NPASS Compound

Structure

NPC66985 OpenBabel06302215212D 33 37 0 0 1 0 0 0 0 0999 V2000 -5.6479 -1.4881 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8542 -1.0299 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.0362 -1.5022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2182 -1.0299 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2182 -0.0854 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.0362 0.3869 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.2374 0.8480 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0362 1.3314 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.8542 1.8038 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6722 1.3315 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.6722 0.3869 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8542 -0.0854 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.7988 -0.0854 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.1445 0.5135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0668 0.5135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6057 -0.2852 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2182 1.8037 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2181 2.7483 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4001 3.2206 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0362 3.2206 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8542 2.7483 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6722 3.2206 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6722 4.1652 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8541 4.6375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9599 3.6319 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4245 0.3728 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6309 -0.0854 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6309 -1.0019 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8372 0.3728 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7414 1.2842 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1550 1.4747 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6132 0.6810 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 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 12 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 26 1 1 0 0 0 6 12 1 0 0 0 0 6 7 1 1 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 8 17 1 6 0 0 0 10 9 1 6 0 0 0 10 11 1 0 0 0 0 10 14 1 0 0 0 0 12 11 1 1 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 16 1 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 18 20 1 0 0 0 0 20 25 2 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 24 25 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 29 33 2 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 31 32 1 0 0 0 0 32 33 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	452.22
Volume:	467.052
LogP:	5.468
LogD:	4.37
LogS:	-4.589
# Rotatable Bonds:	6
TPSA:	74.97
# H-Bond Aceptor:	6
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.576
Synthetic Accessibility Score:	5.493
Fsp3:	0.556
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:	-4.919
MDCK Permeability:	2.9602231734315865e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.984
30% Bioavailability (F30%):	0.985

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.009
Plasma Protein Binding (PPB):	99.61869049072266%
Volume Distribution (VD):	1.613
Pgp-substrate:	6.983031272888184%

ADMET: Metabolism

CYP1A2-inhibitor:	0.174
CYP1A2-substrate:	0.09
CYP2C19-inhibitor:	0.577
CYP2C19-substrate:	0.075
CYP2C9-inhibitor:	0.677
CYP2C9-substrate:	0.242
CYP2D6-inhibitor:	0.307
CYP2D6-substrate:	0.199
CYP3A4-inhibitor:	0.818
CYP3A4-substrate:	0.289

ADMET: Excretion

Clearance (CL):	12.853
Half-life (T1/2):	0.237

ADMET: Toxicity

hERG Blockers:	0.644
Human Hepatotoxicity (H-HT):	0.486
Drug-inuced Liver Injury (DILI):	0.887
AMES Toxicity:	0.009
Rat Oral Acute Toxicity:	0.951
Maximum Recommended Daily Dose:	0.928
Skin Sensitization:	0.098
Carcinogencity:	0.622
Eye Corrosion:	0.004
Eye Irritation:	0.391
Respiratory Toxicity:	0.976

Download Data

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

Natural Product: NPC66985

Natural Product ID:	NPC66985
*Common Name:**	HOEQINATYYOKBA-LIELMZMFSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HOEQINATYYOKBA-LIELMZMFSA-N
Standard InCHI:	InChI=1S/C27H32O6/c1-17-10-11-21(31-24(29)19-12-13-30-16-19)26(4)22(32-23(28)18-8-6-5-7-9-18)14-20-15-27(17,26)33-25(20,2)3/h5-9,12-13,16-17,20-22H,10-11,14-15H2,1-4H3/t17-,20-,21+,22+,26+,27+/m1/s1
SMILES:	C[C@@H]1CC[C@@H]([C@@]2(C)[C@H](C[C@@H]3C[C@]12OC3(C)C)OC(=O)c1ccccc1)OC(=O)c1ccoc1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	102103032
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001550] Sesquiterpenoids [CHEMONTID:0002051] Agarofurans

*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
NPO8412	Monanchora arbuscula	Species	Crambeidae	Eukaryota	n.a.	Caribbean	n.a.	PMID[19743809]
NPO631	Osyris lanceolata	Species	Santalaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20499922]
NPO4016	Ligularia fischeri	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24892518]
NPO8412	Monanchora arbuscula	Species	Crambeidae	Eukaryota	n.a.	n.a.	n.a.	PMID[25924111]
NPO40471	Celastrus subspicata	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28548851]
NPO4016	Ligularia fischeri	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4016	Ligularia fischeri	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8412	Monanchora arbuscula	Species	Crambeidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO631	Osyris lanceolata	Species	Santalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4016	Ligularia fischeri	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8117	Aureolaria virginica	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2871	Canistrocarpus cervicornis	Species	Dictyotaceae	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

Activity Type	# Activity
IC50	1

Activity Type	# Activity
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified		IC50	=	19700.0	nM	PMID[28548851]

☑ 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 NPC66985 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	420
0.1-0.2	1508
0.2-0.3	2739
0.3-0.4	6083
0.4-0.5	11669
0.5-0.6	7264
0.6-0.7	8402
0.7-0.8	4239
0.8-0.85	307
0.85-0.9	56
0.9-0.95	7
0.95-1	3

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 NPC66985 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	348
0.1-0.2	844
0.2-0.3	1507
0.3-0.4	2676
0.4-0.5	2263
0.5-0.6	1068
0.6-0.7	362
0.7-0.8	80
0.8-0.85	2
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