NPASS Compound

Structure

NPC39114 OpenBabel06302215172D 22 24 0 0 1 0 0 0 0 0999 V2000 -2.5164 -3.6675 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7169 -3.0668 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7969 -3.4587 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8375 -2.0741 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9024 -1.7195 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2393 -0.9709 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6015 -0.4855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4676 -0.9855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6015 0.4855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2393 0.9709 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9024 1.7195 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8375 2.0741 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7169 3.0668 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8302 1.9535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6531 1.3855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1179 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.1179 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.5711 -1.3373 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6531 -1.3855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8302 -1.9535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9839 -0.0000 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 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 20 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 22 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 10 22 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 6 0 0 0 12 14 1 0 0 0 0 14 15 1 0 0 0 0 16 15 1 1 0 0 0 16 17 1 0 0 0 0 16 21 1 0 0 0 0 17 18 1 1 0 0 0 17 19 1 0 0 0 0 17 21 1 0 0 0 0 19 20 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	302.22
Volume:	338.478
LogP:	5.851
LogD:	4.938
LogS:	-5.159
# Rotatable Bonds:	1
TPSA:	25.67
# H-Bond Aceptor:	2
# H-Bond Donor:	0
# Rings:	3
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.637
Synthetic Accessibility Score:	5.539
Fsp3:	0.7
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:	-4.609
MDCK Permeability:	2.030474934144877e-05
Pgp-inhibitor:	0.986
Pgp-substrate:	0.006
Human Intestinal Absorption (HIA):	0.002
20% Bioavailability (F20%):	0.015
30% Bioavailability (F30%):	0.02

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.075
Plasma Protein Binding (PPB):	96.63436126708984%
Volume Distribution (VD):	3.1
Pgp-substrate:	2.610243558883667%

ADMET: Metabolism

CYP1A2-inhibitor:	0.392
CYP1A2-substrate:	0.708
CYP2C19-inhibitor:	0.372
CYP2C19-substrate:	0.917
CYP2C9-inhibitor:	0.501
CYP2C9-substrate:	0.372
CYP2D6-inhibitor:	0.178
CYP2D6-substrate:	0.765
CYP3A4-inhibitor:	0.651
CYP3A4-substrate:	0.442

ADMET: Excretion

Clearance (CL):	9.495
Half-life (T1/2):	0.08

ADMET: Toxicity

hERG Blockers:	0.026
Human Hepatotoxicity (H-HT):	0.801
Drug-inuced Liver Injury (DILI):	0.839
AMES Toxicity:	0.018
Rat Oral Acute Toxicity:	0.273
Maximum Recommended Daily Dose:	0.883
Skin Sensitization:	0.243
Carcinogencity:	0.859
Eye Corrosion:	0.003
Eye Irritation:	0.019
Respiratory Toxicity:	0.492

Download Data

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

Natural Product: NPC39114

Natural Product ID:	NPC39114
*Common Name:**	CAYPXRVDKAIIKY-SSCWMJKZSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	CAYPXRVDKAIIKY-SSCWMJKZSA-N
Standard InCHI:	InChI=1S/C20H30O2/c1-13(2)16-8-9-20(5)19(22-20)7-6-14(3)10-17-11-15(4)18(12-16)21-17/h11-14,19H,6-10H2,1-5H3/b16-12+/t14-,19-,20-/m0/s1
SMILES:	CC(C)/C/1=C/c2c(C)cc(C[C@@H](C)CC[C@H]3[C@](C)(CC1)O3)o2
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0004144] Heteroaromatic compounds

*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
NPO19125	Hoppea dichotoma	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/S0031-9422(00)84903-1]
NPO19125	Hoppea dichotoma	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11190384]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	fruit	n.a.	PMID[16417304]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	branch	n.a.	PMID[17202693]
NPO17716	Calendula arvensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1965654]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	Bark	n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17716	Calendula arvensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO16826	Streptomyces refuineus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO15968	Annella mollis	Species	Subergorgiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17716	Calendula arvensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1307	Rabdosia trichocarpa	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18789	Cosmos caudatus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16097	Ottonia corcovadensis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO10708	Colchicum kesselringii	Species	Colchicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19125	Hoppea dichotoma	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7783	Agathosma affinis	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11591	Rhododendron simiarum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18846	Gastrolobium grandiflorum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15604	Bombax oleagineum	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18705	Sinularia crassa	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16964	Aplophyllum tenue	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO18376	Oryctolagus cuniculus	Species	Leporidae	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 NPC39114 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	361
0.1-0.2	1506
0.2-0.3	4445
0.3-0.4	10803
0.4-0.5	8938
0.5-0.6	9526
0.6-0.7	6543
0.7-0.8	531
0.8-0.85	39
0.85-0.9	5
0.9-0.95	0
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 NPC39114 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	337
0.1-0.2	1044
0.2-0.3	1651
0.3-0.4	2817
0.4-0.5	1930
0.5-0.6	1078
0.6-0.7	282
0.7-0.8	11
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