NPASS Compound

Structure

NPC240645 OpenBabel06302215392D 43 47 0 0 1 0 0 0 0 0999 V2000 1.0686 2.2076 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0686 2.2076 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.4314 1.3416 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.4260 1.2371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6339 0.2589 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7678 -0.2411 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5599 -1.2192 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.3911 -1.5283 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.1343 -0.8591 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9264 0.1190 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0247 0.4280 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9264 0.7371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5990 -2.5064 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.3422 -1.8373 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1441 -3.1755 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0638 -4.1537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0149 -4.4627 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2228 -5.4409 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7580 -3.7936 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5501 -2.8154 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.2932 -2.1463 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2443 -2.4553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9874 -1.7862 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4522 -3.4335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0952 -2.8665 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3031 -1.8884 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.2541 -1.5794 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4314 3.0736 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0686 3.9397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0686 3.9397 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5686 4.8057 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5686 3.0736 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0686 2.2076 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0686 2.2076 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0686 3.9397 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4314 3.0736 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9314 2.2076 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4314 1.3416 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9314 2.2076 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4314 1.3416 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9314 0.4756 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4314 1.3416 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 -4.9314 0.4756 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 28 1 0 0 0 0 3 2 1 6 0 0 0 3 4 1 0 0 0 0 3 11 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 6 11 1 0 0 0 0 7 8 1 0 0 0 0 7 26 1 0 0 0 0 8 9 1 0 0 0 0 8 13 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 13 20 1 0 0 0 0 13 14 1 0 0 0 0 13 15 1 0 0 0 0 15 16 2 0 0 0 0 15 25 1 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 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 22 23 2 0 0 0 0 22 24 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 28 29 1 6 0 0 0 28 36 1 0 0 0 0 29 30 1 0 0 0 0 30 35 1 0 0 0 0 30 31 1 1 0 0 0 30 32 1 0 0 0 0 32 33 1 0 0 0 0 32 34 1 0 0 0 0 32 35 1 0 0 0 0 36 37 1 0 0 0 0 37 38 2 0 0 0 0 37 39 1 0 0 0 0 39 40 1 0 0 0 0 40 41 2 0 0 0 0 40 42 1 0 0 0 0 42 43 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	618.32
Volume:	629.486
LogP:	4.253
LogD:	3.966
LogS:	-4.686
# Rotatable Bonds:	11
TPSA:	119.5
# H-Bond Aceptor:	8
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.164
Synthetic Accessibility Score:	5.579
Fsp3:	0.824
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.985
MDCK Permeability:	2.4933315216912888e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.666
Human Intestinal Absorption (HIA):	0.61
20% Bioavailability (F20%):	0.087
30% Bioavailability (F30%):	0.98

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.94
Plasma Protein Binding (PPB):	76.70458221435547%
Volume Distribution (VD):	0.556
Pgp-substrate:	15.04500675201416%

ADMET: Metabolism

CYP1A2-inhibitor:	0.008
CYP1A2-substrate:	0.112
CYP2C19-inhibitor:	0.026
CYP2C19-substrate:	0.554
CYP2C9-inhibitor:	0.15
CYP2C9-substrate:	0.039
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.061
CYP3A4-inhibitor:	0.806
CYP3A4-substrate:	0.672

ADMET: Excretion

Clearance (CL):	8.819
Half-life (T1/2):	0.859

ADMET: Toxicity

hERG Blockers:	0.096
Human Hepatotoxicity (H-HT):	0.12
Drug-inuced Liver Injury (DILI):	0.892
AMES Toxicity:	0.386
Rat Oral Acute Toxicity:	0.66
Maximum Recommended Daily Dose:	0.214
Skin Sensitization:	0.834
Carcinogencity:	0.629
Eye Corrosion:	0.057
Eye Irritation:	0.02
Respiratory Toxicity:	0.984

Download Data

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

Natural Product: NPC240645

Natural Product ID:	NPC240645
*Common Name:**	OHEDEHGBHXSULQ-VVINNDCVSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	OHEDEHGBHXSULQ-VVINNDCVSA-N
Standard InCHI:	InChI=1S/C34H50O8S/c1-18(26(17-33(6)31(3,4)42-33)41-28(38)16-29(39)43-8)22-9-10-23-30-24(11-12-32(22,23)5)34(7)20(14-25(30)37)13-21(36)15-27(34)40-19(2)35/h13,18,22-27,30,37H,9-12,14-17H2,1-8H3/t18-,22+,23-,24-,25+,26+,27-,30-,32+,33-,34-/m0/s1
SMILES:	C[C@@H]([C@H]1CC[C@H]2[C@H]3[C@H](CC[C@]12C)[C@]1(C)C(=CC(=O)C[C@@H]1OC(=O)C)C[C@H]3O)[C@@H](C[C@@]1(C)C(C)(C)O1)OC(=O)CC(=O)SC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	102150666
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001445] Bile acids, alcohols and derivatives [CHEMONTID:0002194] Hydroxy bile acids, alcohols and derivatives [CHEMONTID:0000260] Monohydroxy bile acids, alcohols 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
NPO12929	Polianthes tuberosa	Species	Asparagaceae	Eukaryota	aerial parts	n.a.	n.a.	PMID[11087596]
NPO12929	Polianthes tuberosa	Species	Asparagaceae	Eukaryota	underground parts	n.a.	n.a.	PMID[12398537]
NPO12929	Polianthes tuberosa	Species	Asparagaceae	Eukaryota	fresh tubers	n.a.	n.a.	PMID[14738376]
NPO9060	Sinularia granosa	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[18831569]
NPO9060	Sinularia granosa	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[22672798]
NPO16831	Hypericum patulum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31999455]
NPO16831	Hypericum patulum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12929	Polianthes tuberosa	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14012	Libanotis condensata	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15843	Dalbergia retusa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16831	Hypericum patulum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12929	Polianthes tuberosa	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14012	Libanotis condensata	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3247	Orchis fusca	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13204	Mallotus metcalfianus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16537	Lonicera racemosa	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11780	Alpinia rafflesiana	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1337	Sphyraena japonica	Species	Sphyraenidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16831	Hypericum patulum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15838	Psorospermum molluscum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5115	Abuta panurensis	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14704	Ephedra frustillata	Species	Ephedraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24523	Senecio anteuphorbium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15377	Calea clematidea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4793	Discoglossus pictus	Species	Alytidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14167	Ambrosia artemisioides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15615	Petunia hybrid	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13686	Lepraria lobificans	Species	Stereocaulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6380	Hydrocotyle vulgaris	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15232	Absidia repens	Species	Cunninghamellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8288	Vitis cinerea	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7540	Eucalyptus consideniana	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13502	Senecio algens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22329	Dolomedes okefinokensis	Species	Pisauridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13354	Euryspongia arenaria	Species	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15843	Dalbergia retusa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13841	Allium minutiflorum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14346	Pterocarpus indica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12106	Aristeomorpha foliacea	Species	Aristeidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12655	Tephrosia virginiana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2991	Duboisia leichhardtii	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15742	Euphorbia laurifolia	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10741	Eucalyptus grossa	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16338	Virola calophylloidea	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15121	Solanum habrochaites	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16150	Nepeta argolica	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1069	Meum athamanticum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16260	Stevia yaconensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16498	Adoxophyes orana	Species	Tortricidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14012	Libanotis condensata	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12929	Polianthes tuberosa	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7342	Bostrychia scorpioides	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16574	Heywoodiella oligocephala	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO11547	Lobelia cardinalis	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14968	Mucuna membranacea	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4167	Oxalis repens	Species	Oxalidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16417	Elaeocarpus ganitrus	Species	Elaeocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2295	Cydonia vulgaris	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2725	Casuarina glauca	Species	Casuarinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9060	Sinularia granosa	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9540	Curvularia falcata	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14531	Dalbergia inundata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16053	Allium aflatunense	Species	Amaryllidaceae	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 NPC240645 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	215
0.1-0.2	1483
0.2-0.3	5330
0.3-0.4	10110
0.4-0.5	11313
0.5-0.6	6681
0.6-0.7	5875
0.7-0.8	1673
0.8-0.85	17
0.85-0.9	0
0.9-0.95	0
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 NPC240645 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	185
0.1-0.2	1591
0.2-0.3	4022
0.3-0.4	2286
0.4-0.5	583
0.5-0.6	231
0.6-0.7	152
0.7-0.8	100
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