NPASS Compound

Structure

NPC485313 OpenBabel06302216142D 31 34 0 0 1 0 0 0 0 0999 V2000 -6.1667 -1.5055 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3007 -2.0055 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3007 -3.0055 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4347 -1.5055 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4347 -0.5055 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.3007 -0.0055 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3007 0.9945 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.1667 1.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1667 2.4945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.0327 0.9945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.8988 1.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4347 1.4945 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.3007 1.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4347 2.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5686 2.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7026 2.4945 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8366 2.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8366 3.9945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9706 2.4945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9706 1.4945 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8366 0.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7026 1.4945 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.7026 0.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5686 0.9945 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.5686 -0.0055 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7026 -0.5055 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1045 0.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8090 1.4013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4781 0.6581 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9781 -0.2079 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 2 1 0 0 0 0 2 3 2 0 0 0 0 2 4 1 0 0 0 0 5 4 1 6 0 0 0 5 6 1 0 0 0 0 5 25 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 1 0 0 0 7 12 1 0 0 0 0 8 9 2 0 0 0 0 8 10 1 0 0 0 0 10 11 1 0 0 0 0 12 24 1 0 0 0 0 12 13 1 1 0 0 0 12 14 1 0 0 0 0 14 15 1 0 0 0 0 16 15 1 1 0 0 0 16 17 1 0 0 0 0 16 22 1 0 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 20 27 1 6 0 0 0 21 22 1 0 0 0 0 22 23 1 1 0 0 0 22 24 1 0 0 0 0 24 25 1 1 0 0 0 25 26 2 0 0 0 0 27 31 2 0 0 0 0 27 28 1 0 0 0 0 28 29 2 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:	432.18
Volume:	426.641
LogP:	2.475
LogD:	1.267
LogS:	-3.397
# Rotatable Bonds:	5
TPSA:	109.11
# H-Bond Aceptor:	8
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.53
Synthetic Accessibility Score:	4.625
Fsp3:	0.652
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-4.924
MDCK Permeability:	5.6315137044293806e-05
Pgp-inhibitor:	0.997
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.01
30% Bioavailability (F30%):	0.887

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.501
Plasma Protein Binding (PPB):	60.29365921020508%
Volume Distribution (VD):	2.145
Pgp-substrate:	35.731990814208984%

ADMET: Metabolism

CYP1A2-inhibitor:	0.024
CYP1A2-substrate:	0.237
CYP2C19-inhibitor:	0.173
CYP2C19-substrate:	0.513
CYP2C9-inhibitor:	0.394
CYP2C9-substrate:	0.065
CYP2D6-inhibitor:	0.011
CYP2D6-substrate:	0.182
CYP3A4-inhibitor:	0.702
CYP3A4-substrate:	0.344

ADMET: Excretion

Clearance (CL):	7.252
Half-life (T1/2):	0.351

ADMET: Toxicity

hERG Blockers:	0.032
Human Hepatotoxicity (H-HT):	0.895
Drug-inuced Liver Injury (DILI):	0.879
AMES Toxicity:	0.013
Rat Oral Acute Toxicity:	0.972
Maximum Recommended Daily Dose:	0.724
Skin Sensitization:	0.084
Carcinogencity:	0.052
Eye Corrosion:	0.036
Eye Irritation:	0.064
Respiratory Toxicity:	0.957

Download Data

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

Natural Product: NPC485313

Natural Product ID:	NPC485313
*Common Name:**	OBSYBRPAKCASQB-ASUQIVHDSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	OBSYBRPAKCASQB-ASUQIVHDSA-N
Standard InCHI:	InChI=1S/C23H28O8/c1-12(24)30-16-9-15(20(26)28-4)22(2)7-5-14-21(27)31-17(13-6-8-29-11-13)10-23(14,3)19(22)18(16)25/h6,8,11,14-17,19H,5,7,9-10H2,1-4H3/t14-,15-,16+,17-,19-,22-,23-/m0/s1
SMILES:	CC(=O)O[C@@H]1C[C@@H](C(=O)OC)[C@]2(C)CC[C@H]3C(=O)O[C@@H](C[C@]3(C)[C@H]2C1=O)c1ccoc1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11546512
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones [CHEMONTID:0001538] Diterpene lactones

*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
NPO634	Salvia divinorum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[14510607]
NPO634	Salvia divinorum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15987194]
NPO634	Salvia divinorum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16441078]
NPO634	Salvia divinorum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16621556]
NPO634	Salvia divinorum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16945525]
NPO634	Salvia divinorum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17190459]
NPO634	Salvia divinorum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17580847]
NPO634	Salvia divinorum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21338114]
NPO634	Salvia divinorum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25193297]
NPO634	Salvia divinorum	Species	Lamiaceae	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
EC50	5
Ki	1
Others	3

Activity Type	# Activity
Individual Protein	8
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT272	Individual Protein	Kappa opioid receptor	Homo sapiens	Ki	=	424.0	nM	PMID[16777411]
NPT272	Individual Protein	Kappa opioid receptor	Homo sapiens	EC50	=	306.0	nM	PMID[16777411]
NPT272	Individual Protein	Kappa opioid receptor	Homo sapiens	Ratio EC50	=	1.0	n.a.	PMID[16441078]
NPT272	Individual Protein	Kappa opioid receptor	Homo sapiens	Ratio EC50	=	1.9	n.a.	PMID[16441078]
NPT272	Individual Protein	Kappa opioid receptor	Homo sapiens	EC50	=	385.0	nM	PMID[16441078]
NPT272	Individual Protein	Kappa opioid receptor	Homo sapiens	EC50	=	6.5	nM	PMID[16441078]
NPT145	Individual Protein	Mu opioid receptor	Homo sapiens	EC50	>	10000.0	nM	PMID[27958743]
NPT272	Individual Protein	Kappa opioid receptor	Homo sapiens	EC50	=	110.0	nM	PMID[27958743]
NPT2	Others	Unspecified		Ratio EC50	<	1.1	10^-2No_unit	PMID[27958743]

☑ 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 NPC485313 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	386
0.1-0.2	1454
0.2-0.3	3060
0.3-0.4	6358
0.4-0.5	11539
0.5-0.6	9656
0.6-0.7	8854
0.7-0.8	1025
0.8-0.85	240
0.85-0.9	104
0.9-0.95	19
0.95-1	2

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 NPC485313 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	322
0.1-0.2	990
0.2-0.3	1970
0.3-0.4	2729
0.4-0.5	1933
0.5-0.6	917
0.6-0.7	269
0.7-0.8	18
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