NPASS Compound

Structure

NPC15598 OpenBabel06302215212D 40 43 0 0 1 0 0 0 0 0999 V2000 -1.6925 -4.8934 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8452 -4.4039 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8455 -3.4254 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0023 -4.8929 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8496 -4.4035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8280 -4.4032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3390 -5.2507 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8493 -3.4250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0017 -2.9360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0015 -1.9575 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8461 -1.4685 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8487 -1.4680 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.8272 -1.4677 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8484 -0.4895 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.6954 0.0005 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6951 0.9794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 0.9789 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0006 1.9789 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8487 1.4684 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.8490 2.4479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6974 2.9374 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5456 2.4474 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5453 1.4679 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3929 0.9779 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2407 1.4674 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2410 2.4469 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1072 2.9465 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3934 2.9369 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3937 3.9369 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2594 3.4369 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1067 0.9673 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6969 0.9784 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5628 0.4782 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6966 -0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5625 -0.5007 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8482 -0.4900 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 0.0003 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5617 -0.4990 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3382 -2.3152 0.0000 O 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 2 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 5 8 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 10 12 1 0 0 0 0 12 13 1 6 0 0 0 12 14 1 0 0 0 0 12 40 1 0 0 0 0 14 37 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 15 39 1 1 0 0 0 16 17 1 0 0 0 0 17 37 1 0 0 0 0 17 18 1 1 0 0 0 17 19 1 0 0 0 0 19 32 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 22 28 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 6 0 0 0 23 32 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 25 31 1 6 0 0 0 26 27 2 0 0 0 0 26 28 1 0 0 0 0 28 29 1 0 0 0 0 28 30 1 0 0 0 0 32 33 1 6 0 0 0 32 34 1 0 0 0 0 34 35 2 0 0 0 0 34 36 1 0 0 0 0 36 37 1 0 0 0 0 37 38 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	558.32
Volume:	582.305
LogP:	2.546
LogD:	1.48
LogS:	-4.424
# Rotatable Bonds:	6
TPSA:	138.2
# H-Bond Aceptor:	8
# H-Bond Donor:	3
# Rings:	4
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.265
Synthetic Accessibility Score:	5.399
Fsp3:	0.75
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.126
MDCK Permeability:	1.6463158317492343e-05
Pgp-inhibitor:	0.965
Pgp-substrate:	0.021
Human Intestinal Absorption (HIA):	0.181
20% Bioavailability (F20%):	0.543
30% Bioavailability (F30%):	0.594

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.727
Plasma Protein Binding (PPB):	70.6874008178711%
Volume Distribution (VD):	0.471
Pgp-substrate:	19.62753677368164%

ADMET: Metabolism

CYP1A2-inhibitor:	0.004
CYP1A2-substrate:	0.116
CYP2C19-inhibitor:	0.046
CYP2C19-substrate:	0.818
CYP2C9-inhibitor:	0.093
CYP2C9-substrate:	0.708
CYP2D6-inhibitor:	0.024
CYP2D6-substrate:	0.119
CYP3A4-inhibitor:	0.801
CYP3A4-substrate:	0.574

ADMET: Excretion

Clearance (CL):	3.013
Half-life (T1/2):	0.339

ADMET: Toxicity

hERG Blockers:	0.013
Human Hepatotoxicity (H-HT):	0.109
Drug-inuced Liver Injury (DILI):	0.302
AMES Toxicity:	0.025
Rat Oral Acute Toxicity:	0.874
Maximum Recommended Daily Dose:	0.818
Skin Sensitization:	0.047
Carcinogencity:	0.901
Eye Corrosion:	0.003
Eye Irritation:	0.009
Respiratory Toxicity:	0.234

Download Data

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

Natural Product: NPC15598

Natural Product ID:	NPC15598
*Common Name:**	IXQKXEUSCPEQRD-KQONOONZSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	IXQKXEUSCPEQRD-KQONOONZSA-N
Standard InCHI:	InChI=1S/C32H46O8/c1-17(33)40-27(2,3)13-12-23(36)32(9,39)25-21(35)15-29(6)22-11-10-18-19(14-20(34)26(38)28(18,4)5)31(22,8)24(37)16-30(25,29)7/h10,12-13,19-22,25,34-35,39H,11,14-16H2,1-9H3/b13-12+/t19-,20+,21-,22?,25?,29+,30-,31+,32+/m1/s1
SMILES:	CC(=O)OC(C)(C)/C=C/C(=O)[C@@](C)(C1[C@@H](C[C@@]2(C)C3CC=C4[C@@H](C[C@@H](C(=O)C4(C)C)O)[C@]3(C)C(=O)C[C@]12C)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	25245488
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001686] Cucurbitacins

*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
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.jfca.2004.07.004]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.jfca.2005.08.001]
NPO21707	Trichosanthes kirilowii	Species	Cucurbitaceae	Eukaryota	n.a.	seed	n.a.	DOI[10.1016/S0031-9422(00)97029-8]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12379786]
NPO24454	Begonia nantoensis	Species	Begoniaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[14993759]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18460139]
NPO21707	Trichosanthes kirilowii	Species	Cucurbitaceae	Eukaryota	seeds	n.a.	n.a.	PMID[18603435]
NPO13450	Cucumis melo	Species	Cucurbitaceae	Eukaryota	Stems	n.a.	n.a.	PMID[19348465]
NPO21707	Trichosanthes kirilowii	Species	Cucurbitaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[20469887]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23507362]
NPO1592	Citrullus colocynthis	Species	Cucurbitaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[30183289]
NPO11699	Ecballium elaterium	Species	Cucurbitaceae	Eukaryota	Fruit juice	n.a.	n.a.	PMID[3404148]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO13450	Cucumis melo	Species	Cucurbitaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO13450	Cucumis melo	Species	Cucurbitaceae	Eukaryota	Cotyledon	n.a.	n.a.	Database[FooDB]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO1551	Luffa aegyptiaca	Species	Cucurbitaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	Cotyledon	n.a.	n.a.	Database[FooDB]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO13450	Cucumis melo	Species	Cucurbitaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO1551	Luffa aegyptiaca	Species	Cucurbitaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO1551	Luffa aegyptiaca	Species	Cucurbitaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO13450	Cucumis melo	Species	Cucurbitaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	Seed Oil	n.a.	n.a.	Database[FooDB]
NPO1551	Luffa aegyptiaca	Species	Cucurbitaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO11174	Hemsleya graciliflora	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO30404	Luffa cylindrica	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1592	Citrullus colocynthis	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3344	Bryonia alba	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13450	Cucumis melo	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21707	Trichosanthes kirilowii	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9481	Strophanthus divaricatus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24454	Begonia nantoensis	Species	Begoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11699	Ecballium elaterium	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11699	Ecballium elaterium	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24454	Begonia nantoensis	Species	Begoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27538	Hemsleya macrosperma	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11174	Hemsleya graciliflora	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21707	Trichosanthes kirilowii	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13450	Cucumis melo	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1551	Luffa aegyptiaca	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1592	Citrullus colocynthis	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3344	Bryonia alba	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9481	Strophanthus divaricatus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27538	Hemsleya macrosperma	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21707	Trichosanthes kirilowii	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9481	Strophanthus divaricatus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO1592	Citrullus colocynthis	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO30404	Luffa cylindrica	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO1551	Luffa aegyptiaca	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO21707	Trichosanthes kirilowii	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO13450	Cucumis melo	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11174	Hemsleya graciliflora	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24454	Begonia nantoensis	Species	Begoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1592	Citrullus colocynthis	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3344	Bryonia alba	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11699	Ecballium elaterium	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27538	Hemsleya macrosperma	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1551	Luffa aegyptiaca	Species	Cucurbitaceae	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 NPC15598 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	208
0.1-0.2	1204
0.2-0.3	4021
0.3-0.4	8295
0.4-0.5	12672
0.5-0.6	6215
0.6-0.7	6816
0.7-0.8	2931
0.8-0.85	271
0.85-0.9	50
0.9-0.95	6
0.95-1	8

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 NPC15598 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	180
0.1-0.2	1372
0.2-0.3	3623
0.3-0.4	2591
0.4-0.5	836
0.5-0.6	212
0.6-0.7	158
0.7-0.8	111
0.8-0.85	36
0.85-0.9	30
0.9-0.95	1
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