NPASS Compound

Structure

NPC48075 OpenBabel06302216012D 31 32 0 0 1 0 0 0 0 0999 V2000 -3.2321 -1.1340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2321 -1.1340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 C 0 0 2 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 -1.2321 -2.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7321 -3.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2321 -2.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2321 -2.8660 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 1 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 1.0000 0.0000 C 0 0 1 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 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5411 -0.5878 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.2321 -1.5388 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.3366 -2.5334 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5276 -3.1211 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2321 -1.5388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9230 -0.5878 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1456 -1.9456 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4921 -0.2788 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 -0.8660 2.5000 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 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 3 4 1 6 0 0 0 3 5 1 0 0 0 0 3 11 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 8 10 1 0 0 0 0 12 11 1 1 0 0 0 12 13 1 0 0 0 0 12 28 1 0 0 0 0 13 14 1 0 0 0 0 13 31 1 6 0 0 0 14 15 1 0 0 0 0 14 30 1 1 0 0 0 15 16 1 0 0 0 0 15 29 1 6 0 0 0 16 17 1 1 0 0 0 16 28 1 0 0 0 0 17 18 1 0 0 0 0 19 18 1 1 0 0 0 19 20 1 0 0 0 0 19 25 1 0 0 0 0 20 21 1 0 0 0 0 20 27 1 6 0 0 0 21 22 1 0 0 0 0 21 24 1 0 0 0 0 21 26 1 6 0 0 0 22 23 1 0 0 0 0 24 25 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	448.23
Volume:	437.289
LogP:	1.069
LogD:	0.043
LogS:	-2.324
# Rotatable Bonds:	10
TPSA:	158.3
# H-Bond Aceptor:	10
# H-Bond Donor:	6
# Rings:	2
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.228
Synthetic Accessibility Score:	4.975
Fsp3:	0.81
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:	-5.639
MDCK Permeability:	4.2277391912648454e-05
Pgp-inhibitor:	0.066
Pgp-substrate:	0.984
Human Intestinal Absorption (HIA):	0.828
20% Bioavailability (F20%):	0.83
30% Bioavailability (F30%):	0.915

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.133
Plasma Protein Binding (PPB):	61.69462966918945%
Volume Distribution (VD):	0.459
Pgp-substrate:	29.838605880737305%

ADMET: Metabolism

CYP1A2-inhibitor:	0.005
CYP1A2-substrate:	0.699
CYP2C19-inhibitor:	0.007
CYP2C19-substrate:	0.445
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.016
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.063
CYP3A4-inhibitor:	0.042
CYP3A4-substrate:	0.068

ADMET: Excretion

Clearance (CL):	1.066
Half-life (T1/2):	0.799

ADMET: Toxicity

hERG Blockers:	0.041
Human Hepatotoxicity (H-HT):	0.077
Drug-inuced Liver Injury (DILI):	0.016
AMES Toxicity:	0.222
Rat Oral Acute Toxicity:	0.29
Maximum Recommended Daily Dose:	0.007
Skin Sensitization:	0.826
Carcinogencity:	0.036
Eye Corrosion:	0.003
Eye Irritation:	0.038
Respiratory Toxicity:	0.472

Download Data

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

Natural Product: NPC48075

Natural Product ID:	NPC48075
*Common Name:**	DYFCOKYVRKPCBE-QZAXRJMVSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DYFCOKYVRKPCBE-QZAXRJMVSA-N
Standard InCHI:	InChI=1S/C21H36O10/c1-5-20(4,8-6-7-12(2)3)31-18-16(25)15(24)14(23)13(30-18)9-28-19-17(26)21(27,10-22)11-29-19/h5,7,13-19,22-27H,1,6,8-11H2,2-4H3/t13-,14-,15+,16-,17+,18+,19-,20-,21-/m1/s1
SMILES:	C=C[C@](C)(CCC=C(C)C)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO[C@H]2[C@@H]([C@@](CO)(CO2)O)O)O1)O)O)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:0003909] Fatty Acyls [CHEMONTID:0001766] Fatty acyl glycosides [CHEMONTID:0003861] Fatty acyl glycosides of mono- and disaccharides

*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
NPO9553	Phyllodium pulchellum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15921433]
NPO5131	Scorzonera hispanica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9783	Mikania scandens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9783	Mikania scandens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5131	Scorzonera hispanica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9783	Mikania scandens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12591	Archaster typicus	Species	Archasteridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6386	Gutenbergia cordifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8601	Petrosia volcano	Species	Petrosiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13042	Diospyros abyssinica	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12233	Diospyros peregrina	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4746	Centaurea arenaria	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11333	Trapa japonica	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9553	Phyllodium pulchellum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9361	Aplophyllum villosum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO1326	Cratystylis conocephala	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22899	Phaeotremella fagi	Species	Phaeotremellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9783	Mikania scandens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5131	Scorzonera hispanica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12367	Diospyros elliptifolia	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13555	Beaucarnea recurvata	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7870	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12819	Clitocybe subilludens	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9989	Cotylelobium scabriusculum	Species	Dipterocarpaceae	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 NPC48075 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	140
0.1-0.2	1774
0.2-0.3	7199
0.3-0.4	15689
0.4-0.5	9858
0.5-0.6	6234
0.6-0.7	1611
0.7-0.8	177
0.8-0.85	10
0.85-0.9	4
0.9-0.95	1
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 NPC48075 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	124
0.1-0.2	2158
0.2-0.3	4362
0.3-0.4	1787
0.4-0.5	502
0.5-0.6	186
0.6-0.7	31
0.7-0.8	0
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