NPASS Compound

Structure

NPC147001 OpenBabel06302215572D 33 35 0 0 1 0 0 0 0 0999 V2000 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 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 1 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 2 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 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 2 0 0 0 0 0 0 0 0 0 -2.5981 -2.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4641 -3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3301 -2.5000 0.0000 C 0 0 2 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 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -1.0000 0.0000 O 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 -7.7942 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.3923 -1.0000 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 -3.4641 -4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 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 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 2 1 1 6 0 0 0 2 3 1 0 0 0 0 2 30 1 0 0 0 0 3 4 1 0 0 0 0 3 33 1 1 0 0 0 4 5 1 0 0 0 0 4 32 1 6 0 0 0 5 6 1 0 0 0 0 5 31 1 1 0 0 0 6 7 1 1 0 0 0 6 30 1 0 0 0 0 7 8 1 0 0 0 0 9 8 1 6 0 0 0 9 10 1 0 0 0 0 9 14 1 0 0 0 0 10 11 1 0 0 0 0 10 29 1 1 0 0 0 11 12 1 0 0 0 0 11 28 1 6 0 0 0 12 13 1 0 0 0 0 12 27 1 1 0 0 0 13 14 1 0 0 0 0 13 15 1 6 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 16 18 1 0 0 0 0 18 19 2 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 26 1 0 0 0 0 24 25 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	472.16
Volume:	438.403
LogP:	-0.248
LogD:	-0.187
LogS:	-1.754
# Rotatable Bonds:	7
TPSA:	195.6
# H-Bond Aceptor:	12
# H-Bond Donor:	7
# Rings:	3
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.172
Synthetic Accessibility Score:	4.385
Fsp3:	0.571
Lipinski Rule-of-5:	Rejected
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:	-6.453
MDCK Permeability:	5.509403854375705e-05
Pgp-inhibitor:	0.006
Pgp-substrate:	0.987
Human Intestinal Absorption (HIA):	0.938
20% Bioavailability (F20%):	0.027
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.158
Plasma Protein Binding (PPB):	72.67737579345703%
Volume Distribution (VD):	0.495
Pgp-substrate:	25.586532592773438%

ADMET: Metabolism

CYP1A2-inhibitor:	0.046
CYP1A2-substrate:	0.027
CYP2C19-inhibitor:	0.032
CYP2C19-substrate:	0.076
CYP2C9-inhibitor:	0.005
CYP2C9-substrate:	0.142
CYP2D6-inhibitor:	0.015
CYP2D6-substrate:	0.134
CYP3A4-inhibitor:	0.016
CYP3A4-substrate:	0.015

ADMET: Excretion

Clearance (CL):	1.01
Half-life (T1/2):	0.804

ADMET: Toxicity

hERG Blockers:	0.223
Human Hepatotoxicity (H-HT):	0.036
Drug-inuced Liver Injury (DILI):	0.032
AMES Toxicity:	0.142
Rat Oral Acute Toxicity:	0.399
Maximum Recommended Daily Dose:	0.003
Skin Sensitization:	0.927
Carcinogencity:	0.09
Eye Corrosion:	0.003
Eye Irritation:	0.057
Respiratory Toxicity:	0.025

Download Data

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

Natural Product: NPC147001

Natural Product ID:	NPC147001
*Common Name:**	JLJZYIHYERFTEY-VMVDPQBSSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JLJZYIHYERFTEY-VMVDPQBSSA-N
Standard InCHI:	InChI=1S/C21H28O12/c1-9-14(24)16(26)18(28)20(31-9)30-8-12-15(25)17(27)19(29)21(32-12)33-13(23)7-4-10-2-5-11(22)6-3-10/h2-7,9,12,14-22,24-29H,8H2,1H3/b7-4-/t9-,12-,14-,15-,16+,17+,18-,19-,20+,21+/m1/s1
SMILES:	C[C@@H]1[C@H]([C@@H]([C@H]([C@@H](OC[C@@H]2[C@H]([C@@H]([C@H]([C@@H](O2)OC(=O)/C=Cc2ccc(cc2)O)O)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:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000476] Cinnamic acids and derivatives [CHEMONTID:0001391] Hydroxycinnamic acids and derivatives [CHEMONTID:0003002] Hydroxycinnamic acid esters [CHEMONTID:0003003] Hydroxycinnamic acid 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
NPO6333	Annona glabra	Species	Annonaceae	Eukaryota	n.a.	stem wood	n.a.	DOI[10.1021/np100247r]
NPO6333	Annona glabra	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10395501]
NPO6333	Annona glabra	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10425140]
NPO2166	Ajania fruticulosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10425142]
NPO6333	Annona glabra	Species	Annonaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[15568797]
NPO6333	Annona glabra	Species	Annonaceae	Eukaryota	stem	Taipei Botanical Garden, Taipei, Taiwan, China	2006-MAR	PMID[20828184]
NPO6333	Annona glabra	Species	Annonaceae	Eukaryota	fruits	n.a.	n.a.	PMID[25499882]
NPO7252	Sonchus oleraceus	Species	Asteraceae	Eukaryota	n.a.	Molise Region, Italy	Autumn 2018	PMID[32803719]
NPO7252	Sonchus oleraceus	Species	Asteraceae	Eukaryota	n.a.	Molise Region, Italy	Spring 2019	PMID[32803719]
NPO7252	Sonchus oleraceus	Species	Asteraceae	Eukaryota	n.a.	Molise Region, Italy		PMID[32803719]
NPO7252	Sonchus oleraceus	Species	Asteraceae	Eukaryota	n.a	The rural area of Viçosa, State of Minas Gerais (MG), Brazil	Adult stage	PMID[35282307]
NPO6333	Annona glabra	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9584397]
NPO6333	Annona glabra	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9599260]
NPO6333	Annona glabra	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6333	Annona glabra	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1715	Eucalyptus radiata	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO247	Urceolaria bryophila	Species	Trichodinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7252	Sonchus oleraceus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2166	Ajania fruticulosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6333	Annona glabra	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8566	Astragalus curvicarpus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2901	Ilex taubertiana	Species	Aquifoliaceae	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 NPC147001 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	259
0.1-0.2	1171
0.2-0.3	3122
0.3-0.4	7817
0.4-0.5	10377
0.5-0.6	8123
0.6-0.7	9578
0.7-0.8	1889
0.8-0.85	225
0.85-0.9	101
0.9-0.95	19
0.95-1	16

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 NPC147001 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	219
0.1-0.2	724
0.2-0.3	1536
0.3-0.4	2996
0.4-0.5	2019
0.5-0.6	1254
0.6-0.7	381
0.7-0.8	20
0.8-0.85	0
0.85-0.9	1
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