NPASS Compound

Structure

NPC90493 OpenBabel06302215592D 37 39 0 0 1 0 0 0 0 0999 V2000 1.7321 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5981 3.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4641 3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4641 2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 0.5000 0.0000 O 0 0 0 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 5.1962 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 2.0000 0.0000 C 0 0 0 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 10.3923 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 O 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 1.7321 -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 0.0000 -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 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -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 2.5981 4.5000 0.0000 O 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 6 0 0 0 5 6 1 0 0 0 0 5 23 1 0 0 0 0 6 7 1 0 0 0 0 6 37 1 6 0 0 0 7 8 1 0 0 0 0 7 36 1 6 0 0 0 8 9 1 1 0 0 0 8 22 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 15 20 2 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 18 21 1 0 0 0 0 19 20 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 1 0 0 0 24 25 1 0 0 0 0 25 30 2 0 0 0 0 25 26 1 0 0 0 0 26 27 2 0 0 0 0 27 28 1 0 0 0 0 28 29 2 0 0 0 0 28 31 1 0 0 0 0 29 30 1 0 0 0 0 31 32 2 0 0 0 0 32 33 1 0 0 0 0 33 34 2 0 0 0 0 33 35 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	514.15
Volume:	500.274
LogP:	2.531
LogD:	1.663
LogS:	-3.787
# Rotatable Bonds:	11
TPSA:	169.05
# H-Bond Aceptor:	11
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.283
Synthetic Accessibility Score:	3.853
Fsp3:	0.269
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:	-5.865
MDCK Permeability:	2.937729914265219e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.731
Human Intestinal Absorption (HIA):	0.859
20% Bioavailability (F20%):	0.976
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.066
Plasma Protein Binding (PPB):	94.5218276977539%
Volume Distribution (VD):	0.303
Pgp-substrate:	3.6148056983947754%

ADMET: Metabolism

CYP1A2-inhibitor:	0.391
CYP1A2-substrate:	0.01
CYP2C19-inhibitor:	0.14
CYP2C19-substrate:	0.046
CYP2C9-inhibitor:	0.299
CYP2C9-substrate:	0.68
CYP2D6-inhibitor:	0.361
CYP2D6-substrate:	0.139
CYP3A4-inhibitor:	0.231
CYP3A4-substrate:	0.051

ADMET: Excretion

Clearance (CL):	1.484
Half-life (T1/2):	0.899

ADMET: Toxicity

hERG Blockers:	0.228
Human Hepatotoxicity (H-HT):	0.736
Drug-inuced Liver Injury (DILI):	0.949
AMES Toxicity:	0.274
Rat Oral Acute Toxicity:	0.036
Maximum Recommended Daily Dose:	0.019
Skin Sensitization:	0.956
Carcinogencity:	0.345
Eye Corrosion:	0.003
Eye Irritation:	0.029
Respiratory Toxicity:	0.059

Download Data

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

Natural Product: NPC90493

Natural Product ID:	NPC90493
*Common Name:**	LDYQNDDGKTWQSU-KKORPJHTSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	LDYQNDDGKTWQSU-KKORPJHTSA-N
Standard InCHI:	InChI=1S/C26H26O11/c1-15(27)35-25-24(33)23(32)20(14-34-22(31)13-7-16-2-8-18(28)9-3-16)37-26(25)36-19-10-4-17(5-11-19)6-12-21(29)30/h2-13,20,23-26,28,32-33H,14H2,1H3,(H,29,30)/b12-6+,13-7+/t20-,23-,24-,25-,26-/m1/s1
SMILES:	CC(=O)O[C@@H]1[C@@H]([C@@H]([C@@H](COC(=O)/C=C/c2ccc(cc2)O)O[C@H]1Oc1ccc(cc1)/C=C/C(=O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0002105] Glycosyl compounds [CHEMONTID:0004165] Phenolic glycosides

*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

Show entries

Search:

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO23108	Pinus flexilis	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9834165]
NPO20454	Bidens pilosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[469551]
NPO23440	Aconitum napellus	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23876370]
NPO24718	Streptomyces parvulus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[23423168]
NPO15117	Chromolaena odorata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23186307]
NPO24588	Phellinus igniarius	Species	Hymenochaetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20583752]
NPO23924	Psilotum nudum	Species	Psilotaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20488581]
NPO24811	Cibotium barometz	Species	Cibotiaceae	Eukaryota	rhizomes	n.a.	n.a.	PMID[19739599]
NPO9392	Elaeodendron alluaudianum	Species	Celastraceae	Eukaryota	n.a.	Madagascar Rainforest	n.a.	PMID[19058971]
NPO9392	Elaeodendron alluaudianum	Species	Celastraceae	Eukaryota	n.a.	stem	n.a.	PMID[19058971]

Showing 1 to 10 of 102 entries

Previous1 2 3 4 5…11Next

☑ 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

Show entries

Search:

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

Showing 0 to 0 of 0 entries

PreviousNext

☑ 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

Show entries

Search:

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
No data available in table

Showing 0 to 0 of 0 entries

PreviousNext

☑ 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 NPC90493 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	278
0.1-0.2	1331
0.2-0.3	3736
0.3-0.4	9081
0.4-0.5	9354
0.5-0.6	5299
0.6-0.7	9030
0.7-0.8	3936
0.8-0.85	462
0.85-0.9	165
0.9-0.95	22
0.95-1	3

Show entries

Search:

Similarity Score	Similarity Level	Natural Product ID
No data available in table

Showing 0 to 0 of 0 entries

PreviousNext

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 NPC90493 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	230
0.1-0.2	781
0.2-0.3	1630
0.3-0.4	2801
0.4-0.5	1920
0.5-0.6	1112
0.6-0.7	574
0.7-0.8	100
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Show entries

Search:

Similarity Score	Similarity Level	Drug ID	Developmental Stage
No data available in table

Showing 0 to 0 of 0 entries

PreviousNext

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