NPASS Compound

Structure

NPC185045 OpenBabel06302215342D 35 37 0 0 1 0 0 0 0 0999 V2000 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1962 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1962 -3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.0622 -3.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.9282 -3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.9282 -2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.7942 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -10.3923 -2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -11.2583 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -11.2583 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -10.3923 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -12.1244 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -12.1244 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.3923 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2321 1.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.0000 0.0000 C 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 1 2 1 0 0 0 0 2 35 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 3 29 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 6 0 0 0 6 8 1 0 0 0 0 9 8 1 1 0 0 0 9 10 1 0 0 0 0 9 25 1 0 0 0 0 10 11 1 0 0 0 0 10 28 1 6 0 0 0 11 12 1 0 0 0 0 11 27 1 1 0 0 0 12 13 1 0 0 0 0 12 26 1 6 0 0 0 13 14 1 1 0 0 0 13 25 1 0 0 0 0 14 15 1 0 0 0 0 16 15 1 1 0 0 0 16 17 1 0 0 0 0 16 21 1 0 0 0 0 17 18 1 0 0 0 0 17 24 1 6 0 0 0 18 19 1 0 0 0 0 18 23 1 1 0 0 0 19 20 1 0 0 0 0 19 22 1 1 0 0 0 20 21 1 0 0 0 0 29 30 1 0 0 0 0 29 31 1 0 0 0 0 29 32 1 0 0 0 0 32 33 2 0 0 0 0 32 34 1 0 0 0 0 34 35 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	504.26
Volume:	489.41
LogP:	0.195
LogD:	0.471
LogS:	-2.16
# Rotatable Bonds:	8
TPSA:	175.37
# H-Bond Aceptor:	11
# H-Bond Donor:	6
# Rings:	3
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.227
Synthetic Accessibility Score:	4.995
Fsp3:	0.875
Lipinski Rule-of-5:	Rejected
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:	-5.557
MDCK Permeability:	3.217579433112405e-05
Pgp-inhibitor:	0.953
Pgp-substrate:	0.967
Human Intestinal Absorption (HIA):	0.892
20% Bioavailability (F20%):	0.037
30% Bioavailability (F30%):	0.97

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.116
Plasma Protein Binding (PPB):	83.4697494506836%
Volume Distribution (VD):	0.749
Pgp-substrate:	11.31343936920166%

ADMET: Metabolism

CYP1A2-inhibitor:	0.004
CYP1A2-substrate:	0.096
CYP2C19-inhibitor:	0.014
CYP2C19-substrate:	0.361
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.094
CYP2D6-inhibitor:	0.014
CYP2D6-substrate:	0.114
CYP3A4-inhibitor:	0.01
CYP3A4-substrate:	0.027

ADMET: Excretion

Clearance (CL):	0.989
Half-life (T1/2):	0.813

ADMET: Toxicity

hERG Blockers:	0.012
Human Hepatotoxicity (H-HT):	0.177
Drug-inuced Liver Injury (DILI):	0.045
AMES Toxicity:	0.377
Rat Oral Acute Toxicity:	0.056
Maximum Recommended Daily Dose:	0.01
Skin Sensitization:	0.064
Carcinogencity:	0.145
Eye Corrosion:	0.003
Eye Irritation:	0.018
Respiratory Toxicity:	0.057

Download Data

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

Natural Product: NPC185045

Natural Product ID:	NPC185045
*Common Name:**	DSLCYTQZSJRSJD-QYRTZOEFSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DSLCYTQZSJRSJD-QYRTZOEFSA-N
Standard InCHI:	InChI=1S/C24H40O11/c1-11-5-8-16(26)24(3,4)13(11)7-6-12(2)34-23-21(31)19(29)18(28)15(35-23)10-33-22-20(30)17(27)14(25)9-32-22/h12,14-15,17-23,25,27-31H,5-10H2,1-4H3/t12-,14+,15-,17+,18-,19+,20-,21-,22+,23-/m1/s1
SMILES:	CC1=C(CC[C@@H](C)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO[C@H]3[C@@H]([C@H]([C@H](CO3)O)O)O)O2)O)O)O)C(C)(C)C(=O)CC1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101450245
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0001766] Fatty acyl glycosides [CHEMONTID:0003861] Fatty acyl glycosides of mono- and disaccharides

*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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO9420	Aspergillus arenarius	Species	Aspergillaceae	Eukaryota	sclerotia	n.a.	n.a.	PMID[9599285]
NPO14826	Streptomyces mobaraensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[32998509]
NPO23289	Heracleum sphondylium	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24697288]
NPO12977	Solenopsis invicta	Species	Formicidae	Eukaryota	n.a.	n.a.	n.a.	PMID[21905650]
NPO14555	Porella swartziana	Species	Porellaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[14738381]
NPO14555	Porella swartziana	Species	Porellaceae	Eukaryota	n.a.	Argentine	n.a.	PMID[14738381]
NPO7484	Salacia chinensis	Species	Celastraceae	Eukaryota	stems	Thailand	n.a.	PMID[14510595]
NPO7484	Salacia chinensis	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12951446]
NPO2353	Bituminaria bituminosa	Species	Fabaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[12943781]
NPO24176	Streptomyces fradiae	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[10757717]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
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☑ 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 NPC185045 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	222
0.1-0.2	1532
0.2-0.3	5406
0.3-0.4	12502
0.4-0.5	9984
0.5-0.6	7300
0.6-0.7	4953
0.7-0.8	761
0.8-0.85	32
0.85-0.9	3
0.9-0.95	2
0.95-1	0

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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 NPC185045 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	201
0.1-0.2	2024
0.2-0.3	3973
0.3-0.4	1925
0.4-0.5	543
0.5-0.6	318
0.6-0.7	162
0.7-0.8	3
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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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