NPASS Compound

Structure

NPC202942 OpenBabel06302215192D 31 35 0 0 1 0 0 0 0 0999 V2000 0.8420 1.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8420 0.4861 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6839 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6839 -0.9722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8420 -1.4583 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6839 -1.9444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8420 -2.4306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -2.9167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8420 -2.4306 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8420 -4.3750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8420 -1.4583 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6839 -0.9722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5259 -1.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5259 -2.4306 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3679 -2.9167 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3679 -1.9444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2098 -2.4306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0518 -2.9167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0518 -3.8889 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8938 -4.3750 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2098 -4.3750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6960 -5.2170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7237 -5.2170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3679 -3.8889 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5259 -4.3750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6839 -3.8889 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6839 -2.9167 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8420 -3.4028 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.9722 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8420 0.4861 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 30 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 29 1 0 0 0 0 5 6 1 1 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 27 1 0 0 0 0 9 10 1 0 0 0 0 9 11 1 0 0 0 0 11 12 1 6 0 0 0 11 29 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 14 27 1 0 0 0 0 15 24 1 0 0 0 0 15 16 1 1 0 0 0 15 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 21 23 1 0 0 0 0 21 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 29 30 1 0 0 0 0 30 31 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	424.37
Volume:	488.171
LogP:	6.423
LogD:	5.933
LogS:	-6.31
# Rotatable Bonds:	0
TPSA:	17.07
# H-Bond Aceptor:	1
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	1

MedChem Properties

QED Drug-Likeness Score:	0.358
Synthetic Accessibility Score:	4.822
Fsp3:	0.9
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-5.191
MDCK Permeability:	1.42787212098483e-05
Pgp-inhibitor:	0.062
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.827
30% Bioavailability (F30%):	0.949

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.061
Plasma Protein Binding (PPB):	93.98702239990234%
Volume Distribution (VD):	1.222
Pgp-substrate:	1.9682230949401855%

ADMET: Metabolism

CYP1A2-inhibitor:	0.067
CYP1A2-substrate:	0.705
CYP2C19-inhibitor:	0.121
CYP2C19-substrate:	0.969
CYP2C9-inhibitor:	0.147
CYP2C9-substrate:	0.807
CYP2D6-inhibitor:	0.208
CYP2D6-substrate:	0.898
CYP3A4-inhibitor:	0.516
CYP3A4-substrate:	0.427

ADMET: Excretion

Clearance (CL):	4.759
Half-life (T1/2):	0.195

ADMET: Toxicity

hERG Blockers:	0.009
Human Hepatotoxicity (H-HT):	0.199
Drug-inuced Liver Injury (DILI):	0.036
AMES Toxicity:	0.003
Rat Oral Acute Toxicity:	0.126
Maximum Recommended Daily Dose:	0.844
Skin Sensitization:	0.087
Carcinogencity:	0.009
Eye Corrosion:	0.696
Eye Irritation:	0.836
Respiratory Toxicity:	0.973

Download Data

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

Natural Product: NPC202942

Natural Product ID:	NPC202942
*Common Name:**	ZYOCVAPRXVCQQR-NGVMWHTRSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ZYOCVAPRXVCQQR-NGVMWHTRSA-N
Standard InCHI:	InChI=1S/C30H48O/c1-19-11-14-27(5)17-18-29(7)21(25(27)20(19)2)9-10-23-28(6)15-13-24(31)26(3,4)22(28)12-16-30(23,29)8/h20-23,25H,1,9-18H2,2-8H3/t20-,21-,22+,23-,25-,27-,28+,29-,30-/m1/s1
SMILES:	C=C1CC[C@]2(C)CC[C@]3(C)[C@H](CC[C@@H]4[C@@]5(C)CCC(=O)C(C)(C)[C@@H]5CC[C@@]34C)[C@H]2[C@@H]1C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	14485466
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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
NPO7294	Cunninghamella echinulata	Species	Cunninghamellaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12740180]
NPO10946	Pseudallescheria boydii	Species	Microascaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20509707]
NPO19556	Clathrina clathrus	Species	Clathrinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[20590100]
NPO8087	Aglaia foveolata	Species	Meliaceae	Eukaryota	n.a.	stem	n.a.	PMID[20939540]
NPO8087	Aglaia foveolata	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20939540]
NPO8087	Aglaia foveolata	Species	Meliaceae	Eukaryota	n.a.	twig	n.a.	PMID[20939540]
NPO8087	Aglaia foveolata	Species	Meliaceae	Eukaryota	n.a.	fruit	n.a.	PMID[20939540]
NPO8087	Aglaia foveolata	Species	Meliaceae	Eukaryota	n.a.	leaf	n.a.	PMID[20939540]
NPO8087	Aglaia foveolata	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22817615]
NPO10946	Pseudallescheria boydii	Species	Microascaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23964677]
NPO20453	Cayratia japonica	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11697	Cirsium setosum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15736	Liatris spicata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20453	Cayratia japonica	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11697	Cirsium setosum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15736	Liatris spicata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO23706	Breea segeta	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TM-MC]
NPO11697	Cirsium setosum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO10946	Pseudallescheria boydii	Species	Microascaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20453	Cayratia japonica	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11697	Cirsium setosum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8087	Aglaia foveolata	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26652	Soroseris hookeriana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22090	Aframomum alboviolaceum	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3651	Ajania achilleoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7294	Cunninghamella echinulata	Species	Cunninghamellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9531	Premna latifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15736	Liatris spicata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19556	Clathrina clathrus	Species	Clathrinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4687	Gyromitra esculenta	Species	Discinaceae	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 NPC202942 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	321
0.1-0.2	4224
0.2-0.3	18835
0.3-0.4	8998
0.4-0.5	5972
0.5-0.6	3400
0.6-0.7	832
0.7-0.8	97
0.8-0.85	8
0.85-0.9	10
0.9-0.95	0
0.95-1	0

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 NPC202942 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	329
0.1-0.2	3789
0.2-0.3	3749
0.3-0.4	852
0.4-0.5	275
0.5-0.6	131
0.6-0.7	24
0.7-0.8	1
0.8-0.85	0
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