NPASS Compound

Structure

NPC311956 OpenBabel06302215532D 30 32 0 0 1 0 0 0 0 0999 V2000 -3.0048 1.4135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7969 2.3917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6629 2.8917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6574 2.7872 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4006 2.1180 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.6085 1.1399 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2018 0.2263 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3357 -0.2737 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3412 -0.1691 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.9345 -1.0827 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.9563 -1.2906 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6776 -1.7518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5731 -2.7463 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5437 -1.2518 0.0000 O 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 -2.3902 1.4781 0.0000 C 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 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 -4.8654 1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2666 2.6180 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 16 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 5 30 1 6 0 0 0 6 7 2 0 0 0 0 6 29 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 8 14 1 0 0 0 0 9 10 1 0 0 0 0 9 15 1 0 0 0 0 10 11 1 6 0 0 0 10 12 1 0 0 0 0 12 13 2 0 0 0 0 12 14 1 0 0 0 0 15 16 1 0 0 0 0 15 17 1 0 0 0 0 17 18 1 0 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 0 0 0 0 21 22 1 0 0 0 0 21 26 1 6 0 0 0 22 23 1 1 0 0 0 22 25 1 0 0 0 0 23 24 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	336.23
Volume:	364.615
LogP:	2.627
LogD:	2.555
LogS:	-3.081
# Rotatable Bonds:	5
TPSA:	77.76
# H-Bond Aceptor:	4
# H-Bond Donor:	3
# Rings:	2
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.671
Synthetic Accessibility Score:	4.659
Fsp3:	0.75
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:	-5.321
MDCK Permeability:	2.320573548786342e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	0.044
Human Intestinal Absorption (HIA):	0.007
20% Bioavailability (F20%):	0.48
30% Bioavailability (F30%):	0.005

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.872
Plasma Protein Binding (PPB):	73.87805938720703%
Volume Distribution (VD):	0.4
Pgp-substrate:	24.906787872314453%

ADMET: Metabolism

CYP1A2-inhibitor:	0.007
CYP1A2-substrate:	0.233
CYP2C19-inhibitor:	0.012
CYP2C19-substrate:	0.489
CYP2C9-inhibitor:	0.017
CYP2C9-substrate:	0.142
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.083
CYP3A4-inhibitor:	0.509
CYP3A4-substrate:	0.146

ADMET: Excretion

Clearance (CL):	2.68
Half-life (T1/2):	0.417

ADMET: Toxicity

hERG Blockers:	0.016
Human Hepatotoxicity (H-HT):	0.205
Drug-inuced Liver Injury (DILI):	0.019
AMES Toxicity:	0.008
Rat Oral Acute Toxicity:	0.836
Maximum Recommended Daily Dose:	0.948
Skin Sensitization:	0.277
Carcinogencity:	0.53
Eye Corrosion:	0.195
Eye Irritation:	0.23
Respiratory Toxicity:	0.976

Download Data

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

Natural Product: NPC311956

Natural Product ID:	NPC311956
*Common Name:**	CPKWYFUGBHLPGR-WVYXXGMBSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	CPKWYFUGBHLPGR-WVYXXGMBSA-N
Standard InCHI:	InChI=1S/C21H32O9/c1-9-4-5-12(23)10(2)7-14-16(11(3)20(27)28-14)13(6-9)29-21-19(26)18(25)17(24)15(8-22)30-21/h4,7,11-19,21-26H,5-6,8H2,1-3H3/b9-4+,10-7+/t11-,12+,13-,14+,15+,16+,17+,18-,19+,21+/m0/s1
SMILES:	C/C/1=CC[C@H](/C(=C/[C@@H]2[C@H]([C@H](C)C(=O)O2)[C@H](C1)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)/C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones [CHEMONTID:0001543] Sesquiterpene lactones [CHEMONTID:0001771] Germacranolides and derivatives

*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
NPO27907	Dianthus versicolor	Species	Caryophyllaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[19290648]
NPO27907	Dianthus versicolor	Species	Caryophyllaceae	Eukaryota	aerial parts	Changqing, Shangdong Province, China	2004-JUN	PMID[19290648]
NPO24074	Jatropha dioica	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28771358]
NPO27907	Dianthus versicolor	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28720	Agardhiella subulata	Species	Solieriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24807	Fuscospora fusca	Species	0thofagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28267	Aria dentata	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28496	Rhododendron vaccinioides	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28215	Centaurea africana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27907	Dianthus versicolor	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28406	Hypericum foliosum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28086	Dalbergia sympathetica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28390	Helichrysum rugulosum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28051	Balsamorhiza macrophylla	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29270	Strobilanthes formosana	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28302	Aphis nerii	Species	Aphididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24074	Jatropha dioica	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28653	Picris rhagadioloides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28318	Chromodoris youngbleuthi	Species	Chromodorididae	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 NPC311956 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	177
0.1-0.2	1101
0.2-0.3	4375
0.3-0.4	9649
0.4-0.5	12750
0.5-0.6	7813
0.6-0.7	5535
0.7-0.8	1223
0.8-0.85	70
0.85-0.9	2
0.9-0.95	1
0.95-1	1

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 NPC311956 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	147
0.1-0.2	1516
0.2-0.3	3842
0.3-0.4	2401
0.4-0.5	750
0.5-0.6	378
0.6-0.7	104
0.7-0.8	12
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