NPASS Compound

Structure

NPC271489 OpenBabel06302216172D 30 32 0 0 1 0 0 0 0 0999 V2000 4.1989 -3.3939 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3591 -3.8788 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5193 -3.3939 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6796 -3.8788 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5193 -2.4242 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3591 -1.9394 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8398 -1.4545 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8398 -0.4848 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6796 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6018 -0.2997 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9015 -1.2219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1718 0.4848 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6018 1.2693 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6796 0.9697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8398 1.4545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.9697 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8398 1.4545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6796 0.9697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6796 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8398 -0.4848 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8398 -1.4545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 -0.9697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5193 -0.4848 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3591 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1989 -0.4848 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3591 0.9697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1989 1.4545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0387 0.9697 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 -5.8785 1.4545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 3 5 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 8 7 1 1 0 0 0 8 9 1 0 0 0 0 8 22 1 0 0 0 0 9 14 2 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 10 12 2 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 16 15 1 6 0 0 0 16 17 1 0 0 0 0 16 22 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 19 24 1 1 0 0 0 20 21 1 1 0 0 0 20 22 1 0 0 0 0 22 23 1 1 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 25 27 1 0 0 0 0 27 28 2 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	432.2
Volume:	444.632
LogP:	4.908
LogD:	4.785
LogS:	-5.273
# Rotatable Bonds:	7
TPSA:	65.74
# H-Bond Aceptor:	5
# H-Bond Donor:	0
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.45
Synthetic Accessibility Score:	4.96
Fsp3:	0.583
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:	-4.638
MDCK Permeability:	2.0339088223408908e-05
Pgp-inhibitor:	0.995
Pgp-substrate:	0.027
Human Intestinal Absorption (HIA):	0.011
20% Bioavailability (F20%):	0.033
30% Bioavailability (F30%):	0.925

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.025
Plasma Protein Binding (PPB):	98.09407806396484%
Volume Distribution (VD):	2.824
Pgp-substrate:	2.625840663909912%

ADMET: Metabolism

CYP1A2-inhibitor:	0.321
CYP1A2-substrate:	0.592
CYP2C19-inhibitor:	0.942
CYP2C19-substrate:	0.802
CYP2C9-inhibitor:	0.931
CYP2C9-substrate:	0.058
CYP2D6-inhibitor:	0.857
CYP2D6-substrate:	0.103
CYP3A4-inhibitor:	0.941
CYP3A4-substrate:	0.736

ADMET: Excretion

Clearance (CL):	13.629
Half-life (T1/2):	0.259

ADMET: Toxicity

hERG Blockers:	0.423
Human Hepatotoxicity (H-HT):	0.905
Drug-inuced Liver Injury (DILI):	0.697
AMES Toxicity:	0.016
Rat Oral Acute Toxicity:	0.578
Maximum Recommended Daily Dose:	0.951
Skin Sensitization:	0.604
Carcinogencity:	0.044
Eye Corrosion:	0.015
Eye Irritation:	0.024
Respiratory Toxicity:	0.98

Download Data

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

Natural Product: NPC271489

Natural Product ID:	NPC271489
*Common Name:**	DZIJJEZRPMYRRP-DKYQICBRSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DZIJJEZRPMYRRP-DKYQICBRSA-N
Standard InCHI:	InChI=1S/C24H32O5S/c1-7-14(2)23(26)29-22-21-15(3)13-27-19(21)12-17-8-9-18(16(4)24(17,22)5)28-20(25)10-11-30-6/h7,10-11,13,16-18,22H,8-9,12H2,1-6H3/b11-10-,14-7-/t16-,17+,18-,22+,24+/m0/s1
SMILES:	C/C=C(/C)C(=O)O[C@@H]1c2c(C)coc2C[C@H]2CC[C@@H]([C@H](C)[C@@]12C)OC(=O)/C=CSC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	21602833
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001550] Sesquiterpenoids [CHEMONTID:0003655] Eremophilane, 8,9-secoeremophilane and furoeremophilane sesquiterpenoids

*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
NPO15275	Briareum asbestinum	Species	Briareidae	Eukaryota	n.a.	n.a.	n.a.	PMID[12662092]
NPO1396	Cladogynos orientalis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[15679308]
NPO15275	Briareum asbestinum	Species	Briareidae	Eukaryota	n.a.	Caribbean	n.a.	PMID[1686898]
NPO6741	Metasequoia glyptostroboides	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21226514]
NPO6741	Metasequoia glyptostroboides	Species	Cupressaceae	Eukaryota	n.a.	stem	n.a.	PMID[21226514]
NPO6741	Metasequoia glyptostroboides	Species	Cupressaceae	Eukaryota	n.a.	leaf	n.a.	PMID[21226514]
NPO25140	Sapium sebiferum	Species	Euphorbiaceae	Eukaryota	n.a.	leaf	n.a.	PMID[26281591]
NPO25140	Sapium sebiferum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3404159]
NPO10980	Petasites japonicus	Species	Asteraceae	Eukaryota	Pt	n.a.	n.a.	Database[FooDB]
NPO10980	Petasites japonicus	Species	Asteraceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO6741	Metasequoia glyptostroboides	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5166	Adonis sutchuenensis	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10980	Petasites japonicus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8306	Berneuxia thibetica	Species	Diapensiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10980	Petasites japonicus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5166	Adonis sutchuenensis	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6741	Metasequoia glyptostroboides	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25140	Sapium sebiferum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10980	Petasites japonicus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8306	Berneuxia thibetica	Species	Diapensiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO1396	Cladogynos orientalis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO13682	Lonchocarpus laxiflorus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4836	Sideritis arborescens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1706	Eragrostis curvula	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO643	Astragalus ernestii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8950	Stilpnopappus pickelii	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO8306	Berneuxia thibetica	Species	Diapensiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21493	Bunodosoma caissarum	Species	Actiniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6741	Metasequoia glyptostroboides	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1049	Tethya amamensis	Species	Tethyidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7793	Matricaria matricarioides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19991	Mantella aurantiaca	Species	Mantellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3445	Dumoria heckeli	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO2323	Plantago lundborgii	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15275	Briareum asbestinum	Species	Briareidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25140	Sapium sebiferum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5339	Isophysis tasmanica	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1203	Solanum pseudoquina	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8433	Bongardia chrysogonum	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10980	Petasites japonicus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO117	Acacia armata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17179	Elizabethkingia meningoseptica	Species	Flavobacteriaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO8132	Fritillaria meleagris	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1541	Clusia ellipticifolia	Species	Clusiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2008	Streptomyces ehimensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO5166	Adonis sutchuenensis	Species	Ranunculaceae	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 NPC271489 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	359
0.1-0.2	1443
0.2-0.3	3004
0.3-0.4	6977
0.4-0.5	11863
0.5-0.6	7289
0.6-0.7	8369
0.7-0.8	3245
0.8-0.85	127
0.85-0.9	18
0.9-0.95	3
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 NPC271489 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	308
0.1-0.2	872
0.2-0.3	1764
0.3-0.4	2744
0.4-0.5	2153
0.5-0.6	945
0.6-0.7	307
0.7-0.8	57
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