NPASS Compound

Structure

NPC159464 OpenBabel06302215382D 21 21 0 0 0 0 0 0 0 0999 V2000 3.4641 1.0000 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 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 -0.8660 -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 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -3.5000 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 -2.5981 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -5.0000 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 -1.7321 0.0000 0.0000 O 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 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 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 16 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 19 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 8 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 11 13 1 0 0 0 0 13 14 1 0 0 0 0 15 16 1 0 0 0 0 15 18 1 0 0 0 0 16 17 1 0 0 0 0 19 20 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	116.08
Volume:	127.276
LogP:	-0.365
LogD:	-0.635
LogS:	0.705
# Rotatable Bonds:	2
TPSA:	40.46
# H-Bond Aceptor:	2
# H-Bond Donor:	2
# Rings:	0
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.509
Synthetic Accessibility Score:	4.004
Fsp3:	0.667
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.6
MDCK Permeability:	0.0009047382045537233
Pgp-inhibitor:	0.0
Pgp-substrate:	0.007
Human Intestinal Absorption (HIA):	0.013
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.758

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.737
Plasma Protein Binding (PPB):	11.90453052520752%
Volume Distribution (VD):	1.407
Pgp-substrate:	82.23527526855469%

ADMET: Metabolism

CYP1A2-inhibitor:	0.049
CYP1A2-substrate:	0.579
CYP2C19-inhibitor:	0.027
CYP2C19-substrate:	0.835
CYP2C9-inhibitor:	0.005
CYP2C9-substrate:	0.745
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.248
CYP3A4-inhibitor:	0.008
CYP3A4-substrate:	0.223

ADMET: Excretion

Clearance (CL):	3.778
Half-life (T1/2):	0.828

ADMET: Toxicity

hERG Blockers:	0.013
Human Hepatotoxicity (H-HT):	0.011
Drug-inuced Liver Injury (DILI):	0.045
AMES Toxicity:	0.018
Rat Oral Acute Toxicity:	0.122
Maximum Recommended Daily Dose:	0.022
Skin Sensitization:	0.045
Carcinogencity:	0.045
Eye Corrosion:	0.039
Eye Irritation:	0.978
Respiratory Toxicity:	0.014

Download Data

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

Natural Product: NPC159464

Natural Product ID:	NPC159464
*Common Name:**	SRNFRMCXSNGZTJ-LFYBBSHMSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SRNFRMCXSNGZTJ-LFYBBSHMSA-N
Standard InCHI:	InChI=1S/C17H22O4/c1-11(2)4-7-15-14(10-19)8-13(16(20)17(15)21)6-5-12(3)9-18/h4-5,8,10,18,20-21H,6-7,9H2,1-3H3/b12-5+
SMILES:	CC(=CCc1c(cc(C/C=C(C)/CO)c(c1O)O)C=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	44477997
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0001831] Carbonyl compounds [CHEMONTID:0000124] Aldehydes [CHEMONTID:0003213] Aryl-aldehydes [CHEMONTID:0001345] Benzaldehydes [CHEMONTID:0003978] Hydroxybenzaldehydes

*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
NPO28141	Colpomenia sinuosa	Species	Scytosiphonaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1021/np50097a033]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	fruit	n.a.	PMID[12802735]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	fruit	n.a.	PMID[18384095]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	leaf	n.a.	PMID[22014120]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	fruit	n.a.	PMID[22014120]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	leaf	n.a.	PMID[22014168]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23540838]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24295708]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	leaf	n.a.	PMID[25102361]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	fruit	n.a.	PMID[25306330]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	Oil	n.a.	n.a.	Database[FooDB]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28646	Streptomyces argenteolus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO28195	Phlogacanthus tubiflorus	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28141	Colpomenia sinuosa	Species	Scytosiphonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27829	Aplophyllum pedicellatum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO27905	Eritrichium sericeum	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28556	Streptomyces pentaticus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO28263	Anemone tomentosa	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28070	Chrysosplenium americanum	Species	Saxifragaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21557	Woodsia manchuriensis	Species	Woodsiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20714	Lobophytum schoedei	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23326	Bohadschia vitiensis	Species	Holothuriidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28422	Sabia japonica	Species	Sabiaceae	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 NPC159464 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	309
0.1-0.2	1424
0.2-0.3	3535
0.3-0.4	10156
0.4-0.5	9361
0.5-0.6	5619
0.6-0.7	9490
0.7-0.8	2622
0.8-0.85	152
0.85-0.9	29
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 NPC159464 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	271
0.1-0.2	1006
0.2-0.3	1615
0.3-0.4	2850
0.4-0.5	1931
0.5-0.6	1068
0.6-0.7	376
0.7-0.8	32
0.8-0.85	1
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