NPASS Compound

Structure

NPC82455 OpenBabel06302215162D 26 26 0 0 1 0 0 0 0 0999 V2000 -0.0000 8.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 3.5000 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 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 1 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 1.7321 -1.0000 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 -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 -0.0000 3.0000 0.0000 O 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 4.3301 1.5000 0.0000 O 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 1.7321 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 8.0000 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 26 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 2 0 0 0 0 6 25 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 10 9 1 6 0 0 0 10 11 1 0 0 0 0 10 22 1 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 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 16 21 1 0 0 0 0 17 18 2 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 22 23 2 0 0 0 0 22 24 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	360.19
Volume:	388.712
LogP:	5.345
LogD:	3.664
LogS:	-3.351
# Rotatable Bonds:	10
TPSA:	94.83
# H-Bond Aceptor:	5
# H-Bond Donor:	3
# Rings:	1
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.315
Synthetic Accessibility Score:	3.2
Fsp3:	0.429
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.929
MDCK Permeability:	6.873980055388529e-06
Pgp-inhibitor:	0.008
Pgp-substrate:	0.008
Human Intestinal Absorption (HIA):	0.076
20% Bioavailability (F20%):	0.922
30% Bioavailability (F30%):	0.957

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.043
Plasma Protein Binding (PPB):	97.41109466552734%
Volume Distribution (VD):	0.415
Pgp-substrate:	2.122286081314087%

ADMET: Metabolism

CYP1A2-inhibitor:	0.157
CYP1A2-substrate:	0.112
CYP2C19-inhibitor:	0.144
CYP2C19-substrate:	0.056
CYP2C9-inhibitor:	0.511
CYP2C9-substrate:	0.974
CYP2D6-inhibitor:	0.153
CYP2D6-substrate:	0.247
CYP3A4-inhibitor:	0.074
CYP3A4-substrate:	0.057

ADMET: Excretion

Clearance (CL):	13.451
Half-life (T1/2):	0.864

ADMET: Toxicity

hERG Blockers:	0.012
Human Hepatotoxicity (H-HT):	0.722
Drug-inuced Liver Injury (DILI):	0.042
AMES Toxicity:	0.007
Rat Oral Acute Toxicity:	0.063
Maximum Recommended Daily Dose:	0.044
Skin Sensitization:	0.675
Carcinogencity:	0.615
Eye Corrosion:	0.014
Eye Irritation:	0.475
Respiratory Toxicity:	0.265

Download Data

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

Natural Product: NPC82455

Natural Product ID:	NPC82455
*Common Name:**	PNXHXPQJFNVWQM-AHQMPEJBSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PNXHXPQJFNVWQM-AHQMPEJBSA-N
Standard InCHI:	InChI=1S/C21H28O5/c1-14(2)6-4-7-15(3)8-5-9-16(21(25)26)12-20(24)18-13-17(22)10-11-19(18)23/h6,8,10-11,13,16,22-23H,4-5,7,9,12H2,1-3H3,(H,25,26)/b15-8+/t16-/m0/s1
SMILES:	CC(=CCC/C(=C/CC[C@@H](CC(=O)c1cc(ccc1O)O)C(=O)O)/C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001550] Sesquiterpenoids

*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
NPO26499	Dorstenia kameruniana	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26499	Dorstenia kameruniana	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24129	Bifurcaria bifurcata	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17880	Phlomis spinidens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24680	Evernia illyrica	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25315	Tragopogon dasyrhynchus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25750	Irvingia gabonensis	Species	Irvingiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25882	Salix americana	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10307	Leccinum extremiorientale	Species	Boletaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26441	Sideritis angustifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22023	Scutellaria tenax	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23515	Chrysanthemum yoshinaganthum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24129	Bifurcaria bifurcata	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26499	Dorstenia kameruniana	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17880	Phlomis spinidens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23310	Flourensia resinosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28723	Ia io	Species	Vespertilionidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26067	Acacia sutherlandii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24345	Amoora stellato-squamosa	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO26837	Laurencia grevilleana	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22255	Dendrodochium toxicum	Species	Bionectriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6443	Amesia atrobrunnea	Species	Chaetomiaceae	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 NPC82455 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	270
0.1-0.2	1404
0.2-0.3	3702
0.3-0.4	9411
0.4-0.5	10081
0.5-0.6	6063
0.6-0.7	9306
0.7-0.8	2197
0.8-0.85	175
0.85-0.9	80
0.9-0.95	7
0.95-1	1

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 NPC82455 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	267
0.1-0.2	905
0.2-0.3	1527
0.3-0.4	2620
0.4-0.5	2185
0.5-0.6	1127
0.6-0.7	439
0.7-0.8	70
0.8-0.85	9
0.85-0.9	1
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