NPASS Compound

Structure

NPC305684 OpenBabel06302215482D 26 27 0 0 1 0 0 0 0 0999 V2000 -1.7321 3.0000 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 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 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 -1.7321 -1.0000 0.0000 C 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 -0.8660 -1.5000 0.0000 O 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 0.8660 -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 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 4.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8660 6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3660 5.6340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 7.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 8.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 18 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 17 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 8 10 1 0 0 0 0 10 11 1 0 0 0 0 11 17 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 15 16 1 0 0 0 0 15 17 1 0 0 0 0 18 19 1 0 0 0 0 18 26 1 6 0 0 0 19 20 2 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 21 23 1 0 0 0 0 21 24 1 0 0 0 0 24 25 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	360.16
Volume:	371.649
LogP:	2.024
LogD:	2.301
LogS:	-3.637
# Rotatable Bonds:	7
TPSA:	89.13
# H-Bond Aceptor:	6
# H-Bond Donor:	2
# Rings:	2
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.339
Synthetic Accessibility Score:	3.751
Fsp3:	0.35
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.817
MDCK Permeability:	1.5540650565526448e-05
Pgp-inhibitor:	0.083
Pgp-substrate:	0.282
Human Intestinal Absorption (HIA):	0.54
20% Bioavailability (F20%):	0.75
30% Bioavailability (F30%):	0.985

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.004
Plasma Protein Binding (PPB):	90.75293731689453%
Volume Distribution (VD):	0.787
Pgp-substrate:	3.017348527908325%

ADMET: Metabolism

CYP1A2-inhibitor:	0.83
CYP1A2-substrate:	0.94
CYP2C19-inhibitor:	0.462
CYP2C19-substrate:	0.383
CYP2C9-inhibitor:	0.512
CYP2C9-substrate:	0.941
CYP2D6-inhibitor:	0.47
CYP2D6-substrate:	0.877
CYP3A4-inhibitor:	0.237
CYP3A4-substrate:	0.331

ADMET: Excretion

Clearance (CL):	5.303
Half-life (T1/2):	0.467

ADMET: Toxicity

hERG Blockers:	0.013
Human Hepatotoxicity (H-HT):	0.668
Drug-inuced Liver Injury (DILI):	0.214
AMES Toxicity:	0.644
Rat Oral Acute Toxicity:	0.159
Maximum Recommended Daily Dose:	0.976
Skin Sensitization:	0.56
Carcinogencity:	0.204
Eye Corrosion:	0.007
Eye Irritation:	0.825
Respiratory Toxicity:	0.939

Download Data

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

Natural Product: NPC305684

Natural Product ID:	NPC305684
*Common Name:**	VQIKMKPDMSGMTM-ZKYMSZQWSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	VQIKMKPDMSGMTM-ZKYMSZQWSA-N
Standard InCHI:	InChI=1S/C20H24O6/c1-13(15(21)8-10-20(3,4)26-23)9-11-24-17-12-18(22)25-16-7-5-6-14(2)19(16)17/h5-10,12,15,21,23H,11H2,1-4H3/b10-8+,13-9+/t15-/m1/s1
SMILES:	C/C(=CCOc1cc(=O)oc2cccc(C)c12)/[C@@H](/C=C/C(C)(C)OO)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000145] Coumarins 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
NPO11874	Ambrosia hispida	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14802.1	Lonicera tatarica var. morrowii	Varieties	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11874	Ambrosia hispida	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11695	Petasites hybridus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1965	Alnus incana	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5668	Allium waldsteinii	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7387	Aster batangensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11874	Ambrosia hispida	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10034	Penstemon mucronatus	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14802.1	Lonicera tatarica var. morrowii	Varieties	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6008	Cacalia pilgeriana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1545	Baeckea crenulata	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6402	Sideritis kuegleriana	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10637	Byssochlamys fulva	Species	Thermoascaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2544	Stemona saxorum	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12264	Mutisia orbignyana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8742	Hamamelistes betulae	Species	Hormaphididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3661	Goniothalamus tamirensis	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12388	Saccharopolyspora hirsuta	Species	Pseudonocardiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO12606	Achillea spinulifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7743	Helicoverpa zea	Species	0ctuidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9256	Lecanora nipponica	Species	Lecanoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12491	Astragalus onobrychis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10302	Sphagnum rubellum	Species	Sphagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12036	Fritillaria raddeana	Species	Liliaceae	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 NPC305684 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	326
0.1-0.2	1483
0.2-0.3	3667
0.3-0.4	8732
0.4-0.5	10105
0.5-0.6	4183
0.6-0.7	6661
0.7-0.8	6625
0.8-0.85	801
0.85-0.9	104
0.9-0.95	10
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 NPC305684 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	277
0.1-0.2	937
0.2-0.3	1604
0.3-0.4	2487
0.4-0.5	2038
0.5-0.6	1196
0.6-0.7	446
0.7-0.8	143
0.8-0.85	17
0.85-0.9	5
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