NPASS Compound

Structure

CID129165 OpenBabel06191715482D 30 33 0 0 1 0 0 0 0 0999 V2000 -2.6329 5.3937 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9993 6.3858 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5418 5.6986 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8089 3.7142 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 1.0114 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5364 2.4740 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2057 4.6047 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3514 3.0269 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7482 3.9175 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8448 -1.4642 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6902 -0.9764 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2254 1.4621 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2251 0.4868 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6893 0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8456 1.4631 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8445 0.4882 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6910 1.9508 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8451 -1.4637 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5721 5.5969 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3817 2.9253 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.1753 4.7064 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0003 -0.9759 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6895 -0.9755 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6905 -0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3815 1.9503 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5358 0.4872 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8454 0.4877 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5361 1.4626 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5557 -1.4752 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 7 1 0 0 0 0 2 19 1 0 0 0 0 3 19 1 0 0 0 0 8 9 2 0 0 0 0 8 20 1 0 0 0 0 9 21 1 0 0 0 0 10 11 1 0 0 0 0 10 22 1 0 0 0 0 11 24 2 0 0 0 0 12 13 1 0 0 0 0 12 25 1 0 0 0 0 13 26 1 0 0 0 0 14 16 1 0 0 0 0 14 23 1 0 0 0 0 15 17 1 0 0 0 0 15 27 1 0 0 0 0 16 28 1 0 0 0 0 17 29 1 0 0 0 0 18 22 1 0 0 0 0 18 23 1 0 0 0 0 19 21 1 0 0 0 0 20 4 1 1 0 0 0 20 25 1 0 0 0 0 21 7 1 6 0 0 0 22 28 1 6 0 0 0 23 30 1 6 0 0 0 24 26 1 0 0 0 0 24 27 1 0 0 0 0 25 29 1 6 0 0 0 26 29 1 6 0 0 0 27 28 1 6 0 0 0 28 5 1 6 0 0 0 29 6 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	412.37
Volume:	479.432
LogP:	7.492
LogD:	6.276
LogS:	-6.895
# Rotatable Bonds:	5
TPSA:	20.23
# H-Bond Aceptor:	1
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	1

MedChem Properties

QED Drug-Likeness Score:	0.457
Synthetic Accessibility Score:	4.733
Fsp3:	0.862
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.593
MDCK Permeability:	6.44167885184288e-05
Pgp-inhibitor:	0.228
Pgp-substrate:	0.873
Human Intestinal Absorption (HIA):	0.022
20% Bioavailability (F20%):	0.996
30% Bioavailability (F30%):	0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.007
Plasma Protein Binding (PPB):	88.83643341064453%
Volume Distribution (VD):	1.31
Pgp-substrate:	0.9422650337219238%

ADMET: Metabolism

CYP1A2-inhibitor:	0.097
CYP1A2-substrate:	0.342
CYP2C19-inhibitor:	0.153
CYP2C19-substrate:	0.903
CYP2C9-inhibitor:	0.344
CYP2C9-substrate:	0.056
CYP2D6-inhibitor:	0.05
CYP2D6-substrate:	0.537
CYP3A4-inhibitor:	0.889
CYP3A4-substrate:	0.722

ADMET: Excretion

Clearance (CL):	4.308
Half-life (T1/2):	0.045

ADMET: Toxicity

hERG Blockers:	0.059
Human Hepatotoxicity (H-HT):	0.149
Drug-inuced Liver Injury (DILI):	0.023
AMES Toxicity:	0.002
Rat Oral Acute Toxicity:	0.315
Maximum Recommended Daily Dose:	0.979
Skin Sensitization:	0.459
Carcinogencity:	0.015
Eye Corrosion:	0.12
Eye Irritation:	0.13
Respiratory Toxicity:	0.691

Download Data

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

Natural Product: NPC129165

Natural Product ID:	NPC129165
*Common Name:**	Alpha-Spinasterol
IUPAC Name:	(3S,5S,9R,10S,13R,14R,17R)-17-[(E,2R,5S)-5-ethyl-6-methylhept-3-en-2-yl]-10,13-dimethyl-2,3,4,5,6,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-ol
Synonyms:	Alpha-Spinasterol
Standard InCHIKey:	JZVFJDZBLUFKCA-FXIAWGAOSA-N
Standard InCHI:	InChI=1S/C29H48O/c1-7-21(19(2)3)9-8-20(4)25-12-13-26-24-11-10-22-18-23(30)14-16-28(22,5)27(24)15-17-29(25,26)6/h8-9,11,19-23,25-27,30H,7,10,12-18H2,1-6H3/b9-8+/t20-,21-,22+,23+,25-,26+,27+,28+,29-/m1/s1
SMILES:	CC[C@@H](C(C)C)/C=C/[C@H]([C@H]1CC[C@@H]2[C@]1(C)CC[C@H]1C2=CC[C@@H]2[C@]1(C)CC[C@@H](C2)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL487783
PubChem CID:	5281331
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0002031] Stigmastanes and derivatives

*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
NPO23108	Pinus flexilis	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9834165]
NPO11196	Impatiens balsamina	Species	Balsaminaceae	Eukaryota	Pericarp	n.a.	n.a.	PMID[9748380]
NPO14582	Spinacia oleracea	Species	Chenopodiaceae	Eukaryota	n.a.	leaf	n.a.	PMID[9433811]
NPO14582	Spinacia oleracea	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6821187]
NPO25206	Cucurbita moschata	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6821187]
NPO20454	Bidens pilosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[469551]
NPO13645	Armoracia rusticana	Species	Brassicaceae	Eukaryota	Roots	n.a.	n.a.	PMID[31625742]
NPO25206	Cucurbita moschata	Species	Cucurbitaceae	Eukaryota	n.a.	The ‘Dolina Mogilnicy’ Organic Farming Products Cooperative (Wolkowo, Poland)	2016-Oct	PMID[31416184]
NPO11196	Impatiens balsamina	Species	Balsaminaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28165740]
NPO25206	Cucurbita moschata	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26477735]

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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
No data available in table

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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	3
Others	2

Activity Type	# Activity
Cell Line	1
Individual Protein	2
Others	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT461	Cell Line	PANC-1	Homo sapiens	PC50	=	58.1	uM	PMID[480221]
NPT35	Others	n.a.		IC50	>	50000.0	nM	PMID[480220]
NPT68	Individual Protein	Aldose reductase	Rattus norvegicus	IC50	>	30000.0	nM	PMID[480220]
NPT270	Individual Protein	Nitric oxide synthase, inducible	Mus musculus	IC50	>	50000.0	nM	PMID[480219]
NPT2	Others	Unspecified		Inhibition	=	8.7	%	PMID[480219]

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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 NPC129165 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	155
0.1-0.2	1357
0.2-0.3	7761
0.3-0.4	15608
0.4-0.5	6932
0.5-0.6	5610
0.6-0.7	3761
0.7-0.8	1093
0.8-0.85	247
0.85-0.9	99
0.9-0.95	54
0.95-1	20

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC134330
0.9857	High Similarity	NPC141071
0.9857	High Similarity	NPC471723
0.9857	High Similarity	NPC257347
0.9718	High Similarity	NPC189883

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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 NPC129165 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	162
0.1-0.2	1577
0.2-0.3	4487
0.3-0.4	2071
0.4-0.5	421
0.5-0.6	165
0.6-0.7	154
0.7-0.8	84
0.8-0.85	16
0.85-0.9	10
0.9-0.95	1
0.95-1	2

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9577	High Similarity	NPD7339	Approved
0.9577	High Similarity	NPD6942	Approved
0.8947	High Similarity	NPD7525	Registered
0.8919	High Similarity	NPD3701	Clinical (unspecified phase)
0.8649	High Similarity	NPD4784	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