NPASS Compound

Structure

NPC216663 OpenBabel06302215412D 28 31 0 0 1 0 0 0 0 0999 V2000 3.6538 2.6618 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8981 2.0070 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5299 2.2436 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0922 2.2436 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7240 2.0070 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8559 2.5035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0081 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0040 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.1999 1.9790 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.4722 2.7194 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4495 2.5076 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1216 3.2480 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7547 1.5553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1940 2.0875 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6044 1.1756 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.8911 0.8448 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3110 0.7215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7310 0.8448 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0176 1.1756 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.0799 1.6088 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9272 0.7602 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7704 1.5628 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8640 0.5035 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7280 1.0070 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2315 0.1430 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7280 1.0110 0.0000 C 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 2.5989 1.2803 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 20 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 5 4 1 1 0 0 0 5 6 1 0 0 0 0 5 24 1 0 0 0 0 6 7 1 0 0 0 0 8 7 1 1 0 0 0 8 23 1 0 0 0 0 8 27 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 1 0 0 0 9 14 1 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 15 23 1 0 0 0 0 15 28 1 1 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 22 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 19 21 1 6 0 0 0 23 24 1 0 0 0 0 23 27 1 6 0 0 0 24 25 1 0 0 0 0 24 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	392.22
Volume:	399.674
LogP:	3.361
LogD:	2.958
LogS:	-4.466
# Rotatable Bonds:	2
TPSA:	88.52
# H-Bond Aceptor:	6
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.405
Synthetic Accessibility Score:	6.807
Fsp3:	0.773
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:	-4.998
MDCK Permeability:	9.64261380431708e-06
Pgp-inhibitor:	0.0
Pgp-substrate:	0.802
Human Intestinal Absorption (HIA):	0.049
20% Bioavailability (F20%):	0.959
30% Bioavailability (F30%):	0.307

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.883
Plasma Protein Binding (PPB):	68.68851470947266%
Volume Distribution (VD):	1.018
Pgp-substrate:	44.50537109375%

ADMET: Metabolism

CYP1A2-inhibitor:	0.016
CYP1A2-substrate:	0.777
CYP2C19-inhibitor:	0.142
CYP2C19-substrate:	0.741
CYP2C9-inhibitor:	0.446
CYP2C9-substrate:	0.052
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.318
CYP3A4-inhibitor:	0.131
CYP3A4-substrate:	0.589

ADMET: Excretion

Clearance (CL):	2.557
Half-life (T1/2):	0.671

ADMET: Toxicity

hERG Blockers:	0.01
Human Hepatotoxicity (H-HT):	0.771
Drug-inuced Liver Injury (DILI):	0.263
AMES Toxicity:	0.989
Rat Oral Acute Toxicity:	0.065
Maximum Recommended Daily Dose:	0.925
Skin Sensitization:	0.708
Carcinogencity:	0.975
Eye Corrosion:	0.003
Eye Irritation:	0.06
Respiratory Toxicity:	0.449

Download Data

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

Natural Product: NPC216663

Natural Product ID:	NPC216663
*Common Name:**	CMJANKGYCHNBQY-SBJOWSEZSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	CMJANKGYCHNBQY-SBJOWSEZSA-N
Standard InCHI:	InChI=1S/C22H32O6/c1-13-6-7-16-8-9-20-18(26-15(3)23)27-21(25,12-14(2)11-17(24)10-13)22(20,28-20)19(16,4)5/h11,16-18,24-25H,1,6-10,12H2,2-5H3/b14-11+/t16-,17+,18+,20-,21-,22-/m1/s1
SMILES:	C=C1CC[C@@H]2CC[C@@]34[C@@H](OC(=O)C)O[C@](C/C(=C/[C@H](C1)O)/C)([C@]3(C2(C)C)O4)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	24764026
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001729] Oxepanes

*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
NPO24310	Cespitularia hypotentaculata	Species	Xeniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[12398538]
NPO24310	Cespitularia hypotentaculata	Species	Xeniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[16933873]
NPO22004	Cystodytes solitus	Species	Polycitoridae	Eukaryota	n.a.	n.a.	n.a.	PMID[18484775]
NPO24310	Cespitularia hypotentaculata	Species	Xeniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[19061391]
NPO24805	Thorecta reticulata	Species	Thorectidae	Eukaryota	n.a.	n.a.	n.a.	PMID[21513294]
NPO25343	Tanacetum microphyllum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25548	Balanophora indica	Species	Balanophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25548	Balanophora indica	Species	Balanophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25343	Tanacetum microphyllum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25548	Balanophora indica	Species	Balanophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5278	Acacia cyperophylla	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11177	0ctiluca scintillans	Species	0ctilucaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24616	Ottonia vahlii	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO5543	Persicaria tomentosa	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25205	Thymus borgiae	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3706	Hedypnois rhagadioloides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25343	Tanacetum microphyllum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24310	Cespitularia hypotentaculata	Species	Xeniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24805	Thorecta reticulata	Species	Thorectidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24435	Beschorneria bracteata	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25684	Fagus dombeyi	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25631	Picris kamtschatica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25606	Aster patagonicus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22004	Cystodytes solitus	Species	Polycitoridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25314	Usnea ceratina	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25655	Pseudocyphellaria granulata	Species	Lobariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23999	Rhipidothuria racowitzai	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO2404	Heterophragma quadriloculare	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6639	Flagelloscypha pilatii	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25427	Solanum vespertilio	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24482	Phyllanthus oxyphyllus	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25516	Dahlia sherffii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25452	Crucigenia apiculata	Species	Scenedesmaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25548	Balanophora indica	Species	Balanophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28702	Cyclolepis genistoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23333	Michelia excelsa	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25485	Agathosma lanceolata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20428	Debregeasia salicifolia	Species	Urticaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19210	Quercus lusitanica	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25061	Lactarius glyciosmus	Species	Russulaceae	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 NPC216663 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	178
0.1-0.2	1369
0.2-0.3	4748
0.3-0.4	12359
0.4-0.5	9887
0.5-0.6	6620
0.6-0.7	6264
0.7-0.8	1234
0.8-0.85	38
0.85-0.9	0
0.9-0.95	0
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 NPC216663 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	148
0.1-0.2	1737
0.2-0.3	3913
0.3-0.4	2269
0.4-0.5	654
0.5-0.6	285
0.6-0.7	137
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