NPASS Compound

Structure

NPC295089 OpenBabel06302216202D 23 26 0 0 1 0 0 0 0 0999 V2000 -2.2114 -1.7814 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8730 -0.8798 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4035 -0.0762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3665 -0.0762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9669 0.6767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7526 1.6155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8850 2.0334 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0174 1.6155 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 -1.1907 2.1094 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4656 1.4759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8440 0.5904 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8031 0.6767 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.9016 0.3384 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.9448 -0.6236 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1919 -1.2240 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8584 1.3004 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0699 1.5565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4083 2.4581 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6004 0.7529 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5624 0.7097 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 -2.3641 2.5011 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2206 3.4534 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 14 1 0 0 0 0 2 3 2 0 0 0 0 3 12 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 1 0 0 0 0 8 12 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 21 1 0 0 0 0 13 14 1 0 0 0 0 13 16 1 0 0 0 0 14 15 2 0 0 0 0 16 17 2 0 0 0 0 16 22 1 0 0 0 0 17 18 1 0 0 0 0 17 19 1 0 0 0 0 19 20 2 0 0 0 0 19 21 1 0 0 0 0 22 23 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	317.16
Volume:	321.27
LogP:	3.47
LogD:	3.16
LogS:	-3.871
# Rotatable Bonds:	1
TPSA:	55.84
# H-Bond Aceptor:	5
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.693
Synthetic Accessibility Score:	4.854
Fsp3:	0.667
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.92
MDCK Permeability:	2.7852873245137744e-05
Pgp-inhibitor:	0.211
Pgp-substrate:	0.005
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.985
30% Bioavailability (F30%):	0.955

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.988
Plasma Protein Binding (PPB):	46.61463165283203%
Volume Distribution (VD):	1.328
Pgp-substrate:	66.40660858154297%

ADMET: Metabolism

CYP1A2-inhibitor:	0.106
CYP1A2-substrate:	0.748
CYP2C19-inhibitor:	0.753
CYP2C19-substrate:	0.948
CYP2C9-inhibitor:	0.784
CYP2C9-substrate:	0.062
CYP2D6-inhibitor:	0.727
CYP2D6-substrate:	0.168
CYP3A4-inhibitor:	0.829
CYP3A4-substrate:	0.94

ADMET: Excretion

Clearance (CL):	7.167
Half-life (T1/2):	0.147

ADMET: Toxicity

hERG Blockers:	0.011
Human Hepatotoxicity (H-HT):	0.346
Drug-inuced Liver Injury (DILI):	0.176
AMES Toxicity:	0.91
Rat Oral Acute Toxicity:	0.263
Maximum Recommended Daily Dose:	0.313
Skin Sensitization:	0.043
Carcinogencity:	0.589
Eye Corrosion:	0.004
Eye Irritation:	0.013
Respiratory Toxicity:	0.822

Download Data

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

Natural Product: NPC295089

Natural Product ID:	NPC295089
*Common Name:**	YRGLLFADJRHUKM-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YRGLLFADJRHUKM-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C18H23NO4/c1-11-13-7-4-5-9-19-10-6-8-17(13,19)18(14(11)20)15(22-3)12(2)16(21)23-18/h4-10H2,1-3H3
SMILES:	CC1=C2CCCCN3CCCC23C2(C1=O)C(=C(C)C(=O)O2)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	181709
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000307] Azepanes

*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
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15679323]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	roots	n.a.	n.a.	PMID[16643052]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	Roots; Stems; Tubers	n.a.	n.a.	PMID[16872143]
NPO28230	Stemona japonica	Species	Stemonaceae	Eukaryota	stems and leaves	n.a.	n.a.	PMID[18163592]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	roots	n.a.	n.a.	PMID[18452334]
NPO19780	Stemona sessilifolia	Species	Stemonaceae	Eukaryota	n.a.	root	n.a.	PMID[21902195]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[21902195]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	n.a.	tuberous root	n.a.	PMID[21902195]
NPO28230	Stemona japonica	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19780	Stemona sessilifolia	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28230	Stemona japonica	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20195	Radix stemonae preparata	Species	Lymnaeidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19780	Stemona sessilifolia	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28230	Stemona japonica	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO19780	Stemona sessilifolia	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28230	Stemona japonica	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO19780	Stemona sessilifolia	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28230	Stemona japonica	Species	Stemonaceae	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 NPC295089 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	145
0.1-0.2	1089
0.2-0.3	8617
0.3-0.4	22973
0.4-0.5	8203
0.5-0.6	1556
0.6-0.7	111
0.7-0.8	2
0.8-0.85	0
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 NPC295089 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	113
0.1-0.2	887
0.2-0.3	3653
0.3-0.4	3646
0.4-0.5	791
0.5-0.6	58
0.6-0.7	2
0.7-0.8	0
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