NPASS Compound

Structure

NPC174205 OpenBabel06302215552D 33 37 0 0 1 0 0 0 0 0999 V2000 1.7321 -0.0000 0.0000 C 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 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 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3301 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1962 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0622 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5622 0.6340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 2.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3301 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 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 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 2.5000 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 2 31 1 0 0 0 0 3 4 2 0 0 0 0 3 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 7 31 1 0 0 0 0 8 28 1 0 0 0 0 8 9 1 0 0 0 0 8 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 25 1 0 0 0 0 12 13 1 0 0 0 0 12 14 1 0 0 0 0 14 15 1 0 0 0 0 14 21 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 16 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 21 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 25 28 1 0 0 0 0 26 27 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 29 33 1 0 0 0 0 30 31 1 0 0 0 0 31 32 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	458.38
Volume:	508.388
LogP:	5.336
LogD:	4.476
LogS:	-5.545
# Rotatable Bonds:	1
TPSA:	57.53
# H-Bond Aceptor:	3
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.478
Synthetic Accessibility Score:	5.191
Fsp3:	0.967
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.093
MDCK Permeability:	1.0539118193264585e-05
Pgp-inhibitor:	0.861
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.019
20% Bioavailability (F20%):	0.82
30% Bioavailability (F30%):	0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.2
Plasma Protein Binding (PPB):	94.1507568359375%
Volume Distribution (VD):	1.245
Pgp-substrate:	2.2750442028045654%

ADMET: Metabolism

CYP1A2-inhibitor:	0.008
CYP1A2-substrate:	0.655
CYP2C19-inhibitor:	0.028
CYP2C19-substrate:	0.921
CYP2C9-inhibitor:	0.116
CYP2C9-substrate:	0.133
CYP2D6-inhibitor:	0.013
CYP2D6-substrate:	0.145
CYP3A4-inhibitor:	0.85
CYP3A4-substrate:	0.52

ADMET: Excretion

Clearance (CL):	11.119
Half-life (T1/2):	0.091

ADMET: Toxicity

hERG Blockers:	0.289
Human Hepatotoxicity (H-HT):	0.432
Drug-inuced Liver Injury (DILI):	0.042
AMES Toxicity:	0.017
Rat Oral Acute Toxicity:	0.637
Maximum Recommended Daily Dose:	0.442
Skin Sensitization:	0.327
Carcinogencity:	0.217
Eye Corrosion:	0.014
Eye Irritation:	0.019
Respiratory Toxicity:	0.972

Download Data

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

Natural Product: NPC174205

Natural Product ID:	NPC174205
*Common Name:**	DHNJMOPCFKWKNM-LRESDBCGSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DHNJMOPCFKWKNM-LRESDBCGSA-N
Standard InCHI:	InChI=1S/C30H50O3/c1-19-20(32)8-9-22-27(5)13-14-29(7)23-17-25(2,3)10-11-26(23,4)12-15-30(29,18-31)24(27)21(33)16-28(19,22)6/h19,21-24,31,33H,8-18H2,1-7H3/t19-,21+,22+,23+,24-,26+,27-,28+,29-,30-/m0/s1
SMILES:	C[C@H]1C(=O)CC[C@@H]2[C@]3(C)CC[C@@]4(C)[C@@H]5CC(C)(C)CC[C@]5(C)CC[C@]4(CO)[C@H]3[C@@H](C[C@]12C)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:0001553] Triterpenoids

*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
NPO24176	Streptomyces fradiae	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[10757717]
NPO2353	Bituminaria bituminosa	Species	Fabaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[12943781]
NPO7484	Salacia chinensis	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12951446]
NPO7484	Salacia chinensis	Species	Celastraceae	Eukaryota	stems	Thailand	n.a.	PMID[14510595]
NPO14555	Porella swartziana	Species	Porellaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[14738381]
NPO14555	Porella swartziana	Species	Porellaceae	Eukaryota	n.a.	Argentine	n.a.	PMID[14738381]
NPO12977	Solenopsis invicta	Species	Formicidae	Eukaryota	n.a.	n.a.	n.a.	PMID[21905650]
NPO23289	Heracleum sphondylium	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24697288]
NPO14826	Streptomyces mobaraensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[32998509]
NPO9420	Aspergillus arenarius	Species	Aspergillaceae	Eukaryota	sclerotia	n.a.	n.a.	PMID[9599285]
NPO23289	Heracleum sphondylium	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15510	Kummerowia striata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5728	Gerbera piloselloides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16847	Consolida ajacis	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12416	Quercus mongolica	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15961	Sida cordifolia	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12416	Quercus mongolica	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15961	Sida cordifolia	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14869	Ormosia panamensis	Species	Limoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16847	Consolida ajacis	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15510	Kummerowia striata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5728	Gerbera piloselloides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12450	Cneorum pulverulentum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23289	Heracleum sphondylium	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12416	Quercus mongolica	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16847	Consolida ajacis	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5728	Gerbera piloselloides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5078	Turraeanthus mannii	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23289	Heracleum sphondylium	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15510	Kummerowia striata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12416	Quercus mongolica	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15961	Sida cordifolia	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16428	Millettia conraui	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15393	Eucalyptus flocktoniae	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24176	Streptomyces fradiae	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO13375	Palafoxia rosea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26017	Dalbergia stipulacea	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16847	Consolida ajacis	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24732	Cereus weberi	Species	Sagartiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14218	Spodoptera littoralis	Species	0ctuidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15138	Rheum webbianum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16516	Centaurea seridis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4935	Dinemasporium strigosum	Species	Chaetosphaeriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4267	Ceratocystis clavigera	Species	Ceratocystidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16758	Satureja cuneifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15755	Thymbra spicata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12977	Solenopsis invicta	Species	Formicidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13548	Chrozophora obliqua	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8499	Osmerus mordax	Species	Osmeridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5269	Coleus garckeanus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14555	Porella swartziana	Species	Porellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14034	Salvia coulteri	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7484	Salacia chinensis	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11194	Bombus hortorum	Species	Apidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9780	Merremia umbellata	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11881	Adenopeltis colliguaya	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5552	Solanum sisymbriifolium	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15858	Phoebe formosana	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13859	Senecio flavus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14869	Ormosia panamensis	Species	Limoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16175	Trichia floriformis	Species	Trichiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15015	Meconopsis napaulensis	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2353	Bituminaria bituminosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13230	Pedicularis condensata	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5728	Gerbera piloselloides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16678	Flindersia brayleyana	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11599	Elaeagnus commutata	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13710	Lyophyllum shimeji	Species	Lyophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9420	Aspergillus arenarius	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3391	Jungermannia obovata	Species	Jungermanniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12450	Cneorum pulverulentum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15272	Mascarenhasia arborescens	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12555	Aspergillus quadrilineatus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14826	Streptomyces mobaraensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO12680	Perityle vaseyi	Species	Asteraceae	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 NPC174205 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	447
0.1-0.2	3758
0.2-0.3	13030
0.3-0.4	12751
0.4-0.5	5253
0.5-0.6	4418
0.6-0.7	2400
0.7-0.8	567
0.8-0.85	44
0.85-0.9	13
0.9-0.95	13
0.95-1	3

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 NPC174205 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	538
0.1-0.2	3896
0.2-0.3	3295
0.3-0.4	898
0.4-0.5	246
0.5-0.6	203
0.6-0.7	50
0.7-0.8	23
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