NPASS Compound

Structure

NPC204759 OpenBabel06302215382D 31 34 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 -1.7321 -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 -3.4641 -4.0000 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 -2.5981 -2.5000 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 -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 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 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 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -0.0000 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 -5.1962 2.0000 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 -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 3 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 2 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 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 -4.3301 -4.5000 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 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 3 31 1 0 0 0 0 4 5 2 0 0 0 0 4 30 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 17 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 8 20 1 0 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 11 16 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 12 19 1 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 18 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 21 20 1 6 0 0 0 21 22 1 0 0 0 0 21 26 1 0 0 0 0 22 23 1 0 0 0 0 22 29 1 0 0 0 0 23 24 1 0 0 0 0 23 28 1 0 0 0 0 24 25 1 0 0 0 0 24 27 1 6 0 0 0 25 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	434.08
Volume:	395.851
LogP:	0.639
LogD:	0.788
LogS:	-4.199
# Rotatable Bonds:	3
TPSA:	190.28
# H-Bond Aceptor:	11
# H-Bond Donor:	7
# Rings:	4
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.277
Synthetic Accessibility Score:	3.931
Fsp3:	0.25
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.945
MDCK Permeability:	6.402207418432226e-06
Pgp-inhibitor:	0.007
Pgp-substrate:	0.647
Human Intestinal Absorption (HIA):	0.311
20% Bioavailability (F20%):	0.025
30% Bioavailability (F30%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.021
Plasma Protein Binding (PPB):	90.08566284179688%
Volume Distribution (VD):	0.88
Pgp-substrate:	13.930317878723145%

ADMET: Metabolism

CYP1A2-inhibitor:	0.153
CYP1A2-substrate:	0.053
CYP2C19-inhibitor:	0.025
CYP2C19-substrate:	0.046
CYP2C9-inhibitor:	0.072
CYP2C9-substrate:	0.402
CYP2D6-inhibitor:	0.196
CYP2D6-substrate:	0.167
CYP3A4-inhibitor:	0.1
CYP3A4-substrate:	0.011

ADMET: Excretion

Clearance (CL):	5.093
Half-life (T1/2):	0.852

ADMET: Toxicity

hERG Blockers:	0.053
Human Hepatotoxicity (H-HT):	0.141
Drug-inuced Liver Injury (DILI):	0.977
AMES Toxicity:	0.845
Rat Oral Acute Toxicity:	0.058
Maximum Recommended Daily Dose:	0.033
Skin Sensitization:	0.63
Carcinogencity:	0.061
Eye Corrosion:	0.003
Eye Irritation:	0.249
Respiratory Toxicity:	0.033

Download Data

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

Natural Product: NPC204759

Natural Product ID:	NPC204759
*Common Name:**	PZZRDJXEMZMZFD-RLDUMJPOSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PZZRDJXEMZMZFD-RLDUMJPOSA-N
Standard InCHI:	InChI=1S/C20H18O11/c21-8-4-11(24)14-13(5-8)30-18(7-1-2-9(22)10(23)3-7)19(16(14)27)31-20-17(28)15(26)12(25)6-29-20/h1-5,12,15,17,20-26,28H,6H2/t12-,15?,17?,20-/m0/s1
SMILES:	c1cc(c(cc1c1c(c(=O)c2c(cc(cc2o1)O)O)O[C@H]1C(C([C@H](CO1)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	44259215
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
NPO3359	Psidium guajava	Species	Myrtaceae	Eukaryota	n.a.	leaf	n.a.	DOI[10.1016/j.foodchem.2010.03.088]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	leaf	n.a.	DOI[10.1016/S0031-9422(00)94055-X]
NPO25272	Celastrus angulatus	Species	Celastraceae	Eukaryota	n.a.	seed	n.a.	DOI[10.1016/S0031-9422(99)00216-2]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1078/0176-1617-00195]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	flower	n.a.	DOI[10.3390/70200245]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10757735]
NPO11391	Polygonum cuspidatum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11076555]
NPO11391	Polygonum cuspidatum	Species	Polygonaceae	Eukaryota	Roots	n.a.	n.a.	PMID[11459643]
NPO29463	Pogostemon cablin	Species	Lamiaceae	Eukaryota	n.a.	leaf	n.a.	PMID[12575075]
NPO29463	Pogostemon cablin	Species	Lamiaceae	Eukaryota	n.a.	stem	n.a.	PMID[12575075]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[14735439]
NPO11391	Polygonum cuspidatum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1517743]
NPO29463	Pogostemon cablin	Species	Lamiaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[15577255]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	callus	n.a.	PMID[15715262]
NPO29417	Fallopia multiflora	Species	Polygonaceae	Eukaryota	n.a.	root	n.a.	PMID[16564530]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18220354]
NPO31520	Polygonum multiflorum	Species	Polygonaceae	Eukaryota	roots	n.a.	n.a.	PMID[24499304]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24617303]
NPO25272	Celastrus angulatus	Species	Celastraceae	Eukaryota	seeds and root bark	Henan, China	n.a.	PMID[26295746]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28445039]
NPO29417	Fallopia multiflora	Species	Polygonaceae	Eukaryota	Roots	n.a.	n.a.	PMID[29359942]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	Roots	n.a.	n.a.	PMID[30024167]
NPO29463	Pogostemon cablin	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30188125]
NPO3359	Psidium guajava	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31738062]
NPO29417	Fallopia multiflora	Species	Polygonaceae	Eukaryota	Roots	n.a.	n.a.	PMID[31944695]
NPO3359	Psidium guajava	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[4013523]
NPO29417	Fallopia multiflora	Species	Polygonaceae	Eukaryota	Roots; Tubers	n.a.	n.a.	PMID[7714535]
NPO11391	Polygonum cuspidatum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8277318]
NPO3359	Psidium guajava	Species	Myrtaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO3359	Psidium guajava	Species	Myrtaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO3359	Psidium guajava	Species	Myrtaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO3359	Psidium guajava	Species	Myrtaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO3359	Psidium guajava	Species	Myrtaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO3359	Psidium guajava	Species	Myrtaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO3359	Psidium guajava	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11391	Polygonum cuspidatum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25272	Celastrus angulatus	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14105.2	Panax pseudo-ginseng var. notoginseng	Varieties	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14148.1	Panax pseudo - ginseng var. notoginseng	Varieties	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16741	Codonopsis pilosula	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO31520	Polygonum multiflorum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11329	Echinops grijsii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29463	Pogostemon cablin	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3359	Psidium guajava	Species	Myrtaceae	Eukaryota	Fruits	n.a.		Database[Phenol-Explorer]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29463	Pogostemon cablin	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25272	Celastrus angulatus	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14105.2	Panax pseudo-ginseng var. notoginseng	Varieties	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16741	Codonopsis pilosula	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29417	Fallopia multiflora	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3359	Psidium guajava	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11329	Echinops grijsii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11391	Polygonum cuspidatum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16741	Codonopsis pilosula	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO31520	Polygonum multiflorum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29463	Pogostemon cablin	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11329	Echinops grijsii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11391	Polygonum cuspidatum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3359	Psidium guajava	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO25272	Celastrus angulatus	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16741	Codonopsis pilosula	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO29463	Pogostemon cablin	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO29417	Fallopia multiflora	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO11329	Echinops grijsii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO11391	Polygonum cuspidatum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16741	Codonopsis pilosula	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29463	Pogostemon cablin	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11391	Polygonum cuspidatum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11329	Echinops grijsii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25272	Celastrus angulatus	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3359	Psidium guajava	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 NPC204759 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	463
0.1-0.2	1895
0.2-0.3	4423
0.3-0.4	10023
0.4-0.5	7901
0.5-0.6	4220
0.6-0.7	5307
0.7-0.8	5185
0.8-0.85	1550
0.85-0.9	1099
0.9-0.95	438
0.95-1	193

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 NPC204759 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	421
0.1-0.2	956
0.2-0.3	2010
0.3-0.4	2681
0.4-0.5	1740
0.5-0.6	889
0.6-0.7	294
0.7-0.8	122
0.8-0.85	9
0.85-0.9	17
0.9-0.95	10
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