NPASS Compound

Structure

NPC96123 OpenBabel06302215422D 32 34 0 0 1 0 0 0 0 0999 V2000 5.1962 -1.0000 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 3.4641 -1.0000 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 4.3301 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 0.0000 0.0000 C 0 0 0 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 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 N 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 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 3 0 0 0 0 0 0 0 0 0 0.0000 2.0000 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 -0.8660 0.5000 0.0000 C 0 0 3 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 -2.5981 0.5000 0.0000 O 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 -4.3301 0.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -5.1962 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1962 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 C 0 0 3 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 -5.1962 -3.0000 0.0000 O 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 -6.0622 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 0.5000 0.0000 O 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 -0.0000 -0.0000 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 0.0000 3.0000 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 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 4 5 2 0 0 0 0 4 7 1 0 0 0 0 5 6 1 0 0 0 0 7 8 1 1 0 0 0 7 10 1 0 0 0 0 8 9 3 0 0 0 0 11 10 1 6 0 0 0 11 12 1 0 0 0 0 11 29 1 0 0 0 0 12 13 1 0 0 0 0 12 32 1 0 0 0 0 13 14 1 0 0 0 0 13 31 1 1 0 0 0 14 15 1 0 0 0 0 14 30 1 1 0 0 0 15 16 1 0 0 0 0 15 29 1 0 0 0 0 16 17 1 0 0 0 0 18 17 1 6 0 0 0 18 19 1 0 0 0 0 18 25 1 0 0 0 0 19 20 1 0 0 0 0 19 28 1 0 0 0 0 20 21 1 0 0 0 0 20 27 1 1 0 0 0 21 22 1 0 0 0 0 21 26 1 1 0 0 0 22 23 1 0 0 0 0 22 25 1 0 0 0 0 23 24 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	457.16
Volume:	423.314
LogP:	-1.225
LogD:	-1.31
LogS:	-0.862
# Rotatable Bonds:	7
TPSA:	202.32
# H-Bond Aceptor:	12
# H-Bond Donor:	7
# Rings:	3
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.218
Synthetic Accessibility Score:	4.512
Fsp3:	0.65
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.808
MDCK Permeability:	0.00014783568622078747
Pgp-inhibitor:	0.04
Pgp-substrate:	0.891
Human Intestinal Absorption (HIA):	0.984
20% Bioavailability (F20%):	0.957
30% Bioavailability (F30%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.278
Plasma Protein Binding (PPB):	23.39199447631836%
Volume Distribution (VD):	0.363
Pgp-substrate:	63.52532958984375%

ADMET: Metabolism

CYP1A2-inhibitor:	0.012
CYP1A2-substrate:	0.017
CYP2C19-inhibitor:	0.012
CYP2C19-substrate:	0.056
CYP2C9-inhibitor:	0.001
CYP2C9-substrate:	0.077
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.074
CYP3A4-inhibitor:	0.004
CYP3A4-substrate:	0.02

ADMET: Excretion

Clearance (CL):	1.013
Half-life (T1/2):	0.799

ADMET: Toxicity

hERG Blockers:	0.015
Human Hepatotoxicity (H-HT):	0.289
Drug-inuced Liver Injury (DILI):	0.97
AMES Toxicity:	0.719
Rat Oral Acute Toxicity:	0.098
Maximum Recommended Daily Dose:	0.004
Skin Sensitization:	0.748
Carcinogencity:	0.059
Eye Corrosion:	0.003
Eye Irritation:	0.052
Respiratory Toxicity:	0.9

Download Data

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

Natural Product: NPC96123

Natural Product ID:	NPC96123
*Common Name:**	XUCIJNAGGSZNQT-ZPVJLWCPSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XUCIJNAGGSZNQT-ZPVJLWCPSA-N
Standard InCHI:	InChI=1S/C20H27NO11/c21-6-10(9-4-2-1-3-5-9)30-20-18(28)16(26)14(24)12(32-20)8-29-19-17(27)15(25)13(23)11(7-22)31-19/h1-5,10-20,22-28H,7-8H2/t10-,11?,12?,13+,14+,15+,16+,17?,18?,19+,20+/m0/s1
SMILES:	c1ccc(cc1)[C@H](C#N)O[C@H]1C([C@@H]([C@@H](C(CO[C@H]2C([C@@H]([C@@H](C(CO)O2)O)O)O)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	24801909
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0002105] Glycosyl compounds [CHEMONTID:0002365] Cyanogenic 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
NPO4795	Prunus armeniaca	Species	Rosaceae	Eukaryota	n.a.	kernel	n.a.	PMID[10670815]
NPO4795	Prunus armeniaca	Species	Rosaceae	Eukaryota	Fruits	Malatya Fruit Research Institute	between the first and third weeks of 2005-Jul.	PMID[18038980]
NPO4446	Prunus davidiana	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2045817]
NPO4446	Prunus davidiana	Species	Rosaceae	Eukaryota	seeds	n.a.	n.a.	PMID[23985009]
NPO14992	Prunus persica	Species	Rosaceae	Eukaryota	n.a.	kernel	n.a.	PMID[7092570]
NPO4795	Prunus armeniaca	Species	Rosaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO14992	Prunus persica	Species	Rosaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO4795	Prunus armeniaca	Species	Rosaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO14992	Prunus persica	Species	Rosaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO4795	Prunus armeniaca	Species	Rosaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO14992	Prunus persica	Species	Rosaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO14992	Prunus persica	Species	Rosaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO4795	Prunus armeniaca	Species	Rosaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO14992	Prunus persica	Species	Rosaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO4795	Prunus armeniaca	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[FooDB]
NPO4446	Prunus davidiana	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4795	Prunus armeniaca	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14992	Prunus persica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29249	Prunus humilis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18659	Prunus japonica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4795	Prunus armeniaca	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[Phenol-Explorer]
NPO18659	Prunus japonica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14992	Prunus persica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4446	Prunus davidiana	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29249	Prunus humilis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4795	Prunus armeniaca	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4795	Prunus armeniaca	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4446	Prunus davidiana	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14992	Prunus persica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18659	Prunus japonica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4446	Prunus davidiana	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO20032	Prunus sibirica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO29249	Prunus humilis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO18659	Prunus japonica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO29018	Prunus humillis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO25099	Prunus mandshurica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO14992	Prunus persica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4795	Prunus armeniaca	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO24449	Prunus pedunculata	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4795	Prunus armeniaca	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18659	Prunus japonica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14992	Prunus persica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29249	Prunus humilis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20032	Prunus sibirica	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 NPC96123 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	218
0.1-0.2	1101
0.2-0.3	3014
0.3-0.4	9689
0.4-0.5	13130
0.5-0.6	12226
0.6-0.7	2937
0.7-0.8	361
0.8-0.85	8
0.85-0.9	6
0.9-0.95	4
0.95-1	3

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 NPC96123 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	172
0.1-0.2	715
0.2-0.3	1307
0.3-0.4	3233
0.4-0.5	2290
0.5-0.6	1270
0.6-0.7	156
0.7-0.8	7
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