NPASS Compound

Structure

NPC41730 OpenBabel06302216042D 24 26 0 0 1 0 0 0 0 0999 V2000 -1.3644 2.0957 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7312 2.4613 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7312 3.1925 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0979 2.0957 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5353 2.4613 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0979 1.3645 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7312 0.9989 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3656 0.3656 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.2687 0.3656 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3656 0.3656 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8650 -0.4994 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7299 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7299 0.9690 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5948 -0.4994 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5948 -1.4982 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7299 -1.9975 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8649 -1.4981 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8649 -2.4012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.9975 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8650 -1.4981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8650 -0.4993 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6471 -0.0478 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 3.4340 -0.0149 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 5 2 0 0 0 0 4 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 21 1 0 0 0 0 8 9 1 6 0 0 0 8 10 1 0 0 0 0 11 10 1 1 0 0 0 11 17 1 0 0 0 0 11 23 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 15 1 0 0 0 0 14 24 1 6 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 1 0 0 0 17 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 6 0 0 0 21 23 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	336.23
Volume:	358.695
LogP:	2.098
LogD:	2.064
LogS:	-4.17
# Rotatable Bonds:	4
TPSA:	66.76
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.773
Synthetic Accessibility Score:	6.198
Fsp3:	0.85
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:	-4.811
MDCK Permeability:	1.630931546969805e-05
Pgp-inhibitor:	0.004
Pgp-substrate:	0.182
Human Intestinal Absorption (HIA):	0.008
20% Bioavailability (F20%):	0.069
30% Bioavailability (F30%):	0.06

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.579
Plasma Protein Binding (PPB):	59.24723815917969%
Volume Distribution (VD):	1.606
Pgp-substrate:	27.112049102783203%

ADMET: Metabolism

CYP1A2-inhibitor:	0.008
CYP1A2-substrate:	0.971
CYP2C19-inhibitor:	0.048
CYP2C19-substrate:	0.886
CYP2C9-inhibitor:	0.099
CYP2C9-substrate:	0.033
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.056
CYP3A4-inhibitor:	0.823
CYP3A4-substrate:	0.92

ADMET: Excretion

Clearance (CL):	8.348
Half-life (T1/2):	0.252

ADMET: Toxicity

hERG Blockers:	0.034
Human Hepatotoxicity (H-HT):	0.708
Drug-inuced Liver Injury (DILI):	0.116
AMES Toxicity:	0.059
Rat Oral Acute Toxicity:	0.852
Maximum Recommended Daily Dose:	0.953
Skin Sensitization:	0.244
Carcinogencity:	0.977
Eye Corrosion:	0.01
Eye Irritation:	0.05
Respiratory Toxicity:	0.946

Download Data

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

Natural Product: NPC41730

Natural Product ID:	NPC41730
*Common Name:**	DQHNNRWINMUZIY-OBKDMQGPSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DQHNNRWINMUZIY-OBKDMQGPSA-N
Standard InCHI:	InChI=1S/C20H32O4/c1-13(2)15(21)6-9-18(5)12-19-14(3)16(22)7-8-17(19,4)10-11-20(18,23)24-19/h13,16,22-23H,3,6-12H2,1-2,4-5H3/t16-,17-,18+,19-,20+/m1/s1
SMILES:	CC(C)C(=O)CC[C@@]1(C)C[C@@]23C(=C)[C@@H](CC[C@]2(C)CC[C@]1(O)O3)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10019923
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0002012] Oxanes

*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
NPO6812	Bulbine frutescens	Species	Xanthorrhoeaceae	Eukaryota	n.a.	root	n.a.	PMID[12193014]
NPO8948	Streptomyces pristinaespiralis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[25708513]
NPO8796	Cnemidocarpa bicornuta	Species	Styelidae	Eukaryota	n.a.	New Zealand	n.a.	PMID[9644087]
NPO604	Erysimum crepidifolium	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO604	Erysimum crepidifolium	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8033	Sordaria macrospora	Species	Sordariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6812	Bulbine frutescens	Species	Xanthorrhoeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7039	Espeletia uribei	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5863	Amyris plumieri	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12648	Uragoga ipecacuanha	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO2958	Euphorbia glareosa	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9742	Entada scandens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO604	Erysimum crepidifolium	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26935	Coprinopsis lagopus	Species	Psathyrellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1481	Balfourodendron riedelianum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16389	Anodonta cygnea	Species	Unionidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12335	Aristolochia reticulata	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8796	Cnemidocarpa bicornuta	Species	Styelidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8948	Streptomyces pristinaespiralis	Species	Streptomycetaceae	Bacteria	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 NPC41730 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	194
0.1-0.2	1463
0.2-0.3	4810
0.3-0.4	8592
0.4-0.5	12990
0.5-0.6	6194
0.6-0.7	6836
0.7-0.8	1544
0.8-0.85	68
0.85-0.9	6
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 NPC41730 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	175
0.1-0.2	1933
0.2-0.3	3939
0.3-0.4	2053
0.4-0.5	567
0.5-0.6	231
0.6-0.7	201
0.7-0.8	51
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