NPASS Compound

Structure

NPC219918 OpenBabel06302216222D 22 24 0 0 1 0 0 0 0 0999 V2000 -0.8660 -0.5000 0.0000 C 0 0 2 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 -1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0981 -2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0981 -2.3660 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 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 O 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 -0.0000 1.0000 0.0000 C 0 0 2 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 1.3660 2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3660 2.3660 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 2.5981 1.5000 0.0000 O 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 0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 9 1 0 0 0 0 1 21 1 0 0 0 0 1 2 1 6 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 6 0 0 0 4 6 1 0 0 0 0 4 8 1 0 0 0 0 6 7 2 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 10 12 1 0 0 0 0 13 12 1 6 0 0 0 13 21 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 14 16 1 0 0 0 0 14 17 1 0 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	300.21
Volume:	335.841
LogP:	3.528
LogD:	3.645
LogS:	-4.177
# Rotatable Bonds:	1
TPSA:	34.14
# H-Bond Aceptor:	2
# H-Bond Donor:	0
# Rings:	3
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.668
Synthetic Accessibility Score:	4.428
Fsp3:	0.7
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.613
MDCK Permeability:	2.136762486770749e-05
Pgp-inhibitor:	0.983
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.057
30% Bioavailability (F30%):	0.031

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.775
Plasma Protein Binding (PPB):	78.57231903076172%
Volume Distribution (VD):	0.574
Pgp-substrate:	19.843387603759766%

ADMET: Metabolism

CYP1A2-inhibitor:	0.045
CYP1A2-substrate:	0.702
CYP2C19-inhibitor:	0.363
CYP2C19-substrate:	0.761
CYP2C9-inhibitor:	0.23
CYP2C9-substrate:	0.1
CYP2D6-inhibitor:	0.077
CYP2D6-substrate:	0.054
CYP3A4-inhibitor:	0.933
CYP3A4-substrate:	0.602

ADMET: Excretion

Clearance (CL):	7.203
Half-life (T1/2):	0.444

ADMET: Toxicity

hERG Blockers:	0.012
Human Hepatotoxicity (H-HT):	0.466
Drug-inuced Liver Injury (DILI):	0.042
AMES Toxicity:	0.032
Rat Oral Acute Toxicity:	0.944
Maximum Recommended Daily Dose:	0.964
Skin Sensitization:	0.797
Carcinogencity:	0.916
Eye Corrosion:	0.164
Eye Irritation:	0.5
Respiratory Toxicity:	0.983

Download Data

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

Natural Product: NPC219918

Natural Product ID:	NPC219918
*Common Name:**	IOCKHKBAJGJHFL-FCNFAXOHSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	IOCKHKBAJGJHFL-FCNFAXOHSA-N
Standard InCHI:	InChI=1S/C20H28O2/c1-6-19(4)9-7-14-13(12-19)15(21)11-16-18(2,3)17(22)8-10-20(14,16)5/h6,12,14,16H,1,7-11H2,2-5H3/t14-,16-,19-,20+/m1/s1
SMILES:	C=C[C@]1(C)CC[C@@H]2C(=C1)C(=O)C[C@@H]1C(C)(C)C(=O)CC[C@@]21C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	176495
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids

*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
NPO25302	Viola philippica	Species	Violaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[14519932]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15516765]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20973550]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23700450]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	leaf	n.a.	PMID[23849114]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24310066]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	seed	n.a.	PMID[25433632]
NPO28287	Magnaporthe oryzae	Species	Magnaporthaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26258762]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	seed	n.a.	PMID[26860358]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.		PMID[31861466]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	Petiole	n.a.	n.a.	Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	Protoplast	n.a.	n.a.	Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	Shoot	n.a.	n.a.	Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	seed	n.a.	Database[MetaboLights]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25302	Viola philippica	Species	Violaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO25302	Viola philippica	Species	Violaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16391	Protea neriifolia	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO318	Glycosmis trichanthera	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4567	Senecio chrysocoma	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6773	Bryoria implexa	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25302	Viola philippica	Species	Violaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28287	Magnaporthe oryzae	Species	Magnaporthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3641	Polyporus tuberaster	Species	Polyporaceae	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
NPO8541	NPC219918	Other	Leaf	0.54	0.54	0.54	mg/100g	Database [DUKE]

☑ 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 NPC219918 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	242
0.1-0.2	1958
0.2-0.3	9933
0.3-0.4	15807
0.4-0.5	7891
0.5-0.6	4828
0.6-0.7	1641
0.7-0.8	323
0.8-0.85	55
0.85-0.9	17
0.9-0.95	2
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 NPC219918 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	229
0.1-0.2	2051
0.2-0.3	4373
0.3-0.4	1810
0.4-0.5	369
0.5-0.6	191
0.6-0.7	88
0.7-0.8	35
0.8-0.85	1
0.85-0.9	3
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