NPASS Compound

Structure

NPC236389 OpenBabel06302215082D 34 38 0 0 1 0 0 0 0 0999 V2000 -5.2914 2.1412 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8273 1.3373 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2914 0.5335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8991 1.3373 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.7145 2.2469 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9824 1.4825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5610 0.6555 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2173 -0.0008 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.8826 -1.7339 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4135 -0.4649 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.2367 -0.9402 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4129 -1.3931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6088 -1.8574 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8047 -0.4646 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8418 -1.4152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6088 -0.0003 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6088 0.9288 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8041 1.3934 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.9292 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8047 1.3937 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0185 1.8690 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8044 2.3224 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6088 2.7865 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4134 2.3220 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.4137 1.3933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2369 0.9180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2371 1.8683 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6093 0.9292 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6093 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8046 -0.4646 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 -0.9506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2366 2.7973 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0443 0.4206 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 34 1 0 0 0 0 4 5 1 6 0 0 0 4 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 1 0 0 0 8 10 1 0 0 0 0 8 34 1 0 0 0 0 10 16 1 0 0 0 0 10 11 1 1 0 0 0 10 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 31 1 0 0 0 0 14 15 1 1 0 0 0 14 16 1 0 0 0 0 16 17 1 1 0 0 0 17 18 1 0 0 0 0 19 18 1 6 0 0 0 19 20 1 0 0 0 0 19 31 1 0 0 0 0 20 28 1 0 0 0 0 20 21 1 6 0 0 0 20 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 24 33 1 1 0 0 0 25 26 1 0 0 0 0 25 27 1 0 0 0 0 25 28 1 0 0 0 0 28 29 1 6 0 0 0 29 30 1 0 0 0 0 30 31 1 0 0 0 0 31 32 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	472.43
Volume:	536.826
LogP:	6.553
LogD:	5.358
LogS:	-6.288
# Rotatable Bonds:	2
TPSA:	29.46
# H-Bond Aceptor:	2
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.437
Synthetic Accessibility Score:	5.041
Fsp3:	1.0
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:	-5.085
MDCK Permeability:	1.7791368009056896e-05
Pgp-inhibitor:	0.07
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.012
20% Bioavailability (F20%):	0.637
30% Bioavailability (F30%):	0.882

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.078
Plasma Protein Binding (PPB):	96.36293029785156%
Volume Distribution (VD):	1.378
Pgp-substrate:	2.2996268272399902%

ADMET: Metabolism

CYP1A2-inhibitor:	0.027
CYP1A2-substrate:	0.6
CYP2C19-inhibitor:	0.086
CYP2C19-substrate:	0.979
CYP2C9-inhibitor:	0.143
CYP2C9-substrate:	0.275
CYP2D6-inhibitor:	0.037
CYP2D6-substrate:	0.45
CYP3A4-inhibitor:	0.429
CYP3A4-substrate:	0.864

ADMET: Excretion

Clearance (CL):	4.995
Half-life (T1/2):	0.123

ADMET: Toxicity

hERG Blockers:	0.122
Human Hepatotoxicity (H-HT):	0.299
Drug-inuced Liver Injury (DILI):	0.017
AMES Toxicity:	0.004
Rat Oral Acute Toxicity:	0.038
Maximum Recommended Daily Dose:	0.533
Skin Sensitization:	0.525
Carcinogencity:	0.005
Eye Corrosion:	0.956
Eye Irritation:	0.879
Respiratory Toxicity:	0.725

Download Data

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

Natural Product: NPC236389

Natural Product ID:	NPC236389
*Common Name:**	DEQAVSIRSXMHPJ-FMSLPZACSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DEQAVSIRSXMHPJ-FMSLPZACSA-N
Standard InCHI:	InChI=1S/C32H56O2/c1-21(2)31(9)19-20-32(10,34-31)30(8)18-17-29(7)24(30)12-11-23-27(5)15-14-25(33)26(3,4)22(27)13-16-28(23,29)6/h21-25,33H,11-20H2,1-10H3/t22-,23+,24-,25+,27-,28+,29+,30-,31+,32+/m0/s1
SMILES:	CC(C)[C@@]1(C)CC[C@](C)([C@@]2(C)CC[C@]3(C)[C@@H]2CC[C@@H]2[C@@]4(C)CC[C@H](C(C)(C)[C@@H]4CC[C@@]32C)O)O1
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
NPO4673	Dorstenia psilurus	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19061390]
NPO4673	Dorstenia psilurus	Species	Moraceae	Eukaryota	n.a.	root	n.a.	PMID[19061390]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	flower	n.a.	PMID[21916433]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	flower buds	n.a.	n.a.	PMID[23558238]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27228307]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	Roots	n.a.	n.a.	PMID[31150241]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31860304]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32223193]
NPO6225	Streptomyces griseoplanus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[5481496]
NPO10907	Uvaria macrophylla	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1563	Aloe ballyi	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1563	Aloe ballyi	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10907	Uvaria macrophylla	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9289	Liatris squarrosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9289	Liatris squarrosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO21087	Xanthomendoza fallax	Species	Teloschistaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2657	Baeria californica	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO9289	Liatris squarrosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10589	Aster fruticosus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO824	Ursinia cakilefolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8933	Arctotis aspera	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10907	Uvaria macrophylla	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3971	Alnaster fruticosus	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO4673	Dorstenia psilurus	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9563	Pinus armandii	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1563	Aloe ballyi	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12445	Codium arabicum	Species	Codiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6225	Streptomyces griseoplanus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO6755	Lactobacillus helveticus	Species	Lactobacillaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO10982	Hypoxylon microplacum	Species	Xylariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12978	Amblyraja radiata	Species	Rajidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23683	Ptelea aptera	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10767	Ervum lens	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO5250	Guatteria elata	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8360	Neothyonidium magnum	Species	Phyllophoridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7511	Gaillardia spathulata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10651	Streptosporangium vulgare	Species	Streptosporangiaceae	Bacteria	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 NPC236389 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	375
0.1-0.2	4331
0.2-0.3	17541
0.3-0.4	8405
0.4-0.5	4867
0.5-0.6	4442
0.6-0.7	2051
0.7-0.8	568
0.8-0.85	76
0.85-0.9	37
0.9-0.95	4
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 NPC236389 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	383
0.1-0.2	4298
0.2-0.3	3280
0.3-0.4	672
0.4-0.5	198
0.5-0.6	245
0.6-0.7	48
0.7-0.8	23
0.8-0.85	2
0.85-0.9	1
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