NPASS Compound

Structure

NPC226813 OpenBabel06302216042D 23 22 0 0 1 0 0 0 0 0999 V2000 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 -1.7321 2.0000 0.0000 C 0 0 1 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 1.5000 0.0000 C 0 0 2 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 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1962 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6962 1.1340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 0.0000 O 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 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 -0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 3 23 1 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 6 7 1 0 0 0 0 7 8 1 6 0 0 0 7 9 1 0 0 0 0 9 10 1 1 0 0 0 9 19 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 12 14 1 0 0 0 0 12 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 16 18 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	426.39
Volume:	490.807
LogP:	8.094
LogD:	5.656
LogS:	-6.729
# Rotatable Bonds:	4
TPSA:	20.23
# H-Bond Aceptor:	1
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	1

MedChem Properties

QED Drug-Likeness Score:	0.449
Synthetic Accessibility Score:	5.378
Fsp3:	0.933
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.979
MDCK Permeability:	1.0814539564307779e-05
Pgp-inhibitor:	0.008
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.993
30% Bioavailability (F30%):	0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.082
Plasma Protein Binding (PPB):	95.6999282836914%
Volume Distribution (VD):	1.373
Pgp-substrate:	1.6974971294403076%

ADMET: Metabolism

CYP1A2-inhibitor:	0.047
CYP1A2-substrate:	0.18
CYP2C19-inhibitor:	0.098
CYP2C19-substrate:	0.942
CYP2C9-inhibitor:	0.217
CYP2C9-substrate:	0.192
CYP2D6-inhibitor:	0.136
CYP2D6-substrate:	0.199
CYP3A4-inhibitor:	0.784
CYP3A4-substrate:	0.518

ADMET: Excretion

Clearance (CL):	12.821
Half-life (T1/2):	0.03

ADMET: Toxicity

hERG Blockers:	0.721
Human Hepatotoxicity (H-HT):	0.455
Drug-inuced Liver Injury (DILI):	0.036
AMES Toxicity:	0.001
Rat Oral Acute Toxicity:	0.368
Maximum Recommended Daily Dose:	0.907
Skin Sensitization:	0.948
Carcinogencity:	0.069
Eye Corrosion:	0.367
Eye Irritation:	0.227
Respiratory Toxicity:	0.935

Download Data

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

Natural Product: NPC226813

Natural Product ID:	NPC226813
*Common Name:**	GYTQVGSRQSVLQM-VFGFEDTLSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	GYTQVGSRQSVLQM-VFGFEDTLSA-N
Standard InCHI:	InChI=1S/C19H28O4/c1-8-14(2)10-9-11-15(3)18(22-16(4)20)12-13-19(6,7)23-17(5)21/h8-13,15,18H,1H2,2-7H3/b11-9+,13-12+,14-10+/t15-,18+/m1/s1
SMILES:	C=C/C(=C/C=C/[C@@H](C)[C@H](/C=C/C(C)(C)OC(=O)C)OC(=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
NPO9839	Polanisia dodecandra	Species	Cleomaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[1453183]
NPO5270	Citrus natsudaidai	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17689080]
NPO27241	Prunus tomentosa	Species	Rosaceae	Eukaryota	n.a.	seed	n.a.	PMID[18449498]
NPO27241	Prunus tomentosa	Species	Rosaceae	Eukaryota	leaves	n.a.	n.a.	PMID[24767839]
NPO9839	Polanisia dodecandra	Species	Cleomaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7623025]
NPO27241	Prunus tomentosa	Species	Rosaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO27241	Prunus tomentosa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27241	Prunus tomentosa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5270	Citrus natsudaidai	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Title]
NPO5270	Citrus natsudaidai	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4070	Eupatorium sternbergianum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9636	Micromonospora coerulea	Species	Micromonosporaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO12496	Elsholtzia blanda	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9839	Polanisia dodecandra	Species	Cleomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6821	Tricholoma muscarium	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5270	Citrus natsudaidai	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11588	Astragalus sevangensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10954	Topsentia genitrix	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1260	Chlorosplenium aeruginosum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO5679	Topsentia roquensis	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27241	Prunus tomentosa	Species	Rosaceae	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 NPC226813 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	158
0.1-0.2	3610
0.2-0.3	15707
0.3-0.4	15155
0.4-0.5	5657
0.5-0.6	1998
0.6-0.7	350
0.7-0.8	60
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
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 NPC226813 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	138
0.1-0.2	3321
0.2-0.3	4115
0.3-0.4	1320
0.4-0.5	188
0.5-0.6	59
0.6-0.7	7
0.7-0.8	2
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