NPASS Compound

Structure

NPC18666 OpenBabel06302216012D 25 25 0 0 1 0 0 0 0 0999 V2000 6.9282 7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 8.5000 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 1 0 0 0 0 0 0 0 0 0 4.3301 5.5000 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 3.4641 4.0000 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 2.5981 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 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 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 -0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 O 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 3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 5.5000 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 2 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 5 25 1 6 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 7 24 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 2 0 0 0 0 11 23 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 20 2 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 16 22 1 0 0 0 0 17 18 1 0 0 0 0 17 19 2 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	346.25
Volume:	393.7
LogP:	4.942
LogD:	4.657
LogS:	-4.797
# Rotatable Bonds:	9
TPSA:	60.69
# H-Bond Aceptor:	3
# H-Bond Donor:	3
# Rings:	1
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.413
Synthetic Accessibility Score:	3.373
Fsp3:	0.545
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:	-4.767
MDCK Permeability:	2.4360400857403874e-05
Pgp-inhibitor:	0.48
Pgp-substrate:	0.972
Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.978
30% Bioavailability (F30%):	0.977

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.058
Plasma Protein Binding (PPB):	98.13826751708984%
Volume Distribution (VD):	0.54
Pgp-substrate:	0.9526833891868591%

ADMET: Metabolism

CYP1A2-inhibitor:	0.707
CYP1A2-substrate:	0.466
CYP2C19-inhibitor:	0.639
CYP2C19-substrate:	0.282
CYP2C9-inhibitor:	0.749
CYP2C9-substrate:	0.966
CYP2D6-inhibitor:	0.896
CYP2D6-substrate:	0.86
CYP3A4-inhibitor:	0.407
CYP3A4-substrate:	0.194

ADMET: Excretion

Clearance (CL):	8.918
Half-life (T1/2):	0.803

ADMET: Toxicity

hERG Blockers:	0.013
Human Hepatotoxicity (H-HT):	0.045
Drug-inuced Liver Injury (DILI):	0.012
AMES Toxicity:	0.007
Rat Oral Acute Toxicity:	0.005
Maximum Recommended Daily Dose:	0.967
Skin Sensitization:	0.941
Carcinogencity:	0.029
Eye Corrosion:	0.019
Eye Irritation:	0.908
Respiratory Toxicity:	0.223

Download Data

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

Natural Product: NPC18666

Natural Product ID:	NPC18666
*Common Name:**	JUHGRLPYQZPVAA-NYVZZTIHSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JUHGRLPYQZPVAA-NYVZZTIHSA-N
Standard InCHI:	InChI=1S/C22H34O3/c1-15(2)11-20(23)12-17(4)8-6-7-16(3)9-10-19-14-21(24)18(5)13-22(19)25/h8-9,13-15,20,23-25H,6-7,10-12H2,1-5H3/b16-9+,17-8+/t20-/m0/s1
SMILES:	CC(C)C[C@@H](C/C(=C/CC/C(=C/Cc1cc(c(C)cc1O)O)/C)/C)O
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
NPO25807	Psacalium decompositum	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[10479309]
NPO23229	Cochliobolus lunatus	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12027752]
NPO27387	Erythrina addisoniae	Species	Fabaceae	Eukaryota	Stems; Barks	n.a.	n.a.	PMID[12828487]
NPO27352	Cleistopholis patens	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16643031]
NPO26960	Cyclosorus acuminatus	Species	Thelypteridaceae	Eukaryota	rhizomes	n.a.	n.a.	PMID[17125239]
NPO27387	Erythrina addisoniae	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17517504]
NPO27387	Erythrina addisoniae	Species	Fabaceae	Eukaryota	Barks	n.a.	n.a.	PMID[18302333]
NPO23229	Cochliobolus lunatus	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20527910]
NPO27387	Erythrina addisoniae	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20934335]
NPO27387	Erythrina addisoniae	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23022281]
NPO27190	Pittocaulon filare	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24842703]
NPO25807	Psacalium decompositum	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[32672964]
NPO27352	Cleistopholis patens	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3325614]
NPO23229	Cochliobolus lunatus	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9014347]
NPO27403	Aralia taibaiensis	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27403	Aralia taibaiensis	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27387	Erythrina addisoniae	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23229	Cochliobolus lunatus	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27190	Pittocaulon filare	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27352	Cleistopholis patens	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26960	Cyclosorus acuminatus	Species	Thelypteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25807	Psacalium decompositum	Species	n.a.	n.a.	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 NPC18666 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	250
0.1-0.2	1267
0.2-0.3	3815
0.3-0.4	12514
0.4-0.5	8123
0.5-0.6	10899
0.6-0.7	4634
0.7-0.8	945
0.8-0.85	170
0.85-0.9	62
0.9-0.95	18
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 NPC18666 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	232
0.1-0.2	923
0.2-0.3	1656
0.3-0.4	2958
0.4-0.5	1805
0.5-0.6	1143
0.6-0.7	370
0.7-0.8	57
0.8-0.85	2
0.85-0.9	4
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