NPASS Compound

Structure

NPC59037 OpenBabel06302215332D 22 24 0 0 1 0 0 0 0 0999 V2000 -0.2788 -1.7601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5878 -0.8090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.5388 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4049 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2709 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2709 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.1369 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1369 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.1369 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2709 2.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4049 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4049 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5388 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5878 0.8090 0.0000 O 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 1.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5388 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2709 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0029 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.8690 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8690 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.7350 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 15 1 0 0 0 0 3 4 1 6 0 0 0 3 13 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 12 1 0 0 0 0 6 7 1 6 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 8 19 1 1 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 10 18 1 6 0 0 0 11 12 2 0 0 0 0 11 17 1 0 0 0 0 13 12 1 1 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	308.16
Volume:	312.961
LogP:	1.951
LogD:	1.648
LogS:	-2.753
# Rotatable Bonds:	2
TPSA:	72.83
# H-Bond Aceptor:	5
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.592
Synthetic Accessibility Score:	4.471
Fsp3:	0.765
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.72
MDCK Permeability:	8.150429493980482e-05
Pgp-inhibitor:	0.913
Pgp-substrate:	0.991
Human Intestinal Absorption (HIA):	0.017
20% Bioavailability (F20%):	0.021
30% Bioavailability (F30%):	0.979

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.569
Plasma Protein Binding (PPB):	54.87626266479492%
Volume Distribution (VD):	1.126
Pgp-substrate:	38.85966491699219%

ADMET: Metabolism

CYP1A2-inhibitor:	0.042
CYP1A2-substrate:	0.107
CYP2C19-inhibitor:	0.019
CYP2C19-substrate:	0.703
CYP2C9-inhibitor:	0.011
CYP2C9-substrate:	0.066
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.117
CYP3A4-inhibitor:	0.292
CYP3A4-substrate:	0.317

ADMET: Excretion

Clearance (CL):	7.924
Half-life (T1/2):	0.14

ADMET: Toxicity

hERG Blockers:	0.079
Human Hepatotoxicity (H-HT):	0.703
Drug-inuced Liver Injury (DILI):	0.875
AMES Toxicity:	0.063
Rat Oral Acute Toxicity:	0.749
Maximum Recommended Daily Dose:	0.945
Skin Sensitization:	0.289
Carcinogencity:	0.366
Eye Corrosion:	0.268
Eye Irritation:	0.201
Respiratory Toxicity:	0.959

Download Data

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

Natural Product: NPC59037

Natural Product ID:	NPC59037
*Common Name:**	CRNHYCBDESPWOY-BZPBRVGYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	CRNHYCBDESPWOY-BZPBRVGYSA-N
Standard InCHI:	InChI=1S/C17H24O5/c1-8-11-5-6-17(4)13(21-10(3)18)7-12(19)9(2)14(17)15(11)22-16(8)20/h8,11-13,15,19H,5-7H2,1-4H3/t8-,11-,12-,13-,15-,17-/m0/s1
SMILES:	C[C@H]1[C@@H]2CC[C@@]3(C)[C@H](C[C@@H](C(=C3[C@H]2OC1=O)C)O)OC(=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101674073
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones [CHEMONTID:0001543] Sesquiterpene lactones [CHEMONTID:0001772] Eudesmanolides, secoeudesmanolides, and derivatives

*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
NPO27265	Hopea parviflora	Species	Dipterocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27533	Senecio bergii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27708	Mythimna separata	Species	0ctuidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27304	Stevia sanguinea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27409	Scabiosa atropurpurea	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27155	Aconitum nasutum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27554	Doryanthes palmeri	Species	Doryanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27265	Hopea parviflora	Species	Dipterocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27836	Gymnodinium microadriaticum	Species	Gymnodiniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27355	Pseudokeronopsis rubra	Species	Pseudokeronopsidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27073	Poranthera corymbosa	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27447	Yucca aloifolia	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5306	Infundibulicybe catinus	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27519	Alternaria chrysanthemi	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6164	Lasiosiphon eriocephalus	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27227	Matricaria occidentalis	Species	Asteraceae	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 NPC59037 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	175
0.1-0.2	1145
0.2-0.3	4251
0.3-0.4	10480
0.4-0.5	11603
0.5-0.6	6364
0.6-0.7	6617
0.7-0.8	1986
0.8-0.85	66
0.85-0.9	9
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 NPC59037 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	153
0.1-0.2	1553
0.2-0.3	3665
0.3-0.4	2460
0.4-0.5	787
0.5-0.6	274
0.6-0.7	227
0.7-0.8	30
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