NPASS Compound

Structure

NPC96388 OpenBabel06302215222D 22 22 0 0 1 0 0 0 0 0999 V2000 9.3659 -6.9006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.7726 -5.9870 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1848 -5.1780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1903 -5.2825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6025 -4.4735 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6080 -4.5780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0202 -3.7690 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0257 -3.8735 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4379 -3.0645 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4434 -3.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8556 -2.3600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8611 -2.4646 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2733 -1.6555 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2788 -1.7601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3090 -0.9511 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.3090 -0.9511 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6180 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5691 0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8090 0.5878 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 0.3090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8968 -1.7601 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 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 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 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 15 14 1 6 0 0 0 15 16 1 0 0 0 0 15 20 1 0 0 0 0 16 17 1 0 0 0 0 16 22 1 6 0 0 0 17 18 1 6 0 0 0 17 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	312.27
Volume:	352.358
LogP:	6.857
LogD:	4.095
LogS:	-5.598
# Rotatable Bonds:	13
TPSA:	46.53
# H-Bond Aceptor:	3
# H-Bond Donor:	1
# Rings:	1
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.384
Synthetic Accessibility Score:	3.215
Fsp3:	0.947
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.793
MDCK Permeability:	2.4780370949883945e-05
Pgp-inhibitor:	0.117
Pgp-substrate:	0.004
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	1.0
30% Bioavailability (F30%):	0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.215
Plasma Protein Binding (PPB):	97.49608612060547%
Volume Distribution (VD):	1.361
Pgp-substrate:	2.3796586990356445%

ADMET: Metabolism

CYP1A2-inhibitor:	0.539
CYP1A2-substrate:	0.198
CYP2C19-inhibitor:	0.388
CYP2C19-substrate:	0.086
CYP2C9-inhibitor:	0.29
CYP2C9-substrate:	0.943
CYP2D6-inhibitor:	0.048
CYP2D6-substrate:	0.088
CYP3A4-inhibitor:	0.607
CYP3A4-substrate:	0.083

ADMET: Excretion

Clearance (CL):	5.105
Half-life (T1/2):	0.077

ADMET: Toxicity

hERG Blockers:	0.264
Human Hepatotoxicity (H-HT):	0.093
Drug-inuced Liver Injury (DILI):	0.716
AMES Toxicity:	0.014
Rat Oral Acute Toxicity:	0.066
Maximum Recommended Daily Dose:	0.014
Skin Sensitization:	0.943
Carcinogencity:	0.092
Eye Corrosion:	0.902
Eye Irritation:	0.91
Respiratory Toxicity:	0.944

Download Data

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

Natural Product: NPC96388

Natural Product ID:	NPC96388
*Common Name:**	BEEKFGLUGMQFSX-RCCFBDPRSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	BEEKFGLUGMQFSX-RCCFBDPRSA-N
Standard InCHI:	InChI=1S/C19H36O3/c1-3-4-5-6-7-8-9-10-11-12-13-14-15-17-18(20)16(2)22-19(17)21/h16-18,20H,3-15H2,1-2H3/t16-,17+,18+/m0/s1
SMILES:	CCCCCCCCCCCCCC[C@@H]1[C@@H]([C@H](C)OC1=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11174423
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000050] Lactones [CHEMONTID:0001245] Gamma butyrolactones

*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
NPO16657	Diospyros maritima	Species	Ebenaceae	Eukaryota	bark	Indonesia	n.a.	PMID[15270571]
NPO21076	Nephthea armata	Species	Nephtheidae	Eukaryota	n.a.	Taiwan	n.a.	PMID[15387641]
NPO22180	Dracaena mannii	Species	Asparagaceae	Eukaryota	n.a.	stem	n.a.	PMID[18481024]
NPO22180	Dracaena mannii	Species	Asparagaceae	Eukaryota	stems	Yaound, village of Bangoua, near Bangangt	2007-APR	PMID[20553003]
NPO16657	Diospyros maritima	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22313254]
NPO5386	Citrus paradisi	Species	Rutaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO5386	Citrus paradisi	Species	Rutaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO16657	Diospyros maritima	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5386	Citrus paradisi	Species	Rutaceae	Eukaryota	Fruits	n.a.		Database[Phenol-Explorer]
NPO5386	Citrus paradisi	Species	Rutaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO5386	Citrus paradisi	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19432	Millettia pinnata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16657	Diospyros maritima	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16657	Diospyros maritima	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO22007	Acer spicatum	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21819	Domohinea perrieri	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22125	Helipterum propinquum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29112	Streptomyces luteosporeus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO17813	Pittosporum undulatum	Species	Pittosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5386	Citrus paradisi	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20571	Limnodynastes interioris	Species	Myobatrachidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22180	Dracaena mannii	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16657	Diospyros maritima	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19432	Millettia pinnata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18284	Cytisus ciliatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22064	Mannia fragrans	Species	Aytoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20708	Mesua beccariana	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21076	Nephthea armata	Species	Nephtheidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22525	Lobophytum denticulatum	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22867	Stephanitis rhododendri	Species	Tingidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22923	Parthenium bipinnatifidum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19330	Cephalaria procera	Species	Caprifoliaceae	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 NPC96388 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	417
0.1-0.2	3837
0.2-0.3	13610
0.3-0.4	10899
0.4-0.5	8703
0.5-0.6	4570
0.6-0.7	583
0.7-0.8	66
0.8-0.85	8
0.85-0.9	3
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 NPC96388 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	602
0.1-0.2	3862
0.2-0.3	3037
0.3-0.4	886
0.4-0.5	552
0.5-0.6	179
0.6-0.7	27
0.7-0.8	5
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