NPASS Compound

Structure

NPC123888 OpenBabel06302216032D 26 26 0 0 0 0 0 0 0 0999 V2000 -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 -3.4641 -5.0000 0.0000 C 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 -2.5981 -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 -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 O 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 -2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 0.0000 0.0000 O 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 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 O 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 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 O 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 -3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -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 26 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 2 3 0 0 0 6 25 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 17 2 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 11 14 2 0 0 0 0 12 13 1 0 0 0 0 14 15 1 0 0 0 0 14 23 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 18 19 2 0 0 0 0 18 20 1 0 0 0 0 20 21 1 0 0 0 0 23 24 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	364.19
Volume:	382.842
LogP:	4.923
LogD:	3.49
LogS:	-3.577
# Rotatable Bonds:	10
TPSA:	85.22
# H-Bond Aceptor:	6
# H-Bond Donor:	2
# Rings:	1
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.513
Synthetic Accessibility Score:	2.874
Fsp3:	0.45
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-4.638
MDCK Permeability:	1.0435120202600956e-05
Pgp-inhibitor:	0.146
Pgp-substrate:	0.027
Human Intestinal Absorption (HIA):	0.013
20% Bioavailability (F20%):	0.822
30% Bioavailability (F30%):	0.043

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.323
Plasma Protein Binding (PPB):	82.91490173339844%
Volume Distribution (VD):	1.933
Pgp-substrate:	9.386311531066895%

ADMET: Metabolism

CYP1A2-inhibitor:	0.942
CYP1A2-substrate:	0.735
CYP2C19-inhibitor:	0.791
CYP2C19-substrate:	0.549
CYP2C9-inhibitor:	0.44
CYP2C9-substrate:	0.881
CYP2D6-inhibitor:	0.885
CYP2D6-substrate:	0.343
CYP3A4-inhibitor:	0.657
CYP3A4-substrate:	0.185

ADMET: Excretion

Clearance (CL):	12.042
Half-life (T1/2):	0.722

ADMET: Toxicity

hERG Blockers:	0.019
Human Hepatotoxicity (H-HT):	0.917
Drug-inuced Liver Injury (DILI):	0.321
AMES Toxicity:	0.061
Rat Oral Acute Toxicity:	0.025
Maximum Recommended Daily Dose:	0.018
Skin Sensitization:	0.236
Carcinogencity:	0.257
Eye Corrosion:	0.003
Eye Irritation:	0.089
Respiratory Toxicity:	0.101

Download Data

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

Natural Product: NPC123888

Natural Product ID:	NPC123888
*Common Name:**	VCIDBPJGNGIQDM-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	VCIDBPJGNGIQDM-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C20H28O6/c1-13(2)7-6-8-14(3)9-10-26-19-15(12-21)17(24-4)11-16(22)18(19)20(23)25-5/h7,9,11,21-22H,6,8,10,12H2,1-5H3
SMILES:	CC(=CCCC(=CCOc1c(CO)c(cc(c1C(=O)OC)O)OC)C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	71438032
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0002279] Benzene and substituted derivatives [CHEMONTID:0000176] Benzoic acids and derivatives [CHEMONTID:0002344] Methoxybenzoic acids and derivatives [CHEMONTID:0002346] P-methoxybenzoic acids 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
NPO7058	Australostichopus mollis	Species	Stichopodidae	Eukaryota	n.a.	n.a.	n.a.	PMID[15974605]
NPO7058	Australostichopus mollis	Species	Stichopodidae	Eukaryota	n.a.	n.a.	n.a.	PMID[22271309]
NPO1879	Feijoa sellowiana	Species	Myrtaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO1879	Feijoa sellowiana	Species	Myrtaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO1879	Feijoa sellowiana	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18490	Spiraea kamtschatica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18742	Cereus longispinus	Species	Sagartiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14576	Trichoderma atroviride	Species	Hypocreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18652	Melicope broadbentiana	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7058	Australostichopus mollis	Species	Stichopodidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17564	Puccinia arachidis	Species	Pucciniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22038	Lagarostrobos franklinii	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18403	Lagochilus platycalyx	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1879	Feijoa sellowiana	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22034	Eysenhardtia texana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19147	Rhodiola pamiroalaica	Species	Crassulaceae	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 NPC123888 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	307
0.1-0.2	1460
0.2-0.3	4217
0.3-0.4	9625
0.4-0.5	8896
0.5-0.6	3706
0.6-0.7	6201
0.7-0.8	5570
0.8-0.85	1715
0.85-0.9	860
0.9-0.95	138
0.95-1	2

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 NPC123888 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	261
0.1-0.2	956
0.2-0.3	1858
0.3-0.4	2579
0.4-0.5	1782
0.5-0.6	1122
0.6-0.7	401
0.7-0.8	148
0.8-0.85	26
0.85-0.9	17
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