NPASS Compound

Structure

NPC252065 OpenBabel06302215322D 34 37 0 0 1 0 0 0 0 0999 V2000 0.8477 -3.4161 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6926 -2.9280 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5377 -3.4156 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5380 -4.3913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3831 -4.8789 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3834 -5.8546 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8714 -6.6994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3590 -5.8543 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5385 -6.3427 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2279 -4.3908 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6923 -1.9523 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5368 -1.4637 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5366 -0.4876 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8460 -0.4881 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8463 -1.4642 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8466 -2.4642 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0006 -1.9528 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8455 -1.4647 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8457 -0.4886 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6917 -0.0005 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6915 -1.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5369 -0.4891 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3823 -0.0010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3826 0.9757 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5374 1.4643 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6920 0.9762 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8463 1.4648 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0003 0.9767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8659 0.5002 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8466 2.4648 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5377 2.4643 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2488 1.4753 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2435 0.2197 0.0000 O 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 2 11 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 5 10 1 1 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 6 9 1 0 0 0 0 11 12 1 0 0 0 0 11 15 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 13 34 1 0 0 0 0 14 15 1 0 0 0 0 14 29 1 0 0 0 0 15 16 1 0 0 0 0 15 17 1 0 0 0 0 17 18 1 0 0 0 0 19 18 1 6 0 0 0 19 20 1 0 0 0 0 19 29 1 0 0 0 0 20 26 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 23 24 1 0 0 0 0 24 25 1 0 0 0 0 24 33 1 6 0 0 0 25 26 1 0 0 0 0 25 32 1 6 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 27 31 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	484.34
Volume:	502.854
LogP:	1.867
LogD:	1.825
LogS:	-2.949
# Rotatable Bonds:	5
TPSA:	141.61
# H-Bond Aceptor:	7
# H-Bond Donor:	7
# Rings:	4
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.314
Synthetic Accessibility Score:	5.214
Fsp3:	1.0
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.148
MDCK Permeability:	2.8641356038860977e-05
Pgp-inhibitor:	0.067
Pgp-substrate:	0.978
Human Intestinal Absorption (HIA):	0.53
20% Bioavailability (F20%):	0.032
30% Bioavailability (F30%):	0.687

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.103
Plasma Protein Binding (PPB):	75.97035217285156%
Volume Distribution (VD):	0.476
Pgp-substrate:	11.307196617126465%

ADMET: Metabolism

CYP1A2-inhibitor:	0.012
CYP1A2-substrate:	0.335
CYP2C19-inhibitor:	0.003
CYP2C19-substrate:	0.689
CYP2C9-inhibitor:	0.006
CYP2C9-substrate:	0.504
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.118
CYP3A4-inhibitor:	0.035
CYP3A4-substrate:	0.054

ADMET: Excretion

Clearance (CL):	1.875
Half-life (T1/2):	0.325

ADMET: Toxicity

hERG Blockers:	0.2
Human Hepatotoxicity (H-HT):	0.283
Drug-inuced Liver Injury (DILI):	0.029
AMES Toxicity:	0.024
Rat Oral Acute Toxicity:	0.069
Maximum Recommended Daily Dose:	0.056
Skin Sensitization:	0.53
Carcinogencity:	0.019
Eye Corrosion:	0.008
Eye Irritation:	0.036
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: NPC252065

Natural Product ID:	NPC252065
*Common Name:**	HXDUGHMQOCBJOT-PFYNCICHSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HXDUGHMQOCBJOT-PFYNCICHSA-N
Standard InCHI:	InChI=1S/C27H48O7/c1-14(6-7-20(31)24(2,3)33)15-12-17(29)23-25(15,4)11-9-19-26(5)10-8-16(28)22(32)21(26)18(30)13-27(19,23)34/h14-23,28-34H,6-13H2,1-5H3/t14-,15-,16+,17-,18-,19-,20-,21+,22+,23-,25-,26-,27+/m1/s1
SMILES:	C[C@H](CC[C@H](C(C)(C)O)O)[C@H]1C[C@H]([C@@H]2[C@]1(C)CC[C@@H]1[C@@]3(C)CC[C@@H]([C@@H]([C@@H]3[C@@H](C[C@@]21O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	44566288
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001445] Bile acids, alcohols and derivatives [CHEMONTID:0002194] Hydroxy bile acids, alcohols 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
NPO13814	Tupidanthus calyptratus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11421737]
NPO8018	Henricia leviuscula	Species	Echinasteridae	Eukaryota	n.a.	n.a.	n.a.	PMID[16499320]
NPO13914	Fraxinus ornus	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18207	Radermachera sinica	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13914	Fraxinus ornus	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13914	Fraxinus ornus	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8018	Henricia leviuscula	Species	Echinasteridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25557	Alternaria porri	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1488	Aphis spiraecola	Species	Aphididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18207	Radermachera sinica	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14006	Halostachys caspica	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9076	Tiliacora dinklagei	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22644	Helichrysum argenteum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8371	Fagara rhoifolia	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO11691	Limnothrix rosea	Species	Pseudanabaenaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO13814	Tupidanthus calyptratus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13088	Vicia pseudo-orobus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2586	Alnus rubra	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2159	Helipterum splendidum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4309	Carapa procera	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13914	Fraxinus ornus	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5467	Helenium campestre	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14838	Myriocephalus stuartii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9689	Pertusaria flavicans	Species	Pertusariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14510	Streptomyces acidiscabies	Species	Streptomycetaceae	Bacteria	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

Activity Type	# Activity
Others	1

Activity Type	# Activity
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT27	Others	Unspecified		HC50	=	2.1	10'-4M	PMID[479170]

☑ 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 NPC252065 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

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 NPC252065 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

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