NPASS Compound

Structure

NPC148756 OpenBabel06302215352D 43 47 0 0 1 0 0 0 0 0999 V2000 -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 1 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 -1.7321 -0.0000 0.0000 C 0 0 2 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 -2.5981 -1.5000 0.0000 C 0 0 1 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 O 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 -4.3301 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -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 -4.3301 -4.5000 0.0000 O 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 -2.5981 -5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -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 0.0000 -4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -1.5000 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 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 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 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 -0.8660 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 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 43 1 1 0 0 0 4 5 1 0 0 0 0 4 42 1 1 0 0 0 5 6 1 0 0 0 0 5 30 1 1 0 0 0 6 7 1 0 0 0 0 6 8 1 6 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 29 1 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 15 28 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 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 31 30 1 6 0 0 0 31 32 1 0 0 0 0 31 38 1 0 0 0 0 32 33 1 0 0 0 0 32 41 1 1 0 0 0 33 34 1 0 0 0 0 33 40 1 6 0 0 0 34 35 1 0 0 0 0 34 39 1 6 0 0 0 35 36 1 6 0 0 0 35 38 1 0 0 0 0 36 37 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	610.15
Volume:	552.318
LogP:	-0.049
LogD:	-0.128
LogS:	-4.048
# Rotatable Bonds:	6
TPSA:	269.43
# H-Bond Aceptor:	16
# H-Bond Donor:	10
# Rings:	5
# Heavy Atoms:	16

MedChem Properties

QED Drug-Likeness Score:	0.14
Synthetic Accessibility Score:	4.777
Fsp3:	0.444
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.463
MDCK Permeability:	2.0137393221375532e-05
Pgp-inhibitor:	0.019
Pgp-substrate:	0.99
Human Intestinal Absorption (HIA):	0.875
20% Bioavailability (F20%):	0.009
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.043
Plasma Protein Binding (PPB):	86.9762191772461%
Volume Distribution (VD):	0.685
Pgp-substrate:	16.03548812866211%

ADMET: Metabolism

CYP1A2-inhibitor:	0.092
CYP1A2-substrate:	0.033
CYP2C19-inhibitor:	0.025
CYP2C19-substrate:	0.047
CYP2C9-inhibitor:	0.012
CYP2C9-substrate:	0.13
CYP2D6-inhibitor:	0.042
CYP2D6-substrate:	0.139
CYP3A4-inhibitor:	0.044
CYP3A4-substrate:	0.003

ADMET: Excretion

Clearance (CL):	1.428
Half-life (T1/2):	0.782

ADMET: Toxicity

hERG Blockers:	0.272
Human Hepatotoxicity (H-HT):	0.135
Drug-inuced Liver Injury (DILI):	0.983
AMES Toxicity:	0.839
Rat Oral Acute Toxicity:	0.031
Maximum Recommended Daily Dose:	0.004
Skin Sensitization:	0.893
Carcinogencity:	0.046
Eye Corrosion:	0.003
Eye Irritation:	0.186
Respiratory Toxicity:	0.022

Download Data

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

Natural Product: NPC148756

Natural Product ID:	NPC148756
*Common Name:**	DFNXNCCYQRPZMD-QBPMGZHBSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DFNXNCCYQRPZMD-QBPMGZHBSA-N
Standard InCHI:	InChI=1S/C27H30O16/c1-8-17(33)21(37)25(43-26-22(38)20(36)18(34)15(7-28)41-26)27(39-8)42-24-19(35)16-13(32)5-10(29)6-14(16)40-23(24)9-2-3-11(30)12(31)4-9/h2-6,8,15,17-18,20-22,25-34,36-38H,7H2,1H3/t8-,15+,17+,18-,20-,21+,22+,25+,26-,27-/m0/s1
SMILES:	C[C@H]1[C@H]([C@H]([C@H]([C@@H](O1)Oc1c(=O)c2c(cc(cc2oc1c1ccc(c(c1)O)O)O)O)O[C@H]1[C@@H]([C@H]([C@H]([C@@H](CO)O1)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11968884
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
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	stem	n.a.	DOI[10.1007/s11418-006-0112-9]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	flower	n.a.	DOI[10.1007/s11418-006-0112-9]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	leaf	n.a.	DOI[10.1007/s11418-006-0112-9]
NPO3359	Psidium guajava	Species	Myrtaceae	Eukaryota	n.a.	leaf	n.a.	DOI[10.1016/j.foodchem.2010.03.088]
NPO28679	Prunus mume	Species	Rosaceae	Eukaryota	flowers	n.a.	n.a.	PMID[12193020]
NPO28919	Calendula officinalis	Species	Asteraceae	Eukaryota	flowers	n.a.	n.a.	PMID[17190444]
NPO28919	Calendula officinalis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23327299]
NPO28679	Prunus mume	Species	Rosaceae	Eukaryota	fruits	n.a.	n.a.	PMID[24485782]
NPO3359	Psidium guajava	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31738062]
NPO3359	Psidium guajava	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[4013523]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6387056]
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]
NPO9822	Typha angustifolia	Species	Typhaceae	Eukaryota		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.	Database[FooDB]
NPO3359	Psidium guajava	Species	Myrtaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO21462	Lannea grandis	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3359	Psidium guajava	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28679	Prunus mume	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12859	Diospyros rhombifolia	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5243	Typha angustata	Species	Typhaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28919	Calendula officinalis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9822	Typha angustifolia	Species	Typhaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3359	Psidium guajava	Species	Myrtaceae	Eukaryota	Fruits	n.a.		Database[Phenol-Explorer]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5243	Typha angustata	Species	Typhaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28679	Prunus mume	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12859	Diospyros rhombifolia	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9822	Typha angustifolia	Species	Typhaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21462	Lannea grandis	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3359	Psidium guajava	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28919	Calendula officinalis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5243	Typha angustata	Species	Typhaceae	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]
NPO21462	Lannea grandis	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9822	Typha angustifolia	Species	Typhaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28679	Prunus mume	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9822	Typha angustifolia	Species	Typhaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO28679	Prunus mume	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3359	Psidium guajava	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5243	Typha angustata	Species	Typhaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12859	Diospyros rhombifolia	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9822	Typha angustifolia	Species	Typhaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28919	Calendula officinalis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28679	Prunus mume	Species	Rosaceae	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 NPC148756 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	460
0.1-0.2	1842
0.2-0.3	4252
0.3-0.4	9791
0.4-0.5	8319
0.5-0.6	4578
0.6-0.7	5577
0.7-0.8	5191
0.8-0.85	1537
0.85-0.9	565
0.9-0.95	424
0.95-1	161

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 NPC148756 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	404
0.1-0.2	953
0.2-0.3	1998
0.3-0.4	2741
0.4-0.5	1793
0.5-0.6	852
0.6-0.7	273
0.7-0.8	104
0.8-0.85	18
0.85-0.9	6
0.9-0.95	2
0.95-1	6

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