NPASS Compound

Structure

NPC218701 OpenBabel06302215172D 23 25 0 0 0 0 0 0 0 0999 V2000 5.1962 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 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 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 0.8660 0.5000 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 O 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 0.0000 3.0000 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 -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 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 -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 -1.7321 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 1.5000 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 23 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 10 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 22 1 0 0 0 0 7 8 1 0 0 0 0 8 20 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 9 12 1 0 0 0 0 10 11 1 0 0 0 0 12 13 2 0 0 0 0 12 14 1 0 0 0 0 14 19 2 0 0 0 0 14 15 1 0 0 0 0 15 16 2 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 21 1 0 0 0 0 19 20 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	312.1
Volume:	317.074
LogP:	4.469
LogD:	2.451
LogS:	-3.179
# Rotatable Bonds:	2
TPSA:	90.9
# H-Bond Aceptor:	5
# H-Bond Donor:	3
# Rings:	3
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.497
Synthetic Accessibility Score:	2.751
Fsp3:	0.167
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.906
MDCK Permeability:	1.343966414424358e-05
Pgp-inhibitor:	0.02
Pgp-substrate:	0.072
Human Intestinal Absorption (HIA):	0.026
20% Bioavailability (F20%):	0.48
30% Bioavailability (F30%):	0.929

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.01
Plasma Protein Binding (PPB):	91.76731872558594%
Volume Distribution (VD):	0.653
Pgp-substrate:	10.234244346618652%

ADMET: Metabolism

CYP1A2-inhibitor:	0.934
CYP1A2-substrate:	0.336
CYP2C19-inhibitor:	0.658
CYP2C19-substrate:	0.062
CYP2C9-inhibitor:	0.787
CYP2C9-substrate:	0.836
CYP2D6-inhibitor:	0.706
CYP2D6-substrate:	0.237
CYP3A4-inhibitor:	0.181
CYP3A4-substrate:	0.071

ADMET: Excretion

Clearance (CL):	6.543
Half-life (T1/2):	0.703

ADMET: Toxicity

hERG Blockers:	0.003
Human Hepatotoxicity (H-HT):	0.759
Drug-inuced Liver Injury (DILI):	0.966
AMES Toxicity:	0.685
Rat Oral Acute Toxicity:	0.304
Maximum Recommended Daily Dose:	0.193
Skin Sensitization:	0.899
Carcinogencity:	0.346
Eye Corrosion:	0.004
Eye Irritation:	0.888
Respiratory Toxicity:	0.28

Download Data

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

Natural Product: NPC218701

Natural Product ID:	NPC218701
*Common Name:**	XEHWUYVZHDBZHK-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XEHWUYVZHDBZHK-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C18H16O5/c1-9(2)6-7-10-13(20)8-14-15(16(10)21)17(22)11-4-3-5-12(19)18(11)23-14/h3-6,8,19-21H,7H2,1-2H3
SMILES:	CC(=CCc1c(cc2c(c1O)c(=O)c1cccc(c1o2)O)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	9995643
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000123] Benzopyrans [CHEMONTID:0003410] 1-benzopyrans [CHEMONTID:0002817] Dibenzopyrans [CHEMONTID:0000200] Xanthenes [CHEMONTID:0000204] Xanthones [CHEMONTID:0003517] 2-prenylated xanthones

*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
NPO22503	Salix matsudana	Species	Salicaceae	Eukaryota	n.a.	leaf	n.a.	PMID[18794770]
NPO20091	Iotrochota baculifera	Species	Iotrochotidae	Eukaryota	Chinese	n.a.	n.a.	PMID[20624681]
NPO20458	Strychnos decussata	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7288442]
NPO20458	Strychnos decussata	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7400820]
NPO20458	Strychnos decussata	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27363	Gynochthodes officinalis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20091	Iotrochota baculifera	Species	Iotrochotidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20382	Ramalina paludosa	Species	Ramalinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20458	Strychnos decussata	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20458	Strychnos decussata	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO27363	Gynochthodes officinalis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO20091	Iotrochota baculifera	Species	Iotrochotidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21601	Crocus sieberi	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22503	Salix matsudana	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21034	0cardia alba	Species	0cardiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO20382	Ramalina paludosa	Species	Ramalinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21852	Montanoa karwinskii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20773	Jacobaea persoonii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20458	Strychnos decussata	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20897	Suberites domuncula	Species	Suberitidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20647	Eugenia myrcianthes	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23186	Verbena bonariensis	Species	Verbenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18516	Aplysilla spinifera	Species	Darwinellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27363	Gynochthodes officinalis	Species	Rubiaceae	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

Activity Type	# Activity
IC50	2

Activity Type	# Activity
Cell Line	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT165	Cell Line	HeLa	Homo sapiens	IC50	=	37100.0	nM	PMID[513204]
NPT116	Cell Line	HL-60	Homo sapiens	IC50	=	6300.0	nM	PMID[513204]

☑ 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 NPC218701 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	443
0.1-0.2	1981
0.2-0.3	4979
0.3-0.4	11504
0.4-0.5	5848
0.5-0.6	3876
0.6-0.7	5007
0.7-0.8	4700
0.8-0.85	2220
0.85-0.9	1338
0.9-0.95	629
0.95-1	172

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 NPC218701 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	420
0.1-0.2	1015
0.2-0.3	1744
0.3-0.4	2723
0.4-0.5	1734
0.5-0.6	990
0.6-0.7	357
0.7-0.8	107
0.8-0.85	39
0.85-0.9	11
0.9-0.95	7
0.95-1	3

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