NPASS Compound

Structure

NPC114844 OpenBabel06302215352D 47 47 0 0 0 0 0 0 0 0999 V2000 -16.4545 -28.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -15.5885 -29.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -14.7224 -28.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -14.7224 -27.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -13.8564 -27.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -13.8564 -26.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.9904 -25.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.9904 -24.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.1244 -24.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.1244 -23.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.2583 -22.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.2583 -21.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.3923 -21.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.3923 -20.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 -19.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 -18.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 -18.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 -17.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -16.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -15.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -15.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -14.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -13.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -12.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -12.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -11.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -10.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -9.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -9.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -8.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -6.0000 0.0000 C 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 -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 -0.0000 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 0.0000 O 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 -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 -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 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 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 2.5000 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 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 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 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 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 25 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 30 31 1 0 0 0 0 31 32 1 0 0 0 0 32 33 1 0 0 0 0 33 34 1 0 0 0 0 34 35 1 0 0 0 0 35 36 1 0 0 0 0 36 37 2 0 0 0 0 36 38 1 0 0 0 0 38 39 1 0 0 0 0 39 40 1 0 0 0 0 40 41 1 0 0 0 0 41 46 2 0 0 0 0 41 42 1 0 0 0 0 42 43 2 0 0 0 0 43 44 1 0 0 0 0 44 45 2 0 0 0 0 44 47 1 0 0 0 0 45 46 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	656.61
Volume:	776.848
LogP:	15.969
LogD:	5.598
LogS:	-7.77
# Rotatable Bonds:	38
TPSA:	46.53
# H-Bond Aceptor:	3
# H-Bond Donor:	1
# Rings:	1
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.057
Synthetic Accessibility Score:	2.4
Fsp3:	0.841
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.583
MDCK Permeability:	8.52637072057405e-07
Pgp-inhibitor:	0.0
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.52
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0
Plasma Protein Binding (PPB):	105.56822967529297%
Volume Distribution (VD):	4.979
Pgp-substrate:	0.2049199491739273%

ADMET: Metabolism

CYP1A2-inhibitor:	0.015
CYP1A2-substrate:	0.092
CYP2C19-inhibitor:	0.087
CYP2C19-substrate:	0.035
CYP2C9-inhibitor:	0.01
CYP2C9-substrate:	0.996
CYP2D6-inhibitor:	0.017
CYP2D6-substrate:	0.012
CYP3A4-inhibitor:	0.131
CYP3A4-substrate:	0.014

ADMET: Excretion

Clearance (CL):	4.755
Half-life (T1/2):	0.011

ADMET: Toxicity

hERG Blockers:	0.673
Human Hepatotoxicity (H-HT):	0.005
Drug-inuced Liver Injury (DILI):	0.243
AMES Toxicity:	0.014
Rat Oral Acute Toxicity:	0.005
Maximum Recommended Daily Dose:	0.031
Skin Sensitization:	0.992
Carcinogencity:	0.013
Eye Corrosion:	0.764
Eye Irritation:	0.915
Respiratory Toxicity:	0.314

Download Data

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

Natural Product: NPC114844

Natural Product ID:	NPC114844
*Common Name:**	XXNPILBXOYDBBZ-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XXNPILBXOYDBBZ-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C44H80O3/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22-23-24-25-26-27-28-29-30-31-32-33-34-35-44(46)47-41-40-42-36-38-43(45)39-37-42/h36-39,45H,2-35,40-41H2,1H3
SMILES:	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC(=O)OCCc1ccc(cc1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	102420150
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000134] Phenols [CHEMONTID:0000139] Tyrosols and derivatives

*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]
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]
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]

☑ 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 NPC114844 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	193
0.1-0.2	956
0.2-0.3	2954
0.3-0.4	8868
0.4-0.5	11054
0.5-0.6	8892
0.6-0.7	8088
0.7-0.8	1550
0.8-0.85	123
0.85-0.9	16
0.9-0.95	2
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 NPC114844 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	176
0.1-0.2	772
0.2-0.3	1393
0.3-0.4	2603
0.4-0.5	2136
0.5-0.6	1344
0.6-0.7	601
0.7-0.8	119
0.8-0.85	6
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