NPASS Compound

Structure

NPC163098 OpenBabel06302215472D 24 26 0 0 1 0 0 0 0 0999 V2000 3.0878 0.0570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0878 0.0570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5878 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5878 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.6180 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9511 -1.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9511 -0.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.3578 0.6045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8171 0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6831 -0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6831 -1.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.5491 -1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0491 -0.9430 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5491 -1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5491 -2.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6831 -3.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8171 -2.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9511 -3.3090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8171 -1.8090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9511 -2.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5491 -0.8090 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 0.3090 -2.5691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0878 -1.6750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 3 24 1 0 0 0 0 4 22 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 5 23 1 1 0 0 0 6 7 1 0 0 0 0 6 19 1 0 0 0 0 7 8 1 6 0 0 0 7 9 1 0 0 0 0 7 22 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 19 1 0 0 0 0 11 12 1 0 0 0 0 11 21 1 1 0 0 0 12 13 1 0 0 0 0 12 14 1 0 0 0 0 12 15 1 0 0 0 0 15 16 1 0 0 0 0 16 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 M END $$$$

Physi-Chem Properties

Molecular Weight:	334.21
Volume:	356.058
LogP:	2.498
LogD:	2.27
LogS:	-4.12
# Rotatable Bonds:	1
TPSA:	66.76
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.773
Synthetic Accessibility Score:	5.152
Fsp3:	0.75
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-4.651
MDCK Permeability:	2.774196218524594e-05
Pgp-inhibitor:	0.012
Pgp-substrate:	0.005
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.131

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.953
Plasma Protein Binding (PPB):	79.00200653076172%
Volume Distribution (VD):	1.511
Pgp-substrate:	12.55356502532959%

ADMET: Metabolism

CYP1A2-inhibitor:	0.02
CYP1A2-substrate:	0.508
CYP2C19-inhibitor:	0.329
CYP2C19-substrate:	0.855
CYP2C9-inhibitor:	0.183
CYP2C9-substrate:	0.086
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.156
CYP3A4-inhibitor:	0.396
CYP3A4-substrate:	0.66

ADMET: Excretion

Clearance (CL):	7.44
Half-life (T1/2):	0.662

ADMET: Toxicity

hERG Blockers:	0.008
Human Hepatotoxicity (H-HT):	0.217
Drug-inuced Liver Injury (DILI):	0.124
AMES Toxicity:	0.033
Rat Oral Acute Toxicity:	0.547
Maximum Recommended Daily Dose:	0.099
Skin Sensitization:	0.07
Carcinogencity:	0.791
Eye Corrosion:	0.319
Eye Irritation:	0.287
Respiratory Toxicity:	0.85

Download Data

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

Natural Product: NPC163098

Natural Product ID:	NPC163098
*Common Name:**	DOQXTCHBKSIARN-HAZXEVORSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DOQXTCHBKSIARN-HAZXEVORSA-N
Standard InCHI:	InChI=1S/C20H30O4/c1-7-12(2)15-14(22)16-18(5,24-15)10-11-20(23)17(3,4)9-8-13(21)19(16,20)6/h7,14,16,22-23H,1,8-11H2,2-6H3/b15-12-/t14-,16+,18-,19-,20-/m1/s1
SMILES:	C=C/C(=C1/[C@H]([C@H]2[C@@](C)(CC[C@]3(C(C)(C)CCC(=O)[C@]23C)O)O1)O)/C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001634] Naphthofurans

*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
NPO26872	Piper betle	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/S0031-9422(98)00208-8]
NPO26872	Piper betle	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12951092]
NPO6609	Trigonostemon heterophyllus	Species	Euphorbiaceae	Eukaryota	n.a.	twig	n.a.	PMID[22122667]
NPO6609	Trigonostemon heterophyllus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22122667]
NPO26872	Piper betle	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26872	Piper betle	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26575	Scapania undulata	Species	Scapaniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26872	Piper betle	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO937	Limnodynastes terraereginae	Species	Myobatrachidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26818	Euphorbia kaleniczenkii	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26178	Guarea glabra	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26390	Triphasia trifolia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26519	Acanthodoris nanaimoensis	Species	Onchidorididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26872	Piper betle	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25939	Lupinus macounii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26360	Methysticodendron amesianum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO4408	Alstonia rostrata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6609	Trigonostemon heterophyllus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10837	Matthiola incana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25961	Liatris graminifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26275	Dactynotus rudbeckiae	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO7055	Lychnophora hakeaefolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26575	Scapania undulata	Species	Scapaniaceae	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 NPC163098 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	201
0.1-0.2	1125
0.2-0.3	3706
0.3-0.4	6669
0.4-0.5	12501
0.5-0.6	9740
0.6-0.7	6760
0.7-0.8	1961
0.8-0.85	33
0.85-0.9	1
0.9-0.95	0
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 NPC163098 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	173
0.1-0.2	1326
0.2-0.3	3640
0.3-0.4	2548
0.4-0.5	847
0.5-0.6	349
0.6-0.7	197
0.7-0.8	70
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