NPASS Compound

Structure

NPC65986 OpenBabel06302216002D 21 22 0 0 0 0 0 0 0 0999 V2000 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 O 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 -0.8660 -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 -3.4641 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 0.0000 O 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 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 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 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 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 21 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 16 2 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 7 19 1 0 0 0 0 8 9 1 0 0 0 0 9 15 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 12 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 19 20 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	290.12
Volume:	296.312
LogP:	2.948
LogD:	2.898
LogS:	-3.7
# Rotatable Bonds:	5
TPSA:	57.9
# H-Bond Aceptor:	5
# H-Bond Donor:	0
# Rings:	2
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.625
Synthetic Accessibility Score:	2.519
Fsp3:	0.312
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:	-4.597
MDCK Permeability:	1.7996891983784735e-05
Pgp-inhibitor:	0.491
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.007
20% Bioavailability (F20%):	0.005
30% Bioavailability (F30%):	0.176

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.102
Plasma Protein Binding (PPB):	70.39945220947266%
Volume Distribution (VD):	1.144
Pgp-substrate:	17.046493530273438%

ADMET: Metabolism

CYP1A2-inhibitor:	0.946
CYP1A2-substrate:	0.922
CYP2C19-inhibitor:	0.841
CYP2C19-substrate:	0.664
CYP2C9-inhibitor:	0.306
CYP2C9-substrate:	0.865
CYP2D6-inhibitor:	0.539
CYP2D6-substrate:	0.794
CYP3A4-inhibitor:	0.481
CYP3A4-substrate:	0.387

ADMET: Excretion

Clearance (CL):	12.209
Half-life (T1/2):	0.471

ADMET: Toxicity

hERG Blockers:	0.04
Human Hepatotoxicity (H-HT):	0.964
Drug-inuced Liver Injury (DILI):	0.915
AMES Toxicity:	0.166
Rat Oral Acute Toxicity:	0.046
Maximum Recommended Daily Dose:	0.03
Skin Sensitization:	0.351
Carcinogencity:	0.477
Eye Corrosion:	0.004
Eye Irritation:	0.052
Respiratory Toxicity:	0.102

Download Data

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

Natural Product: NPC65986

Natural Product ID:	NPC65986
*Common Name:**	HYLMQFRADKVWGK-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HYLMQFRADKVWGK-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C16H18O5/c1-10(2)7-8-20-15-12(18-3)9-11-5-6-13(17)21-14(11)16(15)19-4/h5-7,9H,8H2,1-4H3
SMILES:	CC(=CCOc1c(cc2ccc(=O)oc2c1OC)OC)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	13989556
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000145] Coumarins and derivatives

*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
NPO23852	Cryptocarya obovata	Species	Lauraceae	Eukaryota	n.a.	trunk bark	n.a.	PMID[15165150]
NPO23852	Cryptocarya obovata	Species	Lauraceae	Eukaryota	n.a.	fruit	n.a.	PMID[15165150]
NPO23852	Cryptocarya obovata	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15165150]
NPO23852	Cryptocarya obovata	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20558060]
NPO14974.1	0stoc commune var. flagelliforme	Varieties	0stocaceae	Bacteria	n.a.	n.a.	n.a.	Database[MetaboLights]
NPO14974.1	0stoc commune var. flagelliforme	Varieties	0stocaceae	Bacteria	n.a.	n.a.	n.a.	Database[TCMID]
NPO17426	Vismia baccifera	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21835	Buxus rugulosa	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20885	Duguetia furfuracea	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19133	Brickellia baccharidea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14974.1	0stoc commune var. flagelliforme	Varieties	0stocaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO23852	Cryptocarya obovata	Species	Lauraceae	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 NPC65986 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	461
0.1-0.2	2077
0.2-0.3	5746
0.3-0.4	10862
0.4-0.5	6201
0.5-0.6	4093
0.6-0.7	5784
0.7-0.8	5155
0.8-0.85	1687
0.85-0.9	526
0.9-0.95	94
0.95-1	11

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 NPC65986 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	408
0.1-0.2	1045
0.2-0.3	2069
0.3-0.4	2626
0.4-0.5	1645
0.5-0.6	888
0.6-0.7	325
0.7-0.8	104
0.8-0.85	32
0.85-0.9	6
0.9-0.95	2
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