NPASS Compound

Structure

NPC192582 OpenBabel06302216002D 36 40 0 0 1 0 0 0 0 0999 V2000 0.0000 -2.9268 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8449 -2.4390 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6898 -2.9268 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8449 -1.4634 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.9756 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8449 -1.4634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6898 -0.9756 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6898 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5347 -0.4878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8449 0.4878 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8449 1.4634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6898 1.9512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5347 1.4634 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5347 3.4146 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5347 0.4878 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3796 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2245 0.4878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2245 1.4634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0694 1.9512 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.9143 1.4634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7592 1.9512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7348 1.9512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2470 1.1063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7592 2.9268 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9143 3.4146 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0694 2.9268 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2245 3.4146 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3796 2.9268 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3796 1.9512 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5347 2.4390 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0694 3.9024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2245 4.3902 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9143 4.3902 0.0000 O 0 0 0 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 0.9756 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4878 0.8449 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 2 4 1 0 0 0 0 5 4 1 1 0 0 0 5 6 1 0 0 0 0 5 34 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 15 1 0 0 0 0 8 9 1 1 0 0 0 8 10 1 0 0 0 0 10 11 1 6 0 0 0 10 34 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 29 1 0 0 0 0 13 14 1 1 0 0 0 13 15 1 0 0 0 0 15 16 1 6 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 18 29 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 1 0 0 0 19 26 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 21 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 26 31 1 1 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 6 0 0 0 31 32 2 0 0 0 0 31 33 1 0 0 0 0 34 35 1 0 0 0 0 34 36 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	498.37
Volume:	546.497
LogP:	7.409
LogD:	5.092
LogS:	-5.724
# Rotatable Bonds:	3
TPSA:	63.6
# H-Bond Aceptor:	4
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.311
Synthetic Accessibility Score:	4.624
Fsp3:	0.875
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-5.091
MDCK Permeability:	1.435287958884146e-05
Pgp-inhibitor:	0.012
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.013
20% Bioavailability (F20%):	0.303
30% Bioavailability (F30%):	0.942

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.326
Plasma Protein Binding (PPB):	90.25518035888672%
Volume Distribution (VD):	0.701
Pgp-substrate:	6.087602138519287%

ADMET: Metabolism

CYP1A2-inhibitor:	0.011
CYP1A2-substrate:	0.136
CYP2C19-inhibitor:	0.027
CYP2C19-substrate:	0.793
CYP2C9-inhibitor:	0.291
CYP2C9-substrate:	0.518
CYP2D6-inhibitor:	0.012
CYP2D6-substrate:	0.116
CYP3A4-inhibitor:	0.355
CYP3A4-substrate:	0.278

ADMET: Excretion

Clearance (CL):	2.194
Half-life (T1/2):	0.028

ADMET: Toxicity

hERG Blockers:	0.014
Human Hepatotoxicity (H-HT):	0.331
Drug-inuced Liver Injury (DILI):	0.027
AMES Toxicity:	0.008
Rat Oral Acute Toxicity:	0.191
Maximum Recommended Daily Dose:	0.92
Skin Sensitization:	0.331
Carcinogencity:	0.415
Eye Corrosion:	0.527
Eye Irritation:	0.079
Respiratory Toxicity:	0.961

Download Data

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

Natural Product: NPC192582

Natural Product ID:	NPC192582
*Common Name:**	RIXNFYQZWDGQAE-OXEUVWLCSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	RIXNFYQZWDGQAE-OXEUVWLCSA-N
Standard InCHI:	InChI=1S/C32H50O4/c1-20(33)36-25-12-13-29(6)23(28(25,4)5)11-14-31(8)24(29)10-9-21-22-19-27(2,3)15-17-32(22,26(34)35)18-16-30(21,31)7/h9,22-25H,10-19H2,1-8H3,(H,34,35)/t22-,23-,24+,25+,29+,30-,31-,32+/m1/s1
SMILES:	CC(=O)O[C@H]1CC[C@@]2(C)[C@H](CC[C@]3(C)[C@H]2CC=C2[C@H]4CC(C)(C)CC[C@@]4(CC[C@@]32C)C(=O)O)C1(C)C
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
NPO6987	Tolypothrix byssoidea	Species	Tolypothrichaceae	Bacteria	n.a.	n.a.	n.a.	PMID[11429991]
NPO7787	Suregada multiflora	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12088443]
NPO3125	Scaphechinus mirabilis	Species	Scutellidae	Eukaryota	n.a.	n.a.	n.a.	PMID[16180820]
NPO23838	Kitasatospora kifunensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[17191679]
NPO18521	Capparis flavicans	Species	Capparaceae	Eukaryota	aerial parts	Khon Kaen Province, Thailand	2006-Aug	PMID[19943620]
NPO17957	Solanum sodomeum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17392	Ipomoea hederacea	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO228	Physostigma venenosum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5788	Millingtonia hortensis	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17957	Solanum sodomeum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO228	Physostigma venenosum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5788	Millingtonia hortensis	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO829	Vaccaria hispanica	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5114	Canis lupus familiaris	Species	Canidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17392	Ipomoea hederacea	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16834	Baccharis sarothroides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5788	Millingtonia hortensis	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO17392	Ipomoea hederacea	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO228	Physostigma venenosum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO829	Vaccaria hispanica	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15625	Umbilicaria spodochroa	Species	Umbilicariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO829	Vaccaria hispanica	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17720	Andropogon laniger	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23838	Kitasatospora kifunensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO16655	Rabdosia flexicaulis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22716	Petalostemon gattingeri	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16834	Baccharis sarothroides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6710	Sinapis nigra	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5788	Millingtonia hortensis	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15360	Stephania hispidula	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5445	Euonymus nanus	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18712	Malus sieboldii	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13976	Sonchus gummifer	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10196	Echinocereus blanckii	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17957	Solanum sodomeum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19129	Oxytropis pseudoglandulosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4489	Achillea serbica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4214	Centaurea collina	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18521	Capparis flavicans	Species	Capparaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7787	Suregada multiflora	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18517	Phthorimaea operculella	Species	Gelechiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17392	Ipomoea hederacea	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1604	Micranthes stellaris	Species	Saxifragaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5114	Canis lupus familiaris	Species	Canidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11189	Anabaena sphaerica	Species	0stocaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO15872	Stachys mucronata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12652	Xylosalsola richteri	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3125	Scaphechinus mirabilis	Species	Scutellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8231	Jaspis digonoxea	Species	Ancorinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13598	Pedicularis plicata	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18307	Peltigera venosa	Species	Peltigeraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19056	Allium nutans	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8719	Fusarium vasinfectum	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17604	Lasioderma serricorne	Species	Anobiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16926	Thymbra capitata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10826	Rabdosia weisiensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6987	Tolypothrix byssoidea	Species	Tolypothrichaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO228	Physostigma venenosum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3113	Xyris semifuscata	Species	Xyridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11437	Alluaudia ascendens	Species	Didiereaceae	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 NPC192582 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	1292
0.2-0.3	4804
0.3-0.4	14005
0.4-0.5	9076
0.5-0.6	5491
0.6-0.7	4916
0.7-0.8	2109
0.8-0.85	440
0.85-0.9	142
0.9-0.95	175
0.95-1	39

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 NPC192582 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	184
0.1-0.2	1609
0.2-0.3	3832
0.3-0.4	2330
0.4-0.5	724
0.5-0.6	215
0.6-0.7	188
0.7-0.8	60
0.8-0.85	3
0.85-0.9	1
0.9-0.95	3
0.95-1	1

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