NPASS Compound

Structure

NPC269121 OpenBabel06302215262D 31 34 0 0 1 0 0 0 0 0999 V2000 1.2838 -3.6730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0249 -2.7071 0.0000 C 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 2.6559 -2.3827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 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 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 1 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 0.8660 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 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 -0.8660 -0.5000 0.0000 C 0 0 1 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 -1.7321 -0.0000 0.0000 C 0 0 2 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 -3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 2 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 2 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 -0.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 4.0000 0.0000 O 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 -4.3301 1.5000 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 -4.3301 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 10 1 0 0 0 0 3 4 1 1 0 0 0 3 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 24 1 0 0 0 0 8 9 1 6 0 0 0 8 10 1 0 0 0 0 10 11 1 6 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 24 1 0 0 0 0 13 14 1 6 0 0 0 13 15 1 0 0 0 0 15 16 1 6 0 0 0 15 20 1 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 18 19 1 0 0 0 0 18 29 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 6 0 0 0 20 22 1 0 0 0 0 22 23 1 0 0 0 0 22 25 1 1 0 0 0 24 23 1 6 0 0 0 25 26 1 0 0 0 0 26 27 2 0 0 0 0 26 28 1 0 0 0 0 29 30 2 0 0 0 0 29 31 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	428.33
Volume:	477.08
LogP:	5.511
LogD:	4.566
LogS:	-5.377
# Rotatable Bonds:	4
TPSA:	43.37
# H-Bond Aceptor:	3
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.369
Synthetic Accessibility Score:	5.009
Fsp3:	0.857
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.762
MDCK Permeability:	1.396218067384325e-05
Pgp-inhibitor:	0.992
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.008
20% Bioavailability (F20%):	0.09
30% Bioavailability (F30%):	0.935

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.159
Plasma Protein Binding (PPB):	97.41876983642578%
Volume Distribution (VD):	1.243
Pgp-substrate:	2.4483704566955566%

ADMET: Metabolism

CYP1A2-inhibitor:	0.034
CYP1A2-substrate:	0.3
CYP2C19-inhibitor:	0.045
CYP2C19-substrate:	0.892
CYP2C9-inhibitor:	0.161
CYP2C9-substrate:	0.068
CYP2D6-inhibitor:	0.07
CYP2D6-substrate:	0.231
CYP3A4-inhibitor:	0.816
CYP3A4-substrate:	0.483

ADMET: Excretion

Clearance (CL):	13.468
Half-life (T1/2):	0.179

ADMET: Toxicity

hERG Blockers:	0.086
Human Hepatotoxicity (H-HT):	0.314
Drug-inuced Liver Injury (DILI):	0.729
AMES Toxicity:	0.005
Rat Oral Acute Toxicity:	0.528
Maximum Recommended Daily Dose:	0.324
Skin Sensitization:	0.823
Carcinogencity:	0.164
Eye Corrosion:	0.792
Eye Irritation:	0.12
Respiratory Toxicity:	0.967

Download Data

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

Natural Product: NPC269121

Natural Product ID:	NPC269121
*Common Name:**	YZYZCVQQKYLXMA-MRPYZOCESA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YZYZCVQQKYLXMA-MRPYZOCESA-N
Standard InCHI:	InChI=1S/C28H44O3/c1-8-25(4)13-9-14-26(5)21(25)12-15-27(6)22-11-10-20(18(2)29)17-28(22,7)24(16-23(26)27)31-19(3)30/h10,21-24H,8-9,11-17H2,1-7H3/t21-,22-,23+,24-,25-,26-,27-,28+/m0/s1
SMILES:	CC[C@@]1(C)CCC[C@@]2(C)[C@H]1CC[C@@]1(C)[C@@H]3CC=C(C[C@@]3(C)[C@H](C[C@H]21)OC(=O)C)C(=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	14395313
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001552] Sesterterpenoids

*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
NPO2453	Stachybotrys chartarum	Species	Stachybotryaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24387683]
NPO2453	Stachybotrys chartarum	Species	Stachybotryaceae	Eukaryota	Niphates recondita	Weizhou Island, Beibuwan Bay, Guangxi,China	n.a.	PMID[24387683]
NPO2453	Stachybotrys chartarum	Species	Stachybotryaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28530828]
NPO2453	Stachybotrys chartarum	Species	Stachybotryaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31265296]
NPO2453	Stachybotrys chartarum	Species	Stachybotryaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32966070]
NPO12586	Tapirira guianensis	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9514013]
NPO8225	Salvia karabachensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22505	Bombax ceiba	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7116	Monachosorum henryi	Species	Dennstaedtiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11328	Juniperus chinensis	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8225	Salvia karabachensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8857	Hydnum repandum	Species	Hydnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8225	Salvia karabachensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO2431	Penicilliopsis zonata	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28504	Calothrix brevissima	Species	Rivulariaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO13038	Fomes hartigii	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5472	Spongia foliascens	Species	Spongiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12708	Rothia indica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22505	Bombax ceiba	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11328	Juniperus chinensis	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9355	Polygonatum orientale	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12586	Tapirira guianensis	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5958	Senegalia modesta	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10944	Mantella baroni	Species	Mantellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12364	Polyides rotundus	Species	Polyideaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12931	Carex pumila	Species	Cyperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8395.1	Crepis foetida subsp. rhoeadifolia	Subspecies	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9977	Polygonum sieboldi	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6781	Senecio acanthifolius	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3308	Calycadenia fremontii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8225	Salvia karabachensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7116	Monachosorum henryi	Species	Dennstaedtiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2453	Stachybotrys chartarum	Species	Stachybotryaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9147	Frasera albomarginata	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8857	Hydnum repandum	Species	Hydnaceae	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 NPC269121 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	1517
0.2-0.3	5310
0.3-0.4	11561
0.4-0.5	10743
0.5-0.6	6200
0.6-0.7	4908
0.7-0.8	1918
0.8-0.85	263
0.85-0.9	39
0.9-0.95	7
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 NPC269121 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	214
0.1-0.2	1756
0.2-0.3	3923
0.3-0.4	2100
0.4-0.5	716
0.5-0.6	194
0.6-0.7	138
0.7-0.8	96
0.8-0.85	7
0.85-0.9	5
0.9-0.95	1
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