NPASS Compound

Structure

NPC83638 OpenBabel06302216162D 30 32 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 1 0 0 0 0 0 0 0 0 0 0.0000 2.0000 0.0000 C 0 0 2 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 1 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 1 0 0 0 0 0 0 0 0 0 -5.1962 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1962 -1.0000 0.0000 C 0 0 2 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 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 27 1 0 0 0 0 12 13 1 0 0 0 0 12 30 1 1 0 0 0 13 14 1 0 0 0 0 13 29 1 6 0 0 0 14 15 1 0 0 0 0 14 28 1 1 0 0 0 15 16 1 6 0 0 0 15 27 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 23 1 0 0 0 0 19 20 1 0 0 0 0 19 26 1 1 0 0 0 20 21 1 0 0 0 0 20 25 1 6 0 0 0 21 22 1 0 0 0 0 21 24 1 6 0 0 0 22 23 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	427.15
Volume:	397.228
LogP:	-0.71
LogD:	-0.674
LogS:	-1.493
# Rotatable Bonds:	6
TPSA:	182.09
# H-Bond Aceptor:	11
# H-Bond Donor:	6
# Rings:	3
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.283
Synthetic Accessibility Score:	4.504
Fsp3:	0.632
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:	-5.566
MDCK Permeability:	5.6933797168312594e-05
Pgp-inhibitor:	0.407
Pgp-substrate:	0.857
Human Intestinal Absorption (HIA):	0.958
20% Bioavailability (F20%):	0.2
30% Bioavailability (F30%):	0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.2
Plasma Protein Binding (PPB):	27.705324172973633%
Volume Distribution (VD):	0.455
Pgp-substrate:	54.4283332824707%

ADMET: Metabolism

CYP1A2-inhibitor:	0.009
CYP1A2-substrate:	0.047
CYP2C19-inhibitor:	0.024
CYP2C19-substrate:	0.055
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.044
CYP2D6-inhibitor:	0.016
CYP2D6-substrate:	0.08
CYP3A4-inhibitor:	0.007
CYP3A4-substrate:	0.028

ADMET: Excretion

Clearance (CL):	0.978
Half-life (T1/2):	0.797

ADMET: Toxicity

hERG Blockers:	0.031
Human Hepatotoxicity (H-HT):	0.334
Drug-inuced Liver Injury (DILI):	0.958
AMES Toxicity:	0.64
Rat Oral Acute Toxicity:	0.509
Maximum Recommended Daily Dose:	0.006
Skin Sensitization:	0.84
Carcinogencity:	0.059
Eye Corrosion:	0.006
Eye Irritation:	0.456
Respiratory Toxicity:	0.933

Download Data

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

Natural Product: NPC83638

Natural Product ID:	NPC83638
*Common Name:**	YYYCJNDALLBNEG-GNRUMFBNSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YYYCJNDALLBNEG-GNRUMFBNSA-N
Standard InCHI:	InChI=1S/C19H25NO10/c20-6-11(9-4-2-1-3-5-9)29-19-17(26)15(24)14(23)12(30-19)8-28-18-16(25)13(22)10(21)7-27-18/h1-5,10-19,21-26H,7-8H2/t10-,11-,12+,13-,14+,15-,16+,17+,18-,19+/m0/s1
SMILES:	c1ccc(cc1)[C@H](C#N)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO[C@H]2[C@@H]([C@H]([C@H](CO2)O)O)O)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	656493
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
NPO13968	Garcinia scortechinii	Species	Clusiaceae	Eukaryota	fruits	n.a.	n.a.	PMID[16038540]
NPO14358	Rhodobacter sphaeroides	Species	Rhodobacteraceae	Bacteria	n.a.	n.a.	n.a.	PMID[1612412]
NPO8068	Blumea mollis	Species	Asteraceae	Eukaryota	n.a.	leaf	n.a.	PMID[18566831]
NPO14162	Chlorophytum borivilianum	Species	Asparagaceae	Eukaryota	roots	n.a.	n.a.	PMID[19128156]
NPO7016	Gardenia tubifera	Species	Rubiaceae	Eukaryota	exudate	n.a.	n.a.	PMID[20028108]
NPO12357	Lycopus europaeus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20674349]
NPO11492	Kopsia grandifolia	Species	Apocynaceae	Eukaryota	n.a.	stem	n.a.	PMID[21428274]
NPO11492	Kopsia grandifolia	Species	Apocynaceae	Eukaryota	n.a.	leaf	n.a.	PMID[21428274]
NPO8650	Perilla frutescens	Species	Lamiaceae	Eukaryota	leaves	n.a.	n.a.	PMID[22272932]
NPO8650	Perilla frutescens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25320841]
NPO1795	Fragaria vesca	Species	Rosaceae	Eukaryota	n.a.	fruit	n.a.	PMID[26169681]
NPO13014	Ipomoea cairica	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8650	Perilla frutescens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12357	Lycopus europaeus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1795	Fragaria vesca	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3465	Aconitum leucostomum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16703	Isodon lophanthoides	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1795	Fragaria vesca	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13014	Ipomoea cairica	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4004	Aquilegia ecalcarata	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13968	Garcinia scortechinii	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12357	Lycopus europaeus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8650	Perilla frutescens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13014	Ipomoea cairica	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8650	Perilla frutescens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3465	Aconitum leucostomum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8650	Perilla frutescens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4671	Persea mexicana	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10550	Artemisia hanseniana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11492	Kopsia grandifolia	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3465	Aconitum leucostomum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8892	Sordaria araneosa	Species	Sordariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13467	Anarsia lineatella	Species	Gelechiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14358	Rhodobacter sphaeroides	Species	Rhodobacteraceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO14162	Chlorophytum borivilianum	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13968	Garcinia scortechinii	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12509	Dipterocarpus dyeri	Species	Dipterocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13766	Ceanothus velutinus	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13014	Ipomoea cairica	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4004	Aquilegia ecalcarata	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1795	Fragaria vesca	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7016	Gardenia tubifera	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14057	Apollonias barbujana	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO205	Lasianthus fordii	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16703	Isodon lophanthoides	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8068	Blumea mollis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11998	Ledebouria socialis	Species	Hyacinthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5191	Penicillium cinerascens	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO746	Panax innovans	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8650	Perilla frutescens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12357	Lycopus europaeus	Species	Lamiaceae	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 NPC83638 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 NPC83638 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