NPASS Compound

Structure

NPC83008 OpenBabel06302215132D 23 24 0 0 1 0 0 0 0 0999 V2000 -0.4875 -1.5251 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8146 -0.5801 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.8134 -0.6276 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6795 -0.1276 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1377 0.7612 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.1702 1.0142 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1138 0.5440 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6220 1.4052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9600 2.1547 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.0426 1.7567 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4245 2.5427 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.4795 2.8698 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5077 2.6340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1824 1.9103 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3717 0.9284 0.0000 C 0 0 2 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 1.3671 0.8333 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3965 2.1758 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0045 3.3573 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1772 3.1308 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8534 3.8676 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1534 2.9136 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4405 3.8070 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 16 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 5 10 1 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 9 20 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 11 19 1 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 13 18 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 15 17 1 1 0 0 0 20 21 1 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	322.25
Volume:	358.461
LogP:	3.488
LogD:	3.589
LogS:	-3.681
# Rotatable Bonds:	1
TPSA:	60.69
# H-Bond Aceptor:	3
# H-Bond Donor:	3
# Rings:	2
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.648
Synthetic Accessibility Score:	5.236
Fsp3:	0.8
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:	-4.641
MDCK Permeability:	2.167644379369449e-05
Pgp-inhibitor:	0.003
Pgp-substrate:	0.993
Human Intestinal Absorption (HIA):	0.941
20% Bioavailability (F20%):	0.583
30% Bioavailability (F30%):	0.739

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.932
Plasma Protein Binding (PPB):	85.65482330322266%
Volume Distribution (VD):	0.841
Pgp-substrate:	4.948420524597168%

ADMET: Metabolism

CYP1A2-inhibitor:	0.038
CYP1A2-substrate:	0.245
CYP2C19-inhibitor:	0.034
CYP2C19-substrate:	0.807
CYP2C9-inhibitor:	0.075
CYP2C9-substrate:	0.539
CYP2D6-inhibitor:	0.016
CYP2D6-substrate:	0.139
CYP3A4-inhibitor:	0.318
CYP3A4-substrate:	0.335

ADMET: Excretion

Clearance (CL):	7.634
Half-life (T1/2):	0.619

ADMET: Toxicity

hERG Blockers:	0.028
Human Hepatotoxicity (H-HT):	0.388
Drug-inuced Liver Injury (DILI):	0.027
AMES Toxicity:	0.005
Rat Oral Acute Toxicity:	0.499
Maximum Recommended Daily Dose:	0.983
Skin Sensitization:	0.79
Carcinogencity:	0.178
Eye Corrosion:	0.014
Eye Irritation:	0.214
Respiratory Toxicity:	0.948

Download Data

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

Natural Product: NPC83008

Natural Product ID:	NPC83008
*Common Name:**	QWIUMSWXLCXCSM-UQLHANAESA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	QWIUMSWXLCXCSM-UQLHANAESA-N
Standard InCHI:	InChI=1S/C20H34O3/c1-13-6-8-20(5)9-7-16(19(3,4)23)18(20)17(22)12-14(2)11-15(21)10-13/h6,8,11,13,15-18,21-23H,7,9-10,12H2,1-5H3/b8-6+,14-11+/t13-,15+,16-,17+,18-,20+/m1/s1
SMILES:	C[C@@H]1/C=C/[C@@]2(C)CC[C@H]([C@@H]2[C@H](C/C(=C/[C@H](C1)O)/C)O)C(C)(C)O
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:0001551] Diterpenoids [CHEMONTID:0001760] Dolabellane and neodolabellane 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
NPO21169	Salvia blepharochlaena	Species	Lamiaceae	Eukaryota	roots	n.a.	n.a.	PMID[11325249]
NPO18865	Tetracentron sinense	Species	Trochodendraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21306	Alpinia pinnanensis	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18865	Tetracentron sinense	Species	Trochodendraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21306	Alpinia pinnanensis	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27967	Betula glandulosa	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19911	Arachniodes festina	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17330	Pseudopotamilla occelata	Species	Sabellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20488	Abies homolepis	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20420	Helenium brevifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16565	Lindera oldhami	Species	Tineidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20838	Cleome pentaphylla	Species	Cleomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17838	Aster flaccidus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21306	Alpinia pinnanensis	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21169	Salvia blepharochlaena	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20558	Pseudevernia ericetorum	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18865	Tetracentron sinense	Species	Trochodendraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20221	Maytenus truncata	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21494	Eryngium maritimum	Species	Apiaceae	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 NPC83008 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	164
0.1-0.2	1394
0.2-0.3	8343
0.3-0.4	15108
0.4-0.5	8128
0.5-0.6	6618
0.6-0.7	2466
0.7-0.8	436
0.8-0.85	32
0.85-0.9	5
0.9-0.95	3
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 NPC83008 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	147
0.1-0.2	1989
0.2-0.3	4242
0.3-0.4	1932
0.4-0.5	497
0.5-0.6	240
0.6-0.7	60
0.7-0.8	43
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