NPASS Compound

Structure

CID139047 OpenBabel06191715492D 31 32 0 0 1 0 0 0 0 0999 V2000 -9.7488 -0.1904 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.9736 -1.4152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9545 -2.7600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0567 -1.9836 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7355 0.4914 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.3346 -1.6046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4368 -0.8282 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5391 -0.0517 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.3005 -1.8634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6275 -2.3117 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4028 -1.0870 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7297 -1.5353 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5050 -0.3105 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8320 -0.7588 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.0076 -1.1563 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6616 -2.0529 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7638 -1.2765 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4641 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 20 1 0 0 0 0 2 20 1 0 0 0 0 3 21 1 0 0 0 0 4 22 1 0 0 0 0 5 23 1 0 0 0 0 6 24 1 0 0 0 0 7 25 1 0 0 0 0 9 12 1 0 0 0 0 9 13 1 0 0 0 0 10 14 1 0 0 0 0 10 15 1 0 0 0 0 11 16 1 0 0 0 0 11 18 1 0 0 0 0 12 20 2 0 0 0 0 13 21 1 0 0 0 0 14 21 2 0 0 0 0 15 22 1 0 0 0 0 16 22 2 0 0 0 0 17 19 1 0 0 0 0 17 26 1 0 0 0 0 18 29 1 0 0 0 0 19 29 1 0 0 0 0 23 24 1 0 0 0 0 23 27 2 0 0 0 0 24 28 2 0 0 0 0 25 26 2 0 0 0 0 25 27 1 0 0 0 0 26 28 1 0 0 0 0 27 30 1 0 0 0 0 28 31 1 0 0 0 0 29 8 1 6 0 0 0 29 31 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	208.07
Volume:	212.234
LogP:	1.069
LogD:	0.972
LogS:	-2.044
# Rotatable Bonds:	2
TPSA:	66.76
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	1
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.665
Synthetic Accessibility Score:	3.246
Fsp3:	0.182
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.945
MDCK Permeability:	6.180454420245951e-06
Pgp-inhibitor:	0.0
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.012
20% Bioavailability (F20%):	0.14
30% Bioavailability (F30%):	0.031

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.053
Plasma Protein Binding (PPB):	88.10321807861328%
Volume Distribution (VD):	0.761
Pgp-substrate:	13.4730863571167%

ADMET: Metabolism

CYP1A2-inhibitor:	0.937
CYP1A2-substrate:	0.549
CYP2C19-inhibitor:	0.031
CYP2C19-substrate:	0.238
CYP2C9-inhibitor:	0.045
CYP2C9-substrate:	0.693
CYP2D6-inhibitor:	0.02
CYP2D6-substrate:	0.273
CYP3A4-inhibitor:	0.029
CYP3A4-substrate:	0.219

ADMET: Excretion

Clearance (CL):	9.156
Half-life (T1/2):	0.934

ADMET: Toxicity

hERG Blockers:	0.011
Human Hepatotoxicity (H-HT):	0.108
Drug-inuced Liver Injury (DILI):	0.297
AMES Toxicity:	0.381
Rat Oral Acute Toxicity:	0.446
Maximum Recommended Daily Dose:	0.316
Skin Sensitization:	0.921
Carcinogencity:	0.666
Eye Corrosion:	0.536
Eye Irritation:	0.947
Respiratory Toxicity:	0.895

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC139047

Natural Product ID:	NPC139047
*Common Name:**	Alpha-Tocotrienol
IUPAC Name:	(2R)-2,5,7,8-tetramethyl-2-[(3E,7E)-4,8,12-trimethyltrideca-3,7,11-trienyl]-3,4-dihydrochromen-6-ol
Synonyms:	Alpha-Tocotrienol
Standard InCHIKey:	RZFHLOLGZPDCHJ-XZXLULOTSA-N
Standard InCHI:	InChI=1S/C29H44O2/c1-20(2)12-9-13-21(3)14-10-15-22(4)16-11-18-29(8)19-17-26-25(7)27(30)23(5)24(6)28(26)31-29/h12,14,16,30H,9-11,13,15,17-19H2,1-8H3/b21-14+,22-16+/t29-/m1/s1
SMILES:	CC(=CCC/C(=C/CC/C(=C/CC[C@]1(C)CCc2c(C)c(c(C)c(C)c2O1)O)/C)/C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL120276
PubChem CID:	5282347
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001534] Quinone and hydroquinone lipids [CHEMONTID:0001546] Vitamin E compounds [CHEMONTID:0002092] Tocotrienols

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	blood	n.a.	PMID[9949311]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	blood	n.a.	PMID[9892086]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	cerebrospinal fluid	n.a.	PMID[9870205]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	urine	n.a.	PMID[9869364]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	urine	n.a.	PMID[9869358]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	blood	n.a.	PMID[9861496]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	cerebrospinal fluid	n.a.	PMID[9861478]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	urine	n.a.	PMID[9857238]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	urine	n.a.	PMID[9851755]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	cerebrospinal fluid	n.a.	PMID[9818465]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
NPO28907	NPC139047	n.a.	n.a	11.26 ± 1.21	n.a.	n.a.	n.a.	PMID[35282307]
NPO5973	NPC139047	n.a.	n.a	21.58 ±4.51	n.a.	n.a.	n.a.	PMID[35282307]
NPO7252	NPC139047	n.a.	n.a	13.53 ±2.53	n.a.	n.a.	n.a.	PMID[35282307]
NPO7298.3	NPC139047	n.a.	Seeds	0.36±0.07	n.a.	n.a.	mg/kg	PMID[27023318]
NPO7298.3	NPC139047	n.a.	Seeds	1.54±0.28	n.a.	n.a.	mg/kg	PMID[27023318]

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☑ 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
IC50	6
Others	17

Activity Type	# Activity
Cell Line	5
NON-MOLECULAR	1
Organism	15
Subcellular	1
Tissue	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Stability	=	7.0	%	PMID[554019]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Stability	=	5.0	%	PMID[554019]
NPT433	Subcellular	Liver microsomes	Homo sapiens	Stability	=	15.0	%	PMID[554019]
NPT625	Tissue	Liver	Mus musculus	Stability	=	15.0	%	PMID[554019]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	5000.0	nM	PMID[554018]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	>	20000.0	nM	PMID[554017]
NPT82	Cell Line	MDA-MB-231	Homo sapiens	IC50	>	10000.0	nM	PMID[554017]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	=	1603245.39	nM	PMID[554017]
NPT65	Cell Line	HepG2	Homo sapiens	Inhibition	=	32.0	%	PMID[554015]
NPT65	Cell Line	HepG2	Homo sapiens	Inhibition	=	15.0	%	PMID[554015]

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☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC139047 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	346
0.1-0.2	1804
0.2-0.3	4523
0.3-0.4	13345
0.4-0.5	5694
0.5-0.6	8733
0.6-0.7	6972
0.7-0.8	1165
0.8-0.85	81
0.85-0.9	20
0.9-0.95	7
0.95-1	7

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Similarity Score	Similarity Level	Natural Product ID
0.9735	High Similarity	NPC45663
0.9649	High Similarity	NPC48623
0.9649	High Similarity	NPC168707
0.964	High Similarity	NPC242580
0.964	High Similarity	NPC236070

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Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC139047 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	345
0.1-0.2	1078
0.2-0.3	1751
0.3-0.4	2842
0.4-0.5	1595
0.5-0.6	1077
0.6-0.7	399
0.7-0.8	53
0.8-0.85	5
0.85-0.9	1
0.9-0.95	2
0.95-1	2

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.964	High Similarity	NPD7340	Approved
0.9545	High Similarity	NPD1398	Phase 1
0.9035	High Similarity	NPD6671	Approved
0.8917	High Similarity	NPD6696	Suspended
0.8718	High Similarity	NPD7644	Approved

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Bioactivity similarity: Similar Natural Products in NPASS

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