NPASS Compound

Structure

NPC126940 OpenBabel06302215552D 23 26 0 0 1 0 0 0 0 0999 V2000 2.0708 -0.0003 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4144 0.3788 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4145 1.1368 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7580 -0.0001 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.7577 -1.0718 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1704 -1.6075 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0985 -1.0717 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.0984 0.0002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1702 0.5359 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0265 0.5362 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9548 0.0004 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9550 -1.0714 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.8833 -1.6072 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3708 -0.7626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8834 -2.6791 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9553 -3.2151 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0269 -2.6793 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0268 -1.6075 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.1823 -2.0952 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8585 -1.6071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3460 -0.7625 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7195 -0.4153 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 2 1 0 0 0 0 2 3 1 0 0 0 0 4 2 1 1 0 0 0 4 9 1 0 0 0 0 4 23 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 7 6 1 6 0 0 0 7 18 1 0 0 0 0 7 8 1 0 0 0 0 7 22 1 0 0 0 0 8 9 2 0 0 0 0 8 10 1 0 0 0 0 10 11 1 0 0 0 0 12 11 1 6 0 0 0 12 13 1 0 0 0 0 12 18 1 0 0 0 0 13 14 1 6 0 0 0 13 15 1 0 0 0 0 13 20 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 6 0 0 0 20 21 1 0 0 0 0 22 23 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	320.24
Volume:	343.985
LogP:	4.198
LogD:	3.345
LogS:	-5.053
# Rotatable Bonds:	2
TPSA:	38.69
# H-Bond Aceptor:	3
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.605
Synthetic Accessibility Score:	6.2
Fsp3:	0.9
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:	-4.66
MDCK Permeability:	1.868361869128421e-05
Pgp-inhibitor:	0.41
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.011
30% Bioavailability (F30%):	0.028

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.222
Plasma Protein Binding (PPB):	93.37586212158203%
Volume Distribution (VD):	1.543
Pgp-substrate:	2.173032283782959%

ADMET: Metabolism

CYP1A2-inhibitor:	0.096
CYP1A2-substrate:	0.876
CYP2C19-inhibitor:	0.115
CYP2C19-substrate:	0.94
CYP2C9-inhibitor:	0.209
CYP2C9-substrate:	0.058
CYP2D6-inhibitor:	0.036
CYP2D6-substrate:	0.13
CYP3A4-inhibitor:	0.909
CYP3A4-substrate:	0.92

ADMET: Excretion

Clearance (CL):	7.943
Half-life (T1/2):	0.31

ADMET: Toxicity

hERG Blockers:	0.055
Human Hepatotoxicity (H-HT):	0.344
Drug-inuced Liver Injury (DILI):	0.114
AMES Toxicity:	0.081
Rat Oral Acute Toxicity:	0.11
Maximum Recommended Daily Dose:	0.602
Skin Sensitization:	0.371
Carcinogencity:	0.887
Eye Corrosion:	0.089
Eye Irritation:	0.637
Respiratory Toxicity:	0.974

Download Data

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

Natural Product: NPC126940

Natural Product ID:	NPC126940
*Common Name:**	NVECILAMICWAEO-VYJAJWGXSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	NVECILAMICWAEO-VYJAJWGXSA-N
Standard InCHI:	InChI=1S/C20H32O3/c1-14(2)19-10-11-20(23-22-19)15(12-19)6-7-16-17(3,13-21)8-5-9-18(16,20)4/h12,14,16,21H,5-11,13H2,1-4H3/t16-,17-,18-,19-,20+/m0/s1
SMILES:	CC(C)[C@]12CC[C@]3(C(=C1)CC[C@H]1[C@@](C)(CCC[C@]31C)CO)OO2
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11267184
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000368] Dioxanes [CHEMONTID:0001312] 1,2-dioxanes

*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
NPO21179	Streptomyces griseoaurantiacus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[10048567]
NPO18881	Loropetalum chinense	Species	Hamamelidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18881	Loropetalum chinense	Species	Hamamelidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14307	Rhizopus oryzae	Species	Rhizopodaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18881	Loropetalum chinense	Species	Hamamelidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21704	Papaver suaveolens	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23157	Wigandia kunthii	Species	Namaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14307	Rhizopus oryzae	Species	Rhizopodaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13308	Polycitor adriaticus	Species	Polycitoridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21179	Streptomyces griseoaurantiacus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO22530	Vigna luteola	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18881	Loropetalum chinense	Species	Hamamelidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22147	Goniothalamus macrophyllus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21894	Psychotria granadensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22968	Elaeocarpus serratus	Species	Elaeocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15469	Myodocarpus gracilis	Species	Myodocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6953.1	Aconitum sachalinense subsp. yezoense	Subspecies	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20425	Epimedium macranthum	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23194	Berberis beaniana	Species	Berberidaceae	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 NPC126940 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	203
0.1-0.2	1673
0.2-0.3	6095
0.3-0.4	16056
0.4-0.5	8298
0.5-0.6	5736
0.6-0.7	3653
0.7-0.8	878
0.8-0.85	95
0.85-0.9	8
0.9-0.95	0
0.95-1	2

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 NPC126940 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	192
0.1-0.2	1935
0.2-0.3	4149
0.3-0.4	2084
0.4-0.5	435
0.5-0.6	224
0.6-0.7	120
0.7-0.8	10
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