NPASS Compound

Structure

NPC300048 OpenBabel06302215242D 37 40 0 0 1 0 0 0 0 0999 V2000 4.2793 -4.8278 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4494 -3.6805 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5409 -2.9595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4623 -3.3857 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5538 -2.6647 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.3637 -3.1940 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9175 -2.6674 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.5126 -3.1249 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5994 -3.8706 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2885 -4.1682 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3753 -4.9139 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8909 -3.7203 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8280 -1.9221 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7894 -1.4562 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3351 -0.7534 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9453 -1.3078 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2507 -0.3002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1408 0.5170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3781 0.8303 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7934 1.0208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8317 -0.9021 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7721 -1.5256 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.7947 -1.5924 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2606 -1.4379 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.1224 -0.5768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2953 -0.7001 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8059 -0.4053 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3166 -0.7001 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8273 -0.4053 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8273 0.1844 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3166 0.4792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8059 0.1844 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2953 -1.2898 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0963 0.9167 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6596 -1.3845 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5281 -3.2542 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 37 1 0 0 0 0 3 4 1 0 0 0 0 5 4 1 6 0 0 0 5 6 1 0 0 0 0 5 22 1 0 0 0 0 6 7 1 0 0 0 0 7 24 1 0 0 0 0 7 8 1 6 0 0 0 7 13 1 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 10 12 1 0 0 0 0 13 14 2 0 0 0 0 13 15 1 0 0 0 0 15 34 1 0 0 0 0 15 16 1 1 0 0 0 15 21 1 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 18 19 1 0 0 0 0 18 20 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 6 0 0 0 22 24 1 0 0 0 0 24 25 1 0 0 0 0 24 36 1 6 0 0 0 25 26 2 0 0 0 0 25 34 1 0 0 0 0 26 27 1 0 0 0 0 26 33 1 0 0 0 0 27 32 2 0 0 0 0 27 28 1 0 0 0 0 28 29 2 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 31 32 1 0 0 0 0 34 35 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	502.31
Volume:	556.531
LogP:	7.781
LogD:	5.193
LogS:	-4.775
# Rotatable Bonds:	8
TPSA:	71.44
# H-Bond Aceptor:	4
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.24
Synthetic Accessibility Score:	5.998
Fsp3:	0.545
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.093
MDCK Permeability:	1.8873075532610528e-05
Pgp-inhibitor:	0.239
Pgp-substrate:	0.809
Human Intestinal Absorption (HIA):	0.008
20% Bioavailability (F20%):	0.891
30% Bioavailability (F30%):	0.796

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.621
Plasma Protein Binding (PPB):	86.58435821533203%
Volume Distribution (VD):	2.447
Pgp-substrate:	8.51702880859375%

ADMET: Metabolism

CYP1A2-inhibitor:	0.036
CYP1A2-substrate:	0.162
CYP2C19-inhibitor:	0.761
CYP2C19-substrate:	0.707
CYP2C9-inhibitor:	0.492
CYP2C9-substrate:	0.064
CYP2D6-inhibitor:	0.558
CYP2D6-substrate:	0.009
CYP3A4-inhibitor:	0.924
CYP3A4-substrate:	0.762

ADMET: Excretion

Clearance (CL):	10.932
Half-life (T1/2):	0.035

ADMET: Toxicity

hERG Blockers:	0.008
Human Hepatotoxicity (H-HT):	0.937
Drug-inuced Liver Injury (DILI):	0.562
AMES Toxicity:	0.057
Rat Oral Acute Toxicity:	0.951
Maximum Recommended Daily Dose:	0.126
Skin Sensitization:	0.217
Carcinogencity:	0.403
Eye Corrosion:	0.007
Eye Irritation:	0.017
Respiratory Toxicity:	0.985

Download Data

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

Natural Product: NPC300048

Natural Product ID:	NPC300048
*Common Name:**	SEJBFXIKYPRBLV-BIXGDQOPSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SEJBFXIKYPRBLV-BIXGDQOPSA-N
Standard InCHI:	InChI=1S/C33H42O4/c1-21(2)13-14-25-19-32(18-16-23(5)6)29(36)31(17-15-22(3)4)20-30(25,7)33(32,37)26(28(31)35)27(34)24-11-9-8-10-12-24/h8-13,15-16,25,34,37H,14,17-20H2,1-7H3/b27-26+/t25-,30+,31+,32+,33-/m1/s1
SMILES:	CC(=CC[C@@H]1C[C@@]2(CC=C(C)C)C(=O)[C@@]3(CC=C(C)C)C[C@]1(C)[C@@]2(/C(=C(c1ccccc1)/O)/C3=O)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:0001549] Monoterpenoids [CHEMONTID:0000051] Aromatic monoterpenoids

*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
NPO19764	Tithonia diversifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11975495]
NPO24016	Cladanthus mixtus	Species	Asteraceae	Eukaryota	Roots	n.a.	n.a.	PMID[14738379]
NPO19764	Tithonia diversifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19299148]
NPO19764	Tithonia diversifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23501116]
NPO21003	Cystoseira tamariscifolia	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25640118]
NPO20116	Ilex cornuta	Species	Aquifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20116	Ilex cornuta	Species	Aquifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19764	Tithonia diversifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20116	Ilex cornuta	Species	Aquifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20116	Ilex cornuta	Species	Aquifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO21003	Cystoseira tamariscifolia	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3338	Vatica obscura	Species	Dipterocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27328	Echinopsis candicans	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20927	Scirpophaga incertulas	Species	Crambidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15534	Parablechnum procerum	Species	Blechnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19764	Tithonia diversifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20116	Ilex cornuta	Species	Aquifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24016	Cladanthus mixtus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16024	Piper sumatranum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13990	Montanoa atriplicifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19000	Crepis crocea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO825	Stranvaesia davidiana	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9019	Asplenium antiquum	Species	Aspleniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21675	Persicaria sibirica	Species	Polygonaceae	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 NPC300048 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	317
0.1-0.2	1390
0.2-0.3	2213
0.3-0.4	5815
0.4-0.5	12253
0.5-0.6	16300
0.6-0.7	4012
0.7-0.8	392
0.8-0.85	1
0.85-0.9	2
0.9-0.95	0
0.95-1	2

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 NPC300048 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	277
0.1-0.2	841
0.2-0.3	1270
0.3-0.4	3042
0.4-0.5	2390
0.5-0.6	1151
0.6-0.7	164
0.7-0.8	15
0.8-0.85	0
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