NPASS Compound

Structure

NPC240733 OpenBabel06302216122D 29 33 0 0 1 0 0 0 0 0999 V2000 4.7102 -2.1970 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8442 -1.6970 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8442 -0.6970 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9781 -2.1970 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4781 -1.3309 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7281 -1.7639 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8621 -1.2639 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7281 -2.6300 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4781 -3.0630 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.4781 -3.0630 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9781 -2.1970 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8736 -3.1915 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.9890 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.1045 -2.9836 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8090 -3.3903 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.0169 -4.3684 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.9680 -4.6775 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2738 -5.0376 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4781 -2.6472 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4727 -2.7517 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9781 -1.7811 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1045 -0.9945 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8090 -0.5878 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.4781 -1.3309 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.2872 -0.7431 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9781 -3.9290 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0219 -3.9290 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8442 -2.6970 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 9 1 0 0 0 0 4 5 1 0 0 0 0 4 29 1 1 0 0 0 5 6 1 1 0 0 0 5 24 1 0 0 0 0 6 7 2 0 0 0 0 6 8 1 0 0 0 0 9 8 1 1 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 10 27 1 1 0 0 0 11 24 1 0 0 0 0 11 12 1 6 0 0 0 11 13 1 0 0 0 0 13 21 1 0 0 0 0 13 14 1 1 0 0 0 13 22 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 6 0 0 0 15 19 1 0 0 0 0 16 17 1 6 0 0 0 16 18 1 0 0 0 0 19 20 2 0 0 0 0 19 21 1 0 0 0 0 22 23 1 0 0 0 0 22 26 1 6 0 0 0 23 24 1 0 0 0 0 23 26 1 6 0 0 0 24 25 1 6 0 0 0 27 28 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	410.16
Volume:	382.897
LogP:	0.83
LogD:	-0.154
LogS:	-4.073
# Rotatable Bonds:	3
TPSA:	135.05
# H-Bond Aceptor:	9
# H-Bond Donor:	3
# Rings:	5
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.306
Synthetic Accessibility Score:	6.958
Fsp3:	0.8
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.669
MDCK Permeability:	6.700761878164485e-05
Pgp-inhibitor:	0.019
Pgp-substrate:	0.734
Human Intestinal Absorption (HIA):	0.241
20% Bioavailability (F20%):	0.169
30% Bioavailability (F30%):	0.983

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.124
Plasma Protein Binding (PPB):	30.151893615722656%
Volume Distribution (VD):	0.567
Pgp-substrate:	72.48353576660156%

ADMET: Metabolism

CYP1A2-inhibitor:	0.005
CYP1A2-substrate:	0.908
CYP2C19-inhibitor:	0.009
CYP2C19-substrate:	0.673
CYP2C9-inhibitor:	0.001
CYP2C9-substrate:	0.021
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.1
CYP3A4-inhibitor:	0.02
CYP3A4-substrate:	0.231

ADMET: Excretion

Clearance (CL):	2.649
Half-life (T1/2):	0.112

ADMET: Toxicity

hERG Blockers:	0.03
Human Hepatotoxicity (H-HT):	0.195
Drug-inuced Liver Injury (DILI):	0.199
AMES Toxicity:	0.053
Rat Oral Acute Toxicity:	0.219
Maximum Recommended Daily Dose:	0.007
Skin Sensitization:	0.174
Carcinogencity:	0.122
Eye Corrosion:	0.011
Eye Irritation:	0.03
Respiratory Toxicity:	0.964

Download Data

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

Natural Product: NPC240733

Natural Product ID:	NPC240733
*Common Name:**	CYSMUZXOFOZYHN-SYZJHQASSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	CYSMUZXOFOZYHN-SYZJHQASSA-N
Standard InCHI:	InChI=1S/C20H26O9/c1-7(2)19(24)10-16(23)28-13(19)11(26-5)17(4)18(12-14(27-12)20(10,17)25)6-9(8(3)21)15(22)29-18/h8-14,21,24-25H,1,6H2,2-5H3/t8-,9-,10+,11-,12-,13+,14+,17+,18-,19-,20+/m1/s1
SMILES:	C=C(C)[C@]1([C@@H]2C(=O)O[C@H]1[C@H]([C@@]1(C)[C@@]3(C[C@H]([C@@H](C)O)C(=O)O3)[C@H]3[C@@H]([C@@]21O)O3)OC)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000050] Lactones [CHEMONTID:0001245] Gamma butyrolactones

*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
NPO22706	Aglaia forbesii	Species	Meliaceae	Eukaryota	n.a.	leaf	n.a.	PMID[17707871]
NPO21789	Sciadotenia toxifera	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20961068]
NPO20900	Dendrobium chrysotoxum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20900	Dendrobium chrysotoxum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20900	Dendrobium chrysotoxum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO22706	Aglaia forbesii	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22960	Hydnocarpus hainanensis	Species	Achariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20778	Pinus longifolia	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21789	Sciadotenia toxifera	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20287	Passalora fulva	Species	Mycosphaerellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22567	Ectatosoma tiaratum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO22892	Valeriana microphylla	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22446	Caloplaca murorum	Species	Teloschistaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20900	Dendrobium chrysotoxum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20588	Soulamea pancheri	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11289	Eurybia divaricata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20385	Quercus canariensis	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4527	Coprinellus heptemerus	Species	Psathyrellaceae	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 NPC240733 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	301
0.1-0.2	2160
0.2-0.3	6465
0.3-0.4	12470
0.4-0.5	9532
0.5-0.6	7245
0.6-0.7	3848
0.7-0.8	657
0.8-0.85	17
0.85-0.9	1
0.9-0.95	0
0.95-1	1

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 NPC240733 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	319
0.1-0.2	2755
0.2-0.3	3817
0.3-0.4	1478
0.4-0.5	431
0.5-0.6	264
0.6-0.7	83
0.7-0.8	2
0.8-0.85	1
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