NPASS Compound

Structure

NPC81260 OpenBabel06302216192D 25 24 0 0 1 0 0 0 0 0999 V2000 10.3923 14.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 14.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 15.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 14.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 13.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 13.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 12.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 11.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 10.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 10.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 9.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 8.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 2.0000 0.0000 C 0 0 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 2 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 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 1 2 3 0 0 0 0 2 3 1 0 0 0 0 3 4 2 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 3 0 0 0 0 12 13 1 0 0 0 0 13 14 3 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 3 0 0 0 0 19 20 1 0 0 0 0 20 21 3 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 22 25 1 1 0 0 0 23 24 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	334.19
Volume:	394.944
LogP:	5.409
LogD:	2.839
LogS:	-5.489
# Rotatable Bonds:	9
TPSA:	40.46
# H-Bond Aceptor:	2
# H-Bond Donor:	2
# Rings:	0
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.503
Synthetic Accessibility Score:	4.283
Fsp3:	0.478
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:	-4.237
MDCK Permeability:	0.00012180383055238053
Pgp-inhibitor:	0.026
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.909
20% Bioavailability (F20%):	0.968
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.001
Plasma Protein Binding (PPB):	103.35517120361328%
Volume Distribution (VD):	1.725
Pgp-substrate:	1.1323130130767822%

ADMET: Metabolism

CYP1A2-inhibitor:	0.668
CYP1A2-substrate:	0.134
CYP2C19-inhibitor:	0.747
CYP2C19-substrate:	0.169
CYP2C9-inhibitor:	0.599
CYP2C9-substrate:	0.98
CYP2D6-inhibitor:	0.239
CYP2D6-substrate:	0.126
CYP3A4-inhibitor:	0.618
CYP3A4-substrate:	0.09

ADMET: Excretion

Clearance (CL):	7.813
Half-life (T1/2):	0.107

ADMET: Toxicity

hERG Blockers:	0.001
Human Hepatotoxicity (H-HT):	0.532
Drug-inuced Liver Injury (DILI):	0.985
AMES Toxicity:	0.729
Rat Oral Acute Toxicity:	0.966
Maximum Recommended Daily Dose:	0.993
Skin Sensitization:	0.972
Carcinogencity:	0.195
Eye Corrosion:	0.948
Eye Irritation:	0.984
Respiratory Toxicity:	0.869

Download Data

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

Natural Product: NPC81260

Natural Product ID:	NPC81260
*Common Name:**	CXKNSXTVPUUYQM-GYLQWBMOSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	CXKNSXTVPUUYQM-GYLQWBMOSA-N
Standard InCHI:	InChI=1S/C23H26O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-23(25)22-24/h1,3-4,23-25H,5-10,15-17,22H2/b4-3-/t23-/m1/s1
SMILES:	C#C/C=CCCCCCCC#CC#CCCCC#CC#C[C@H](CO)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	23425929
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0001334] Fatty alcohols

*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
NPO29092	Machilus japonica	Species	Lauraceae	Eukaryota	leaves	n.a.	n.a.	PMID[19719245]
NPO29092	Machilus japonica	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29316	Thalictrum baicalense	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29092	Machilus japonica	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3251	Jacobaea maritima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29316	Thalictrum baicalense	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29304	Pseudosindora palustris	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29092	Machilus japonica	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29501	Pinus oocarpa	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29425	Teucrium africanum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3251	Jacobaea maritima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29316	Thalictrum baicalense	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15777	Didymella pinodes	Species	Didymellaceae	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 NPC81260 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	147
0.1-0.2	7593
0.2-0.3	21186
0.3-0.4	10117
0.4-0.5	2780
0.5-0.6	614
0.6-0.7	125
0.7-0.8	61
0.8-0.85	60
0.85-0.9	13
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 NPC81260 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	151
0.1-0.2	5008
0.2-0.3	3236
0.3-0.4	591
0.4-0.5	142
0.5-0.6	19
0.6-0.7	3
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