NPASS Compound

Structure

NPC254607 OpenBabel06302215542D 35 37 0 0 1 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 -4.3301 -5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -6.0000 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 -5.1962 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -2.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4641 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.6720 -0.0219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6665 0.0827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0733 -0.8309 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.8164 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7675 -1.1910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.5106 -1.8601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3027 -2.8383 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.4617 -1.5511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0243 -0.5219 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 C 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 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 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 1 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 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 0.8660 0.5000 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 2.0000 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 2.5981 0.5000 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 0.8660 -2.5000 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 5 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 8 7 1 1 0 0 0 8 9 1 0 0 0 0 8 22 1 0 0 0 0 9 10 1 0 0 0 0 9 13 1 0 0 0 0 10 11 1 6 0 0 0 10 20 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 13 19 1 6 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 16 18 1 0 0 0 0 20 21 2 0 0 0 0 20 23 1 0 0 0 0 21 22 1 0 0 0 0 23 24 1 0 0 0 0 25 24 1 6 0 0 0 25 26 1 0 0 0 0 25 32 1 0 0 0 0 26 27 1 0 0 0 0 26 35 1 1 0 0 0 27 28 1 0 0 0 0 27 34 1 1 0 0 0 28 29 1 0 0 0 0 28 33 1 1 0 0 0 29 30 1 6 0 0 0 29 32 1 0 0 0 0 30 31 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	504.22
Volume:	478.268
LogP:	0.526
LogD:	0.071
LogS:	-2.384
# Rotatable Bonds:	11
TPSA:	181.44
# H-Bond Aceptor:	12
# H-Bond Donor:	5
# Rings:	3
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.241
Synthetic Accessibility Score:	4.978
Fsp3:	0.826
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.945
MDCK Permeability:	0.00013054559531155974
Pgp-inhibitor:	0.002
Pgp-substrate:	0.993
Human Intestinal Absorption (HIA):	0.672
20% Bioavailability (F20%):	0.007
30% Bioavailability (F30%):	0.988

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.16
Plasma Protein Binding (PPB):	30.998748779296875%
Volume Distribution (VD):	0.43
Pgp-substrate:	48.781558990478516%

ADMET: Metabolism

CYP1A2-inhibitor:	0.023
CYP1A2-substrate:	0.044
CYP2C19-inhibitor:	0.009
CYP2C19-substrate:	0.145
CYP2C9-inhibitor:	0.003
CYP2C9-substrate:	0.019
CYP2D6-inhibitor:	0.013
CYP2D6-substrate:	0.039
CYP3A4-inhibitor:	0.072
CYP3A4-substrate:	0.132

ADMET: Excretion

Clearance (CL):	1.589
Half-life (T1/2):	0.845

ADMET: Toxicity

hERG Blockers:	0.037
Human Hepatotoxicity (H-HT):	0.218
Drug-inuced Liver Injury (DILI):	0.533
AMES Toxicity:	0.926
Rat Oral Acute Toxicity:	0.032
Maximum Recommended Daily Dose:	0.288
Skin Sensitization:	0.398
Carcinogencity:	0.924
Eye Corrosion:	0.003
Eye Irritation:	0.024
Respiratory Toxicity:	0.147

Download Data

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

Natural Product: NPC254607

Natural Product ID:	NPC254607
*Common Name:**	YYQCJTVJAARIPW-VRYXWLBUSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YYQCJTVJAARIPW-VRYXWLBUSA-N
Standard InCHI:	InChI=1S/C23H36O12/c1-11(2)6-16(26)35-21-17-14(4-5-23(17,30)10-33-12(3)25)13(8-31-21)9-32-22-20(29)19(28)18(27)15(7-24)34-22/h8,11,14-15,17-22,24,27-30H,4-7,9-10H2,1-3H3/t14-,15-,17-,18-,19-,20-,21+,22-,23+/m1/s1
SMILES:	CC(C)CC(=O)O[C@H]1[C@H]2[C@H](CC[C@@]2(COC(=O)C)O)C(=CO1)CO[C@H]1[C@@H]([C@@H]([C@@H]([C@@H](CO)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101316457
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides

*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
NPO22437	Eurya japonica	Species	Pentaphylacaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23540981]
NPO11313	Juniperus formosana	Species	Cupressaceae	Eukaryota	n.a.	leaf	n.a.	PMID[24273878]
NPO11313	Juniperus formosana	Species	Cupressaceae	Eukaryota	n.a.	fruit	n.a.	PMID[24273878]
NPO19964	Stephania sasakii	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22437	Eurya japonica	Species	Pentaphylacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19964	Stephania sasakii	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17951	Styrax japonicus	Species	Styracaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22437	Eurya japonica	Species	Pentaphylacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20380	Tanacetum balsamitoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20020	Murdannia triquetra	Species	Commelinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15900	Diaphus coeruleus	Species	Myctophidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20138	Gasterosteus aculeatus	Species	Gasterosteidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22630	Calea cuneifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22437	Eurya japonica	Species	Pentaphylacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20644	Mucuna urens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11313	Juniperus formosana	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28240	0tholaena lemmonii	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21781	Eucalyptus kitsoni	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19964	Stephania sasakii	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21031	Dracocephalum moldavica	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17951	Styrax japonicus	Species	Styracaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25742	Rhinella icterica	Species	Bufonidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20834	Artemisia pedemontana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8512	Helichrysum dendroideum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21277	Eucalyptus rubida	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21598	Hypselodoris porterae	Species	Chromodorididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20966	Phlomis nissolii	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21531	Pseudocyphellaria aurata	Species	Lobariaceae	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 NPC254607 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	194
0.1-0.2	1567
0.2-0.3	5455
0.3-0.4	13084
0.4-0.5	9792
0.5-0.6	7758
0.6-0.7	4315
0.7-0.8	473
0.8-0.85	22
0.85-0.9	23
0.9-0.95	13
0.95-1	1

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 NPC254607 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	182
0.1-0.2	2125
0.2-0.3	3947
0.3-0.4	1959
0.4-0.5	512
0.5-0.6	343
0.6-0.7	78
0.7-0.8	4
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