NPASS Compound

Structure

NPC239572 OpenBabel06302215162D 25 29 0 0 1 0 0 0 0 0999 V2000 4.0458 -0.6308 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2774 -0.2887 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6881 -0.7168 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0227 -0.4205 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.8592 -0.3326 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2013 0.4357 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.7069 1.1162 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8704 1.0283 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.5283 0.2599 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.7284 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 0.4205 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7284 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7284 -0.8411 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 -1.2616 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.2020 -2.0781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7284 -0.8411 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.5283 -1.1010 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7882 -1.9009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2254 -2.5260 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6109 -2.0758 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3642 -0.6308 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2053 -0.6308 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 -1.4568 -1.2616 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3760 1.7087 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 6 1 0 0 0 0 2 3 1 0 0 0 0 4 3 1 1 0 0 0 4 17 1 0 0 0 0 4 5 1 0 0 0 0 4 9 1 0 0 0 0 6 5 1 6 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 8 25 1 0 0 0 0 9 10 1 0 0 0 0 10 16 1 0 0 0 0 10 23 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 13 24 1 0 0 0 0 14 15 1 6 0 0 0 14 16 1 0 0 0 0 14 21 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 18 20 1 0 0 0 0 21 22 2 0 0 0 0 21 23 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	348.16
Volume:	339.23
LogP:	0.937
LogD:	0.452
LogS:	-3.461
# Rotatable Bonds:	1
TPSA:	104.06
# H-Bond Aceptor:	6
# H-Bond Donor:	3
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.484
Synthetic Accessibility Score:	6.604
Fsp3:	0.789
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.952
MDCK Permeability:	0.00016050398699007928
Pgp-inhibitor:	0.0
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.096
20% Bioavailability (F20%):	0.169
30% Bioavailability (F30%):	0.672

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.281
Plasma Protein Binding (PPB):	36.2673454284668%
Volume Distribution (VD):	0.29
Pgp-substrate:	53.86595916748047%

ADMET: Metabolism

CYP1A2-inhibitor:	0.002
CYP1A2-substrate:	0.297
CYP2C19-inhibitor:	0.008
CYP2C19-substrate:	0.163
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.085
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.11
CYP3A4-inhibitor:	0.059
CYP3A4-substrate:	0.026

ADMET: Excretion

Clearance (CL):	8.087
Half-life (T1/2):	0.437

ADMET: Toxicity

hERG Blockers:	0.033
Human Hepatotoxicity (H-HT):	0.647
Drug-inuced Liver Injury (DILI):	0.105
AMES Toxicity:	0.018
Rat Oral Acute Toxicity:	0.329
Maximum Recommended Daily Dose:	0.896
Skin Sensitization:	0.185
Carcinogencity:	0.802
Eye Corrosion:	0.004
Eye Irritation:	0.013
Respiratory Toxicity:	0.978

Download Data

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

Natural Product: NPC239572

Natural Product ID:	NPC239572
*Common Name:**	NYLKJADFYRJQOI-DMQYUYNFSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	NYLKJADFYRJQOI-DMQYUYNFSA-N
Standard InCHI:	InChI=1S/C19H24O6/c1-8-6-18-7-9(8)5-10(20)13(18)19-4-3-11(21)17(2,16(24)25-19)14(19)12(18)15(22)23/h9-14,20-21H,1,3-7H2,2H3,(H,22,23)/t9-,10+,11+,12-,13-,14-,17-,18-,19-/m1/s1
SMILES:	C=C1C[C@@]23C[C@H]1C[C@@H]([C@H]3[C@]13CC[C@@H]([C@](C)([C@H]1[C@@H]2C(=O)O)C(=O)O3)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	21596345
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0001767] Gibberellins [CHEMONTID:0002998] C19-gibberellins [CHEMONTID:0004013] C19-gibberellin 6-carboxylic acids

*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
NPO6447	Kopsia teoi	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9544563]
NPO2342	Cytisus scoparius	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2342	Cytisus scoparius	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2342	Cytisus scoparius	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9464	Stevia paniculata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11306	Crotalaria medicaginea	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9852	Polyporus pargamenus	Species	Polyporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12164	Monnieria trifolia	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO26187	Fritillaria stenanthera	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6447	Kopsia teoi	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10968	Striga lutea	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2342	Cytisus scoparius	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7108	Rubus lambertianus	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10089	Polyalthia barnesii	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12374	Psychotria st	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5289	Calocephalus citreus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12280	Sidastrum burrerense	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15185	Yucca recurvifolia	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6052	Genista pichisermolliana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO621	Eria floribunda	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8762	Brickellia cylindracea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12053	Eria alba	Species	Orchidaceae	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 NPC239572 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	252
0.1-0.2	1954
0.2-0.3	6571
0.3-0.4	13683
0.4-0.5	7292
0.5-0.6	6226
0.6-0.7	5535
0.7-0.8	1112
0.8-0.85	61
0.85-0.9	10
0.9-0.95	1
0.95-1	0

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 NPC239572 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	252
0.1-0.2	2443
0.2-0.3	4020
0.3-0.4	1631
0.4-0.5	354
0.5-0.6	225
0.6-0.7	171
0.7-0.8	53
0.8-0.85	1
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