NPASS Compound

Structure

NPC232512 OpenBabel06302216212D 33 37 0 0 1 0 0 0 0 0999 V2000 -0.0026 2.9813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8733 2.4776 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8724 1.4718 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0008 0.9696 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8384 1.4551 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6786 0.9711 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5492 1.4748 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6794 0.0015 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8401 -0.4841 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8404 -1.4541 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5204 -1.4536 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5207 -2.4536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3612 -1.9387 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2016 -1.4531 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2013 -0.4831 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3606 0.0019 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5201 -0.4836 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5199 0.5164 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0423 -1.9382 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.0421 -0.9382 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8822 -1.4526 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7224 -1.9377 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7226 -2.9083 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.8828 -3.3938 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8830 -4.3938 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7488 -3.8938 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0426 -2.9088 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2022 -3.3943 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3614 -2.9093 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5887 -3.4083 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 0.8376 2.4610 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7448 2.9798 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 33 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 4 31 1 0 0 0 0 5 6 1 0 0 0 0 5 32 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 8 17 1 0 0 0 0 9 10 1 0 0 0 0 9 31 1 0 0 0 0 10 11 1 0 0 0 0 11 17 1 0 0 0 0 11 12 1 0 0 0 0 11 13 1 0 0 0 0 13 29 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 14 19 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 19 27 1 0 0 0 0 19 20 1 0 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 23 30 1 0 0 0 0 24 25 1 0 0 0 0 24 26 1 0 0 0 0 24 27 1 0 0 0 0 27 28 1 1 0 0 0 28 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	456.36
Volume:	505.751
LogP:	5.748
LogD:	4.411
LogS:	-5.62
# Rotatable Bonds:	1
TPSA:	49.69
# H-Bond Aceptor:	3
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.447
Synthetic Accessibility Score:	5.263
Fsp3:	0.867
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.778
MDCK Permeability:	1.2803435311070643e-05
Pgp-inhibitor:	0.983
Pgp-substrate:	0.008
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.913
30% Bioavailability (F30%):	0.92

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.023
Plasma Protein Binding (PPB):	94.19660186767578%
Volume Distribution (VD):	2.059
Pgp-substrate:	2.3028862476348877%

ADMET: Metabolism

CYP1A2-inhibitor:	0.03
CYP1A2-substrate:	0.519
CYP2C19-inhibitor:	0.19
CYP2C19-substrate:	0.939
CYP2C9-inhibitor:	0.237
CYP2C9-substrate:	0.447
CYP2D6-inhibitor:	0.02
CYP2D6-substrate:	0.154
CYP3A4-inhibitor:	0.618
CYP3A4-substrate:	0.598

ADMET: Excretion

Clearance (CL):	6.045
Half-life (T1/2):	0.048

ADMET: Toxicity

hERG Blockers:	0.068
Human Hepatotoxicity (H-HT):	0.414
Drug-inuced Liver Injury (DILI):	0.042
AMES Toxicity:	0.013
Rat Oral Acute Toxicity:	0.334
Maximum Recommended Daily Dose:	0.875
Skin Sensitization:	0.217
Carcinogencity:	0.057
Eye Corrosion:	0.081
Eye Irritation:	0.099
Respiratory Toxicity:	0.932

Download Data

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

Natural Product: NPC232512

Natural Product ID:	NPC232512
*Common Name:**	VJTZKDXTRQJBLI-FPXHUTALSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	VJTZKDXTRQJBLI-FPXHUTALSA-N
Standard InCHI:	InChI=1S/C30H48O3/c1-17(2)15-21-26(32)18(3)25-22(33-21)16-30(8)20-9-10-23-27(4,5)24(31)12-13-28(23,6)19(20)11-14-29(25,30)7/h15,18,21-26,31-32H,9-14,16H2,1-8H3/t18-,21-,22+,23+,24+,25-,26+,28+,29+,30-/m0/s1
SMILES:	CC(=C[C@H]1[C@@H]([C@@H](C)[C@H]2[C@@H](C[C@@]3(C)C4=C(CC[C@]23C)[C@@]2(C)CC[C@H](C(C)(C)[C@H]2CC4)O)O1)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	n.a.	small food enterprises (Zvijezda d.d., Zagreb, Croatia)	n.a.	DOI[10.1002/EJLT.200900231]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1007/s11746-997-0093-1]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16660462]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	flower petals	n.a.	n.a.	PMID[17480100]
NPO12687	Planktothrix rubescens	Species	Microcoleaceae	Bacteria	n.a.	n.a.	n.a.	PMID[17935298]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22537213]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	Flowers	n.a.	n.a.	PMID[6361218]
NPO18949	Erythrina eriotricha	Species	Fabaceae	Eukaryota	n.a.	root	n.a.	PMID[8590641]
NPO26686	Eleutherobia aurea	Species	Parasphaerascleridae	Eukaryota	n.a.	n.a.	n.a.	PMID[9322360]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	Flower	n.a.	n.a.	Database[FooDB]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	Flower Essent. Oil	n.a.	n.a.	Database[FooDB]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	Oil	n.a.	n.a.	Database[FooDB]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	Pericarp	n.a.	n.a.	Database[FooDB]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	Pollen Or Spore	n.a.	n.a.	Database[FooDB]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	Shoot	n.a.	n.a.	Database[FooDB]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15187	Aloe marlothii	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13846	Crinodendron hookerianum	Species	Elaeocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18139	Potentilla anserina	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18139	Potentilla anserina	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15187	Aloe marlothii	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13846	Crinodendron hookerianum	Species	Elaeocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18139	Potentilla anserina	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15187	Aloe marlothii	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12687	Planktothrix rubescens	Species	Microcoleaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO26686	Eleutherobia aurea	Species	Parasphaerascleridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18139	Potentilla anserina	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13846	Crinodendron hookerianum	Species	Elaeocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15187	Aloe marlothii	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18949	Erythrina eriotricha	Species	Fabaceae	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	NP ID	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

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ 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 NPC232512 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	186
0.1-0.2	1430
0.2-0.3	4928
0.3-0.4	13727
0.4-0.5	9628
0.5-0.6	6242
0.6-0.7	4918
0.7-0.8	1483
0.8-0.85	127
0.85-0.9	27
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID

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 NPC232512 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	180
0.1-0.2	1592
0.2-0.3	4110
0.3-0.4	2254
0.4-0.5	576
0.5-0.6	194
0.6-0.7	181
0.7-0.8	62
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

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