NPASS Compound

Structure

NPC32226 OpenBabel06302216212D 33 36 0 0 1 0 0 0 0 0999 V2000 5.1962 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -0.5000 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 -2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 2 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 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 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 1.0000 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 3.4641 4.0000 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 1.7321 4.0000 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 0.8660 2.5000 0.0000 O 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 -0.8660 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 0.0000 -0.0000 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 -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 2.5981 5.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 2.5000 0.0000 O 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 3.4641 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 7 1 0 0 0 0 3 4 1 0 0 0 0 3 33 1 6 0 0 0 4 5 1 0 0 0 0 4 32 1 1 0 0 0 5 6 1 0 0 0 0 5 31 1 1 0 0 0 6 7 1 0 0 0 0 6 8 1 1 0 0 0 8 9 1 0 0 0 0 9 19 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 10 12 1 0 0 0 0 12 17 2 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 13 30 1 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 15 29 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 25 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 22 28 1 0 0 0 0 23 24 2 0 0 0 0 23 27 1 0 0 0 0 24 25 1 0 0 0 0 24 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	464.1
Volume:	421.937
LogP:	1.319
LogD:	0.121
LogS:	-3.518
# Rotatable Bonds:	3
TPSA:	210.51
# H-Bond Aceptor:	12
# H-Bond Donor:	8
# Rings:	4
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.244
Synthetic Accessibility Score:	4.149
Fsp3:	0.286
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.417
MDCK Permeability:	6.819861027906882e-06
Pgp-inhibitor:	0.011
Pgp-substrate:	0.984
Human Intestinal Absorption (HIA):	0.75
20% Bioavailability (F20%):	0.767
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.007
Plasma Protein Binding (PPB):	89.73974609375%
Volume Distribution (VD):	0.822
Pgp-substrate:	14.378531455993652%

ADMET: Metabolism

CYP1A2-inhibitor:	0.484
CYP1A2-substrate:	0.076
CYP2C19-inhibitor:	0.024
CYP2C19-substrate:	0.046
CYP2C9-inhibitor:	0.295
CYP2C9-substrate:	0.245
CYP2D6-inhibitor:	0.089
CYP2D6-substrate:	0.147
CYP3A4-inhibitor:	0.112
CYP3A4-substrate:	0.009

ADMET: Excretion

Clearance (CL):	5.94
Half-life (T1/2):	0.888

ADMET: Toxicity

hERG Blockers:	0.022
Human Hepatotoxicity (H-HT):	0.232
Drug-inuced Liver Injury (DILI):	0.982
AMES Toxicity:	0.777
Rat Oral Acute Toxicity:	0.081
Maximum Recommended Daily Dose:	0.218
Skin Sensitization:	0.936
Carcinogencity:	0.035
Eye Corrosion:	0.003
Eye Irritation:	0.878
Respiratory Toxicity:	0.083

Download Data

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

Natural Product: NPC32226

Natural Product ID:	NPC32226
*Common Name:**	DCYOADKBABEMIQ-YIFFCZEQSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DCYOADKBABEMIQ-YIFFCZEQSA-N
Standard InCHI:	InChI=1S/C21H20O12/c1-6-14(26)17(29)18(30)21(31-6)33-20-16(28)13-9(23)4-8(22)5-12(13)32-19(20)7-2-10(24)15(27)11(25)3-7/h2-6,14,17-18,21-27,29-30H,1H3/t6-,14-,17+,18+,21+/m0/s1
SMILES:	C[C@H]1[C@@H]([C@H]([C@H]([C@H](O1)Oc1c(=O)c2c(cc(cc2oc1c1cc(c(c(c1)O)O)O)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	16103933
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003531] Flavonoid-3-O-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
NPO27524	Eugenia hyemalis	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18763827]
NPO27524	Eugenia hyemalis	Species	Myrtaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[18763827]
NPO27799	Agelas dispar	Species	Agelasidae	Eukaryota	n.a.	n.a.	n.a.	PMID[18800848]
NPO27061	Drimys winteri	Species	Winteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29634269]
NPO27434	Rabdosia ternifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9182128]
NPO27799	Agelas dispar	Species	Agelasidae	Eukaryota	n.a.	n.a.	n.a.	PMID[9461661]
NPO27799	Agelas dispar	Species	Agelasidae	Eukaryota	n.a.	n.a.	n.a.	PMID[9748394]
NPO16807	Cyclamen purpurascens	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27309	Rubus chroosepalus	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27309	Rubus chroosepalus	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO27799	Agelas dispar	Species	Agelasidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27393	Artemisia schischkinii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27710	Phora affinis	Species	Phoridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27654	Phyllospongia lamellosa	Species	Thorectidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27434	Rabdosia ternifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18126	Pojarkovia stenocephala	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27469	Hygrocybe punicea	Species	Hygrophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27639	Tephrosia viridiflora	Species	Geometridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16807	Cyclamen purpurascens	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26909	Scalesia baurii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11105	Cacalia floridana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27061	Drimys winteri	Species	Winteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27309	Rubus chroosepalus	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27214	Coccinella transversoguttata	Species	Coccinellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9880	Ecklonia arborea	Species	Lessoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27524	Eugenia hyemalis	Species	Myrtaceae	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 NPC32226 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	436
0.1-0.2	1848
0.2-0.3	4246
0.3-0.4	9769
0.4-0.5	8340
0.5-0.6	4264
0.6-0.7	5258
0.7-0.8	5204
0.8-0.85	1579
0.85-0.9	1102
0.9-0.95	467
0.95-1	184

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 NPC32226 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	403
0.1-0.2	962
0.2-0.3	2043
0.3-0.4	2664
0.4-0.5	1747
0.5-0.6	889
0.6-0.7	279
0.7-0.8	126
0.8-0.85	10
0.85-0.9	17
0.9-0.95	9
0.95-1	1

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