NPASS Compound

Structure

NPC170913 OpenBabel06302215232D 28 30 0 0 1 0 0 0 0 0999 V2000 0.8660 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -4.0000 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 0.8660 -2.5000 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 -1.0000 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 -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 2 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 -2.5981 1.5000 0.0000 C 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 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 0.5000 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 -5.2812 0.1910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.8690 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2812 1.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 C 0 0 2 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 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 3.0000 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 0.8660 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -4.5000 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 28 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 20 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 6 0 0 0 9 19 1 0 0 0 0 10 15 2 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 13 18 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 14 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 19 20 1 0 0 0 0 19 21 1 1 0 0 0 21 22 2 3 0 0 0 21 27 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 24 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	383.25
Volume:	419.539
LogP:	6.462
LogD:	4.671
LogS:	-6.022
# Rotatable Bonds:	8
TPSA:	47.56
# H-Bond Aceptor:	4
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.645
Synthetic Accessibility Score:	3.555
Fsp3:	0.542
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.602
MDCK Permeability:	2.444903839204926e-05
Pgp-inhibitor:	0.997
Pgp-substrate:	0.003
Human Intestinal Absorption (HIA):	0.001
20% Bioavailability (F20%):	0.987
30% Bioavailability (F30%):	0.955

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.115
Plasma Protein Binding (PPB):	96.56282806396484%
Volume Distribution (VD):	5.404
Pgp-substrate:	2.947676420211792%

ADMET: Metabolism

CYP1A2-inhibitor:	0.687
CYP1A2-substrate:	0.155
CYP2C19-inhibitor:	0.951
CYP2C19-substrate:	0.659
CYP2C9-inhibitor:	0.93
CYP2C9-substrate:	0.941
CYP2D6-inhibitor:	0.932
CYP2D6-substrate:	0.757
CYP3A4-inhibitor:	0.942
CYP3A4-substrate:	0.26

ADMET: Excretion

Clearance (CL):	17.895
Half-life (T1/2):	0.06

ADMET: Toxicity

hERG Blockers:	0.107
Human Hepatotoxicity (H-HT):	0.717
Drug-inuced Liver Injury (DILI):	0.275
AMES Toxicity:	0.02
Rat Oral Acute Toxicity:	0.013
Maximum Recommended Daily Dose:	0.434
Skin Sensitization:	0.2
Carcinogencity:	0.9
Eye Corrosion:	0.003
Eye Irritation:	0.014
Respiratory Toxicity:	0.669

Download Data

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

Natural Product: NPC170913

Natural Product ID:	NPC170913
*Common Name:**	HCTXZDQPRLPYOB-RTWAWAEBSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HCTXZDQPRLPYOB-RTWAWAEBSA-N
Standard InCHI:	InChI=1S/C24H33NO3/c1-16(2)6-5-7-18-8-10-20(21(12-18)24(26)25-14-17(3)4)19-9-11-22-23(13-19)28-15-27-22/h6,8-9,11,13,17,20-21H,5,7,10,12,14-15H2,1-4H3,(H,25,26)/t20-,21+/m1/s1
SMILES:	CC(=CCCC1=CC[C@H](c2ccc3c(c2)OCO3)[C@H](C1)C(=NCC(C)C)O)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:0001549] Monoterpenoids [CHEMONTID:0001564] Bicyclic monoterpenoids

*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
NPO4756	Mesua elegans	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20943395]
NPO5710	Michelia rajaniana	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3236012]
NPO9469	Digitalis obscura	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25530	Daphne blagayana	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29440	Sarcomyxa serotina	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4442	Artemisia austriaca	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO81	Erythrina orientalis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3215	Phora atra	Species	Phoridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5710	Michelia rajaniana	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9318	Stevia serrata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4756	Mesua elegans	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO924	Russula subnigricans	Species	Russulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28383	Vernonia tufnellae	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11244	Chrysolaena propinqua	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12990	Umbelopsis vinacea	Species	Umbelopsidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8378	Fagara heitzii	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO6557	Lotus villosus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5060	Onychopetalum amazonicum	Species	Annonaceae	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 NPC170913 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	179
0.1-0.2	1274
0.2-0.3	4419
0.3-0.4	13427
0.4-0.5	5478
0.5-0.6	11585
0.6-0.7	5068
0.7-0.8	1193
0.8-0.85	55
0.85-0.9	2
0.9-0.95	16
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 NPC170913 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	148
0.1-0.2	732
0.2-0.3	1135
0.3-0.4	2530
0.4-0.5	2433
0.5-0.6	1411
0.6-0.7	659
0.7-0.8	95
0.8-0.85	7
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