NPASS Compound

Structure

NPC254688 OpenBabel06302215172D 27 30 0 0 0 0 0 0 0 0999 V2000 -1.7321 -3.0000 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 -0.8660 -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 0.0000 -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 0.8660 -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 2.5981 -0.5000 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 3.4641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 0.0000 O 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 4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -0.5000 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 0.0000 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 -4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 7 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 4 26 1 0 0 0 0 5 6 2 0 0 0 0 6 25 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 8 10 1 0 0 0 0 10 23 2 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 11 25 1 0 0 0 0 12 13 1 0 0 0 0 13 19 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 14 23 1 0 0 0 0 15 16 2 0 0 0 0 15 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 2 0 0 0 0 21 22 1 0 0 0 0 23 24 1 0 0 0 0 26 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	366.07
Volume:	355.417
LogP:	3.745
LogD:	2.496
LogS:	-4.873
# Rotatable Bonds:	2
TPSA:	103.04
# H-Bond Aceptor:	7
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.696
Synthetic Accessibility Score:	2.789
Fsp3:	0.15
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.983
MDCK Permeability:	3.890393054462038e-05
Pgp-inhibitor:	0.985
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.032
20% Bioavailability (F20%):	0.008
30% Bioavailability (F30%):	0.934

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.007
Plasma Protein Binding (PPB):	85.24761199951172%
Volume Distribution (VD):	0.516
Pgp-substrate:	10.49055290222168%

ADMET: Metabolism

CYP1A2-inhibitor:	0.882
CYP1A2-substrate:	0.948
CYP2C19-inhibitor:	0.728
CYP2C19-substrate:	0.111
CYP2C9-inhibitor:	0.833
CYP2C9-substrate:	0.863
CYP2D6-inhibitor:	0.506
CYP2D6-substrate:	0.363
CYP3A4-inhibitor:	0.559
CYP3A4-substrate:	0.131

ADMET: Excretion

Clearance (CL):	1.255
Half-life (T1/2):	0.222

ADMET: Toxicity

hERG Blockers:	0.007
Human Hepatotoxicity (H-HT):	0.828
Drug-inuced Liver Injury (DILI):	0.925
AMES Toxicity:	0.674
Rat Oral Acute Toxicity:	0.719
Maximum Recommended Daily Dose:	0.944
Skin Sensitization:	0.644
Carcinogencity:	0.724
Eye Corrosion:	0.005
Eye Irritation:	0.673
Respiratory Toxicity:	0.425

Download Data

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

Natural Product: NPC254688

Natural Product ID:	NPC254688
*Common Name:**	JZXLAKYPIMLXFU-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JZXLAKYPIMLXFU-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C20H14O7/c1-8-4-9(25-2)5-12-15(8)19(23)17-13(27-12)6-10-16(20(17)24)11(21)7-14(26-3)18(10)22/h4-7,24H,1-3H3
SMILES:	Cc1cc(cc2c1c(=O)c1c(cc3c(C(=O)C=C(C3=O)OC)c1O)o2)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	44419567
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

*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
NPO29266	Fusarium oxysporum	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16562855]
NPO29266	Fusarium oxysporum	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17286429]
NPO168	Agelas sventres	Species	Agelasidae	Eukaryota	n.a.	n.a.	n.a.	PMID[21207971]
NPO1825	Isaria sinclairii	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21456524]
NPO4053	Sageretia theezans	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30106290]
NPO1825	Isaria sinclairii	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8893839]
NPO29266	Fusarium oxysporum	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9014349]
NPO4053	Sageretia theezans	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO356	Cladonia rangiferina	Species	Cladoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO356	Cladonia rangiferina	Species	Cladoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4053	Sageretia theezans	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4053	Sageretia theezans	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO391	Goodyera schlechtendaliana	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2702	Orophea enterocarpa	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1175	Pseuduvaria macrophylla	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29266	Fusarium oxysporum	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1825	Isaria sinclairii	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4286	Arenochalina mirabilis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO4053	Sageretia theezans	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7095	Podocarpus fasciculus	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6198	Lamprometra palmata	Species	Mariametridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5364	Clathrotropis glaucophylla	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO871	Swartzia ulei	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7751	Merulius corium	Species	Meruliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO168	Agelas sventres	Species	Agelasidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6616	Baccharis ochracea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1986	Dipterocarpus indicus	Species	Dipterocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6526	Triclisia gilletii	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO732	Randia tetrasperma	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2273	Davidia involucrata	Species	Nyssaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO356	Cladonia rangiferina	Species	Cladoniaceae	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 NPC254688 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

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 NPC254688 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

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