NPASS Compound

Structure

NPC248837 OpenBabel06302215212D 27 28 0 0 1 0 0 0 0 0999 V2000 -3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -2.5000 0.0000 C 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 -6.9282 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -1.0000 0.0000 C 0 0 1 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 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -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 -4.3301 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1962 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -2.5000 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 -1.7321 -1.0000 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 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 1 2 1 0 0 0 0 1 18 1 0 0 0 0 2 3 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 7 1 0 0 0 0 7 8 2 0 0 0 0 9 7 1 6 0 0 0 9 10 1 0 0 0 0 9 15 1 0 0 0 0 10 11 2 0 0 0 0 10 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 14 17 1 6 0 0 0 15 16 2 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 27 2 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 26 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	372.23
Volume:	408.593
LogP:	5.383
LogD:	3.857
LogS:	-3.609
# Rotatable Bonds:	12
TPSA:	80.92
# H-Bond Aceptor:	4
# H-Bond Donor:	4
# Rings:	2
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.222
Synthetic Accessibility Score:	2.678
Fsp3:	0.478
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.076
MDCK Permeability:	1.761659950716421e-05
Pgp-inhibitor:	0.099
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.039
20% Bioavailability (F20%):	1.0
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.018
Plasma Protein Binding (PPB):	99.48512268066406%
Volume Distribution (VD):	1.182
Pgp-substrate:	0.47520092129707336%

ADMET: Metabolism

CYP1A2-inhibitor:	0.541
CYP1A2-substrate:	0.223
CYP2C19-inhibitor:	0.829
CYP2C19-substrate:	0.062
CYP2C9-inhibitor:	0.308
CYP2C9-substrate:	0.958
CYP2D6-inhibitor:	0.79
CYP2D6-substrate:	0.328
CYP3A4-inhibitor:	0.152
CYP3A4-substrate:	0.152

ADMET: Excretion

Clearance (CL):	6.717
Half-life (T1/2):	0.787

ADMET: Toxicity

hERG Blockers:	0.029
Human Hepatotoxicity (H-HT):	0.017
Drug-inuced Liver Injury (DILI):	0.019
AMES Toxicity:	0.479
Rat Oral Acute Toxicity:	0.09
Maximum Recommended Daily Dose:	0.14
Skin Sensitization:	0.967
Carcinogencity:	0.046
Eye Corrosion:	0.005
Eye Irritation:	0.943
Respiratory Toxicity:	0.417

Download Data

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

Natural Product: NPC248837

Natural Product ID:	NPC248837
*Common Name:**	YKNFYZLEJAATOF-YADHBBJMSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YKNFYZLEJAATOF-YADHBBJMSA-N
Standard InCHI:	InChI=1S/C23H32O4/c24-19(22-20(25)16-17-21(26)23(22)27)15-11-6-4-2-1-3-5-8-12-18-13-9-7-10-14-18/h7,9-10,13-14,21-22,26H,1-6,8,11-12,15-17H2/t21-,22+/m1/s1
SMILES:	C(CCCCCC(=O)[C@H]1C(=O)CC[C@H](C1=O)O)CCCCc1ccccc1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0001831] Carbonyl compounds [CHEMONTID:0000133] 1,3-dicarbonyl compounds [CHEMONTID:0003926] Beta-diketones

*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
NPO28014	Garcinia gaudichaudii	Species	Clusiaceae	Eukaryota	n.a.	bark	n.a.	PMID[11101460]
NPO27888	Sarcococca saligna	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[14584959]
NPO27888	Sarcococca saligna	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[14643329]
NPO27718	Peperomia dindygulensis	Species	Piperaceae	Eukaryota	whole plant	Yunnan Province, China	2002-FEB	PMID[16309318]
NPO27718	Peperomia dindygulensis	Species	Piperaceae	Eukaryota	whole plant	Yunnan Province, China	2002-FEB	PMID[16724842]
NPO27888	Sarcococca saligna	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9548847]
NPO27888	Sarcococca saligna	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16710	Pandanus tectorius	Species	Pandanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27842	Gentiana makinoi	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28014	Garcinia gaudichaudii	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27888	Sarcococca saligna	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27842	Gentiana makinoi	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16710	Pandanus tectorius	Species	Pandanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16710	Pandanus tectorius	Species	Pandanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28014	Garcinia gaudichaudii	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28133	Geigeria filifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27439	Letharia vulpina	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27842	Gentiana makinoi	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27888	Sarcococca saligna	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13728	Metanarthecium luteoviride	Species	Nartheciaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22405	Litsea monopetala	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19590	Daedaleopsis tricolor	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16710	Pandanus tectorius	Species	Pandanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27184	Bonellia macrocarpa	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27718	Peperomia dindygulensis	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27953	Eugenia formosa	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27401	Aniba riparia	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17271	Aegialitis annulata	Species	Plumbaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27135	Tubularia larynx	Species	Tubulariidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27362	Hypericum elodes	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28066	Aloe speciosa	Species	Xanthorrhoeaceae	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 NPC248837 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	192
0.1-0.2	821
0.2-0.3	2096
0.3-0.4	8024
0.4-0.5	15817
0.5-0.6	13991
0.6-0.7	1604
0.7-0.8	142
0.8-0.85	9
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 NPC248837 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	177
0.1-0.2	740
0.2-0.3	1319
0.3-0.4	3124
0.4-0.5	2473
0.5-0.6	1114
0.6-0.7	181
0.7-0.8	22
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