NPASS Compound

Structure

NPC20220 OpenBabel06302215342D 30 31 0 0 1 0 0 0 0 0999 V2000 5.5755 7.0379 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8684 7.7450 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1272 8.7110 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9025 7.4862 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6437 6.5203 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6778 6.2615 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4189 5.2956 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.4530 5.0367 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1260 4.5884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8672 3.6225 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9013 3.3637 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6425 2.3978 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.6766 2.1390 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3496 1.6907 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0908 0.7247 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1248 0.4659 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 1.6594 -1.1088 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 0.0000 -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 -1.7321 -2.0000 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 -2.5981 -1.5000 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 -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 O 0 0 0 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 1 2 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 1 0 0 0 7 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 1 0 0 0 12 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 29 1 0 0 0 0 17 18 1 6 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 28 2 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 22 24 2 0 0 0 0 24 25 1 0 0 0 0 24 30 1 0 0 0 0 25 26 2 0 0 0 0 26 27 1 0 0 0 0 26 28 1 0 0 0 0 28 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	416.37
Volume:	485.402
LogP:	9.463
LogD:	6.439
LogS:	-6.622
# Rotatable Bonds:	12
TPSA:	29.46
# H-Bond Aceptor:	2
# H-Bond Donor:	1
# Rings:	2
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.37
Synthetic Accessibility Score:	3.817
Fsp3:	0.786
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.815
MDCK Permeability:	1.1923718375328463e-05
Pgp-inhibitor:	0.313
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.002
20% Bioavailability (F20%):	0.989
30% Bioavailability (F30%):	0.912

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.741
Plasma Protein Binding (PPB):	98.63823699951172%
Volume Distribution (VD):	4.704
Pgp-substrate:	2.0862057209014893%

ADMET: Metabolism

CYP1A2-inhibitor:	0.118
CYP1A2-substrate:	0.197
CYP2C19-inhibitor:	0.322
CYP2C19-substrate:	0.788
CYP2C9-inhibitor:	0.184
CYP2C9-substrate:	0.953
CYP2D6-inhibitor:	0.146
CYP2D6-substrate:	0.137
CYP3A4-inhibitor:	0.349
CYP3A4-substrate:	0.118

ADMET: Excretion

Clearance (CL):	9.177
Half-life (T1/2):	0.027

ADMET: Toxicity

hERG Blockers:	0.046
Human Hepatotoxicity (H-HT):	0.226
Drug-inuced Liver Injury (DILI):	0.041
AMES Toxicity:	0.027
Rat Oral Acute Toxicity:	0.023
Maximum Recommended Daily Dose:	0.175
Skin Sensitization:	0.954
Carcinogencity:	0.086
Eye Corrosion:	0.008
Eye Irritation:	0.04
Respiratory Toxicity:	0.725

Download Data

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

Natural Product: NPC20220

Natural Product ID:	NPC20220
*Common Name:**	WGVKWNUPNGFDFJ-VPYPWEPUSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	WGVKWNUPNGFDFJ-VPYPWEPUSA-N
Standard InCHI:	InChI=1S/C28H48O2/c1-20(2)11-8-12-21(3)13-9-14-22(4)15-10-17-28(7)18-16-25-24(6)26(29)19-23(5)27(25)30-28/h19-22,29H,8-18H2,1-7H3/t21-,22-,28-/m0/s1
SMILES:	CC(C)CCC[C@H](C)CCC[C@H](C)CCC[C@@]1(C)CCc2c(C)c(cc(C)c2O1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	76959905
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:0000201] Tocopherols

*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
NPO1482	Gossypium barbadense	Species	Malvaceae	Eukaryota	n.a.	Zambia; France; West Africa; USA; South Africa	n.a.	DOI[10.1002/jsfa.2731]
NPO1482	Gossypium barbadense	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1021/ie801365k]
NPO6363	Conyza filaginoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11374974]
NPO7436	Annona foetida	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16499336]
NPO997	Peltodon longipes	Species	Lamiaceae	Eukaryota	roots	Santa Maria, South Brazil	2007-Dec	PMID[21775156]
NPO1482	Gossypium barbadense	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22537213]
NPO2853	Eschweilera coriacea	Species	Lecythidaceae	Eukaryota	bark	Suriname rainforest	n.a.	PMID[9677272]
NPO14149	Saccharina japonica	Species	Laminariaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO14149	Saccharina japonica	Species	Laminariaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO9493	Lactuca virosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5665	Ulva pertusa	Species	Ulvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14149	Saccharina japonica	Species	Laminariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8652	Onychium japonicum	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5502	Rhaponticum repens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3809	Eucalyptus cladocalyx	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9493	Lactuca virosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5665	Ulva pertusa	Species	Ulvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5665	Ulva pertusa	Species	Ulvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14149	Saccharina japonica	Species	Laminariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO6621	Salvadora persica	Species	Salvadoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14149	Saccharina japonica	Species	Laminariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3899	Spodoptera frugiperda	Species	0ctuidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8491	Piper montealegreanum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8860	Hippospongia equina	Species	Spongiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21275	Phoenix paludosa	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2853	Eschweilera coriacea	Species	Lecythidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4301	Wedelia triloba	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7852	Senecio mairetianus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7436	Annona foetida	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6363	Conyza filaginoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8652	Onychium japonicum	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1482	Gossypium barbadense	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21060	Hydnocarpus annamensis	Species	Achariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO997	Peltodon longipes	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3809	Eucalyptus cladocalyx	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5615	Dipteryx alata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10260	Tubifera dimorphotheca	Species	Reticulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1709	Pyrola virens	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5502	Rhaponticum repens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8957	Mananthes patentiflora	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO4134	Campanula persicifolia	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5665	Ulva pertusa	Species	Ulvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9493	Lactuca virosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23741	Aspergillus violaceus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9875	Primula spectabilis	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13596	Lambertella corni-maris	Species	Rutstroemiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1920	Podocarpus elongata	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19467	Aeglopsis chevalieri	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10007	Desmostachya bipinnata	Species	Poaceae	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 NPC20220 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	373
0.1-0.2	1822
0.2-0.3	4477
0.3-0.4	13072
0.4-0.5	5369
0.5-0.6	7365
0.6-0.7	8300
0.7-0.8	1739
0.8-0.85	130
0.85-0.9	32
0.9-0.95	12
0.95-1	6

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 NPC20220 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	346
0.1-0.2	1057
0.2-0.3	1572
0.3-0.4	2804
0.4-0.5	1661
0.5-0.6	1114
0.6-0.7	500
0.7-0.8	85
0.8-0.85	4
0.85-0.9	3
0.9-0.95	4
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