NPASS Compound

Structure

NPC285965 OpenBabel06302215542D 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 1 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 -0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 34 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 1 0 0 0 0 32 35 1 6 0 0 0 33 34 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	506.27
Volume:	492.047
LogP:	0.3
LogD:	0.335
LogS:	-2.542
# Rotatable Bonds:	8
TPSA:	178.53
# H-Bond Aceptor:	11
# H-Bond Donor:	7
# Rings:	3
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.199
Synthetic Accessibility Score:	5.046
Fsp3:	0.917
Lipinski Rule-of-5:	Rejected
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:	-5.751
MDCK Permeability:	4.2813462641788647e-05
Pgp-inhibitor:	0.239
Pgp-substrate:	0.752
Human Intestinal Absorption (HIA):	0.916
20% Bioavailability (F20%):	0.106
30% Bioavailability (F30%):	0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.067
Plasma Protein Binding (PPB):	83.58238983154297%
Volume Distribution (VD):	0.536
Pgp-substrate:	11.399011611938477%

ADMET: Metabolism

CYP1A2-inhibitor:	0.005
CYP1A2-substrate:	0.054
CYP2C19-inhibitor:	0.012
CYP2C19-substrate:	0.122
CYP2C9-inhibitor:	0.001
CYP2C9-substrate:	0.081
CYP2D6-inhibitor:	0.014
CYP2D6-substrate:	0.115
CYP3A4-inhibitor:	0.004
CYP3A4-substrate:	0.022

ADMET: Excretion

Clearance (CL):	0.9
Half-life (T1/2):	0.622

ADMET: Toxicity

hERG Blockers:	0.027
Human Hepatotoxicity (H-HT):	0.157
Drug-inuced Liver Injury (DILI):	0.016
AMES Toxicity:	0.235
Rat Oral Acute Toxicity:	0.115
Maximum Recommended Daily Dose:	0.913
Skin Sensitization:	0.586
Carcinogencity:	0.035
Eye Corrosion:	0.003
Eye Irritation:	0.023
Respiratory Toxicity:	0.117

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

Natural Product: NPC285965

Natural Product ID:	NPC285965
*Common Name:**	YFLZJBSUUWZAOW-PMFOAENNSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YFLZJBSUUWZAOW-PMFOAENNSA-N
Standard InCHI:	InChI=1S/C24H42O11/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/h12,14-23,25-31H,5-10H2,1-4H3/t12-,14+,15-,16-,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@@H](CC1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101843551
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.	Argentine	n.a.	PMID[14738381]
NPO14555	Porella swartziana	Species	Porellaceae	Eukaryota	n.a.	n.a.	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 NPC285965 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	230
0.1-0.2	1978
0.2-0.3	6206
0.3-0.4	14470
0.4-0.5	9254
0.5-0.6	6983
0.6-0.7	3153
0.7-0.8	395
0.8-0.85	24
0.85-0.9	2
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 NPC285965 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	193
0.1-0.2	2379
0.2-0.3	4002
0.3-0.4	1777
0.4-0.5	449
0.5-0.6	282
0.6-0.7	65
0.7-0.8	3
0.8-0.85	0
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