity	<	15.0	%	PMID[16279782]
NPT2	Others	Unspecified	n.a.	Potency	n.a.	48557.7	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	61130.6	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	4896.6	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	76958.8	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	30637.9	nM	PubChem BioAssay data set

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 NPC55903 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	28103
0.1-0.2	18504
0.2-0.3	2998
0.3-0.4	205
0.4-0.5	35
0.5-0.6	10
0.6-0.7	1
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	Natural Product ID
0.6	Remote Similarity	NPC27974
0.5556	Remote Similarity	NPC34715
0.5417	Remote Similarity	NPC150837
0.5385	Remote Similarity	NPC180862
0.5385	Remote Similarity	NPC312304
0.5385	Remote Similarity	NPC600256
0.5357	Remote Similarity	NPC602862
0.52	Remote Similarity	NPC603378
0.5185	Remote Similarity	NPC163734
0.5185	Remote Similarity	NPC599916
0.5172	Remote Similarity	NPC606762

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC55903 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4821
0.1-0.2	3987
0.2-0.3	291
0.3-0.4	39
0.4-0.5	11
0.5-0.6	1
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
0.5385	Remote Similarity	NPD289	Clinical (unspecified phase)

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