NPASS Compound

Structure

NPC122848 OpenBabel06302215512D 35 40 0 0 1 0 0 0 0 0999 V2000 -3.0958 -0.8856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2613 -0.4038 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2613 0.5598 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0958 1.0417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4268 1.0417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4268 2.0053 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5922 0.5598 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5922 -0.4038 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.4268 -0.8856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6458 -1.1186 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.5428 -1.4706 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1204 -1.6061 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.1198 -2.5351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6850 -2.9997 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4897 -1.6058 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.2950 -1.1409 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.1003 -1.6058 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9056 -1.1408 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.9057 -0.2109 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7107 0.2535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7104 1.1829 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9051 1.6479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1001 1.1834 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2907 1.6507 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1004 0.2540 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.2910 0.7213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2951 -0.2110 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.4903 0.2537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6850 -0.2113 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.6849 -1.1412 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.4943 -0.6739 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6850 0.7233 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 4.7150 -1.6081 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9297 -2.0734 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 9 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 3 5 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 8 33 1 0 0 0 0 8 9 1 1 0 0 0 8 10 1 0 0 0 0 10 11 1 6 0 0 0 10 12 1 0 0 0 0 12 30 1 0 0 0 0 12 13 1 0 0 0 0 12 35 1 6 0 0 0 13 14 1 0 0 0 0 15 14 1 6 0 0 0 15 16 1 0 0 0 0 15 30 1 0 0 0 0 16 17 1 1 0 0 0 16 27 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 18 34 1 6 0 0 0 19 25 1 0 0 0 0 19 20 2 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 23 25 1 0 0 0 0 25 26 1 6 0 0 0 25 27 1 0 0 0 0 27 28 1 6 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 29 32 1 6 0 0 0 29 33 1 0 0 0 0 30 31 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	484.25
Volume:	489.855
LogP:	2.732
LogD:	2.622
LogS:	-4.529
# Rotatable Bonds:	0
TPSA:	110.13
# H-Bond Aceptor:	7
# H-Bond Donor:	2
# Rings:	6
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.507
Synthetic Accessibility Score:	6.085
Fsp3:	0.75
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:	-4.92
MDCK Permeability:	2.31727390200831e-05
Pgp-inhibitor:	0.997
Pgp-substrate:	0.97
Human Intestinal Absorption (HIA):	0.023
20% Bioavailability (F20%):	0.908
30% Bioavailability (F30%):	0.987

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.934
Plasma Protein Binding (PPB):	71.74650573730469%
Volume Distribution (VD):	0.489
Pgp-substrate:	19.567611694335938%

ADMET: Metabolism

CYP1A2-inhibitor:	0.017
CYP1A2-substrate:	0.951
CYP2C19-inhibitor:	0.537
CYP2C19-substrate:	0.817
CYP2C9-inhibitor:	0.353
CYP2C9-substrate:	0.031
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.062
CYP3A4-inhibitor:	0.932
CYP3A4-substrate:	0.826

ADMET: Excretion

Clearance (CL):	11.153
Half-life (T1/2):	0.211

ADMET: Toxicity

hERG Blockers:	0.046
Human Hepatotoxicity (H-HT):	0.607
Drug-inuced Liver Injury (DILI):	0.055
AMES Toxicity:	0.034
Rat Oral Acute Toxicity:	0.35
Maximum Recommended Daily Dose:	0.946
Skin Sensitization:	0.796
Carcinogencity:	0.718
Eye Corrosion:	0.004
Eye Irritation:	0.015
Respiratory Toxicity:	0.973

Download Data

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

Natural Product: NPC122848

Natural Product ID:	NPC122848
*Common Name:**	QWEIHMIYLYYENY-CXDIKLOLSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	QWEIHMIYLYYENY-CXDIKLOLSA-N
Standard InCHI:	InChI=1S/C28H36O7/c1-14-12-27(34-23(31)15(14)2)16(3)26(32)10-9-18-17-11-21(29)19-7-6-8-22(30)24(19,4)20(17)13-28(33,35-27)25(18,26)5/h6-8,16-18,20-21,29,32-33H,9-13H2,1-5H3/t16-,17-,18-,20-,21+,24-,25-,26+,27+,28-/m0/s1
SMILES:	CC1=C(C)C(=O)O[C@@]2(C1)[C@@H](C)[C@@]1(CC[C@H]3[C@@H]4C[C@H](C5=CC=CC(=O)[C@]5(C)[C@H]4C[C@]([C@]13C)(O)O2)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	44583787
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001125] Steroid lactones [CHEMONTID:0001560] Withanolides 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
NPO25879	Calophyllum soulattri	Species	Calophyllaceae	Eukaryota	n.a.	bark	n.a.	DOI[10.1039/P19770001505]
NPO16930	Jaborosa rotacea	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16724841]
NPO15768	Lyonia ovalifolia	Species	Ericaceae	Eukaryota	Twigs; Leaves	n.a.	n.a.	PMID[27792321]
NPO15768	Lyonia ovalifolia	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15929	Corydalis ledebouriana	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15929	Corydalis ledebouriana	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15768	Lyonia ovalifolia	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15768	Lyonia ovalifolia	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15929	Corydalis ledebouriana	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15768	Lyonia ovalifolia	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17008	Cephalaria coriacea	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14324	Lopholaena segmentata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16930	Jaborosa rotacea	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14823	Pinus reflexa	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13821	Halophila stipulacea	Species	Hydrocharitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10240	Canarium commun	Species	Strombidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15929	Corydalis ledebouriana	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17080	Melicope patulinervia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27896	Malacosoma californicum	Species	Lasiocampidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25879	Calophyllum soulattri	Species	Calophyllaceae	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 NPC122848 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

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 NPC122848 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

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