NPASS Compound

Structure

NPC63988 OpenBabel06302216112D 40 45 0 0 1 0 0 0 0 0999 V2000 2.4090 -3.3300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7128 -2.3955 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.6740 -2.1914 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.9778 -1.2569 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3204 -0.5266 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.3593 -0.7307 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.0555 -1.6652 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7019 -0.0004 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8508 -0.4916 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8508 -1.4747 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.9662 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8509 -1.4746 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8509 -2.4573 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1207 -3.1148 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7023 -1.9662 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7023 -2.9487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5537 -3.4402 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4052 -2.9487 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4052 -3.9520 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2566 -3.4402 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1068 -2.9486 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1068 -1.9661 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4051 -1.9661 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5537 -1.4746 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5537 -0.4915 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7023 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8508 -0.4915 0.0000 C 0 0 2 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 -0.8508 0.5118 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4051 -0.9628 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2566 -4.4223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6561 -5.3195 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9263 -5.9766 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0289 -6.9534 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0757 -5.4856 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2799 -4.5250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6242 0.4079 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9390 -1.0528 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5964 -1.7831 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3314 -2.9217 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 6 0 0 0 2 3 1 0 0 0 0 2 7 1 0 0 0 0 3 4 1 0 0 0 0 3 40 1 1 0 0 0 4 5 1 0 0 0 0 4 38 1 6 0 0 0 5 6 1 0 0 0 0 5 37 1 1 0 0 0 6 7 1 0 0 0 0 6 8 1 6 0 0 0 9 8 1 1 0 0 0 9 10 1 0 0 0 0 9 28 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 27 1 0 0 0 0 12 13 1 1 0 0 0 12 15 1 0 0 0 0 13 14 2 0 0 0 0 15 16 1 1 0 0 0 15 24 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 23 1 0 0 0 0 18 19 1 1 0 0 0 18 20 1 0 0 0 0 20 21 1 0 0 0 0 20 31 1 1 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 23 30 1 1 0 0 0 24 25 1 6 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 27 29 1 1 0 0 0 31 36 1 0 0 0 0 31 32 2 0 0 0 0 32 33 1 0 0 0 0 33 34 2 0 0 0 0 33 35 1 0 0 0 0 35 36 1 0 0 0 0 38 39 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	290.15
Volume:	313.374
LogP:	2.912
LogD:	2.725
LogS:	-3.265
# Rotatable Bonds:	9
TPSA:	63.6
# H-Bond Aceptor:	4
# H-Bond Donor:	1
# Rings:	1
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.429
Synthetic Accessibility Score:	2.26
Fsp3:	0.412
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	2
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.718
MDCK Permeability:	2.47344869421795e-05
Pgp-inhibitor:	0.43
Pgp-substrate:	0.016
Human Intestinal Absorption (HIA):	0.043
20% Bioavailability (F20%):	0.02
30% Bioavailability (F30%):	0.009

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.518
Plasma Protein Binding (PPB):	95.96932220458984%
Volume Distribution (VD):	0.358
Pgp-substrate:	2.054713726043701%

ADMET: Metabolism

CYP1A2-inhibitor:	0.922
CYP1A2-substrate:	0.898
CYP2C19-inhibitor:	0.693
CYP2C19-substrate:	0.574
CYP2C9-inhibitor:	0.778
CYP2C9-substrate:	0.932
CYP2D6-inhibitor:	0.028
CYP2D6-substrate:	0.865
CYP3A4-inhibitor:	0.362
CYP3A4-substrate:	0.296

ADMET: Excretion

Clearance (CL):	12.511
Half-life (T1/2):	0.943

ADMET: Toxicity

hERG Blockers:	0.042
Human Hepatotoxicity (H-HT):	0.213
Drug-inuced Liver Injury (DILI):	0.49
AMES Toxicity:	0.512
Rat Oral Acute Toxicity:	0.72
Maximum Recommended Daily Dose:	0.293
Skin Sensitization:	0.928
Carcinogencity:	0.668
Eye Corrosion:	0.466
Eye Irritation:	0.942
Respiratory Toxicity:	0.954

Download Data

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

Natural Product: NPC63988

Natural Product ID:	NPC63988
*Common Name:**	DPKLBEWKXLCUQW-UQQDFEJISA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DPKLBEWKXLCUQW-UQQDFEJISA-N
Standard InCHI:	InChI=1S/C30H44O10/c1-16-23(33)25(37-3)24(34)26(39-16)40-18-4-9-28(15-31)20-5-8-27(2)19(17-12-22(32)38-14-17)7-11-30(27,36)21(20)6-10-29(28,35)13-18/h12,15-16,18-21,23-26,33-36H,4-11,13-14H2,1-3H3/t16-,18-,19+,20-,21+,23-,24-,25+,26+,27+,28-,29-,30-/m0/s1
SMILES:	C[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)O[C@H]1CC[C@]2(C=O)[C@H]3CC[C@]4(C)[C@H](CC[C@@]4([C@@H]3CC[C@@]2(C1)O)O)C1=CC(=O)OC1)O)OC)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:0000258] Steroids and steroid derivatives [CHEMONTID:0001125] Steroid lactones [CHEMONTID:0001555] Cardenolides and derivatives [CHEMONTID:0001559] Cardenolide glycosides and derivatives

*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
NPO6427	Wardomyces anomalus	Species	Microascaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1021/np020518b]
NPO6427	Wardomyces anomalus	Species	Microascaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12762814]
NPO19460	Karenia brevis	Species	Kareniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15679307]
NPO5167	Peripentadenia mearsii	Species	Elaeocarpaceae	Eukaryota	n.a.	Australian rainforest	n.a.	PMID[18039010]
NPO19460	Karenia brevis	Species	Kareniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20218657]
NPO10455	Vaccinium uliginosum	Species	Ericaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO10455	Vaccinium uliginosum	Species	Ericaceae	Eukaryota	Fruits	n.a.		Database[Phenol-Explorer]
NPO960	Phlomis aurea	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24924	Saara hardwickii	Species	Agamidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4348	Watasenia scintillans	Species	Enoploteuthidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5167	Peripentadenia mearsii	Species	Elaeocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9565	Linum maritimum	Species	Linaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10455	Vaccinium uliginosum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO960	Phlomis aurea	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2124	Bulgaria inquinans	Species	Bulgariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17202	Lasallia asiae-orientalis	Species	Umbilicariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6423	Vitex cauliflora	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3546	Shorea balangeran	Species	Dipterocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9794	Dysoxylum fraseranum	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10273	Dictyota flabellata	Species	Dictyotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25866	Kaunia lasiophthalma	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8878	Polygala arenaria	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13058	Psychotria brachyceras	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11158	Diplopterygium rufopilosum	Species	Gleicheniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19460	Karenia brevis	Species	Kareniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7535	Mansonia altissima	Species	Culicidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6878	Vesperus xatarti	Species	Cerambycidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11354	Streptomyces galbus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO11510	Astragalus flavescens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6427	Wardomyces anomalus	Species	Microascaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12123	Geodia gigas	Species	Geodiidae	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 NPC63988 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	289
0.1-0.2	1666
0.2-0.3	4908
0.3-0.4	8103
0.4-0.5	11634
0.5-0.6	7417
0.6-0.7	5223
0.7-0.8	2841
0.8-0.85	396
0.85-0.9	100
0.9-0.95	78
0.95-1	42

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 NPC63988 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	251
0.1-0.2	1894
0.2-0.3	3932
0.3-0.4	1973
0.4-0.5	574
0.5-0.6	292
0.6-0.7	158
0.7-0.8	60
0.8-0.85	3
0.85-0.9	10
0.9-0.95	1
0.95-1	2

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