NPASS Compound

Structure

NPC165157 OpenBabel06302215242D 27 27 0 0 0 0 0 0 0 0999 V2000 3.4641 -12.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -12.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -12.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -11.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -10.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -9.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -9.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -8.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 C 0 0 0 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 0 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 1.7321 -0.0000 0.0000 C 0 0 0 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 0.8660 1.5000 0.0000 C 0 0 0 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 0 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 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 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 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 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 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 23 2 0 0 0 0 18 19 1 0 0 0 0 19 20 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 22 27 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	374.28
Volume:	428.292
LogP:	7.734
LogD:	4.572
LogS:	-2.567
# Rotatable Bonds:	16
TPSA:	57.53
# H-Bond Aceptor:	3
# H-Bond Donor:	2
# Rings:	1
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.236
Synthetic Accessibility Score:	2.346
Fsp3:	0.625
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.108
MDCK Permeability:	2.3433223759639077e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.026
20% Bioavailability (F20%):	1.0
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.017
Plasma Protein Binding (PPB):	100.41960906982422%
Volume Distribution (VD):	1.033
Pgp-substrate:	0.32843953371047974%

ADMET: Metabolism

CYP1A2-inhibitor:	0.309
CYP1A2-substrate:	0.196
CYP2C19-inhibitor:	0.516
CYP2C19-substrate:	0.06
CYP2C9-inhibitor:	0.16
CYP2C9-substrate:	0.93
CYP2D6-inhibitor:	0.758
CYP2D6-substrate:	0.117
CYP3A4-inhibitor:	0.165
CYP3A4-substrate:	0.02

ADMET: Excretion

Clearance (CL):	1.985
Half-life (T1/2):	0.721

ADMET: Toxicity

hERG Blockers:	0.497
Human Hepatotoxicity (H-HT):	0.109
Drug-inuced Liver Injury (DILI):	0.732
AMES Toxicity:	0.018
Rat Oral Acute Toxicity:	0.04
Maximum Recommended Daily Dose:	0.019
Skin Sensitization:	0.911
Carcinogencity:	0.055
Eye Corrosion:	0.013
Eye Irritation:	0.936
Respiratory Toxicity:	0.89

Download Data

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

Natural Product: NPC165157

Natural Product ID:	NPC165157
*Common Name:**	KFSFAHOBWUACJO-WAYWQWQTSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	KFSFAHOBWUACJO-WAYWQWQTSA-N
Standard InCHI:	InChI=1S/C24H38O3/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-18-21-19-17-20-22(25)23(21)24(26)27/h5-6,17,19-20,25H,2-4,7-16,18H2,1H3,(H,26,27)/b6-5-
SMILES:	CCCC/C=CCCCCCCCCCCCc1cccc(c1C(=O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	92036223
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0002279] Benzene and substituted derivatives [CHEMONTID:0000176] Benzoic acids and derivatives [CHEMONTID:0001248] Hydroxybenzoic acid derivatives [CHEMONTID:0000487] Salicylic acid and derivatives [CHEMONTID:0002514] Salicylic acids

*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
NPO4957	Epimedium brevicornu	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4957	Epimedium brevicornu	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO2600	Alicyclobacillus acidoterrestris	Species	Alicyclobacillaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO7774	Cliona copiosa	Species	Clionaidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9687	Evernia esorediosa	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1623	Acarospora gobiensis	Species	Acarosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11344	Pilea cavaleriei	Species	Urticaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6734	Gladiolus atroviolaceus	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO987	Cruciata taurica	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12319	Xanthogaleruca luteola	Species	Chrysomelidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4632	Crataegus pyracantha	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4339	Carthamus oxyacanthus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4957	Epimedium brevicornu	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7911	Bignonia gracilis	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7502	Salpa thompsoni	Species	Salpidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO561	Lindsaea chienii	Species	Lindsaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10410	Zephyranthes andersoniana	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10974	Acarus immobilis	Species	Acaridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11121	Myrothamnus flabellifolia	Species	Myrothamnaceae	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 NPC165157 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	259
0.1-0.2	1373
0.2-0.3	3401
0.3-0.4	9461
0.4-0.5	10026
0.5-0.6	6039
0.6-0.7	9315
0.7-0.8	2456
0.8-0.85	263
0.85-0.9	74
0.9-0.95	7
0.95-1	23

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 NPC165157 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	265
0.1-0.2	917
0.2-0.3	1425
0.3-0.4	2553
0.4-0.5	2206
0.5-0.6	1212
0.6-0.7	475
0.7-0.8	83
0.8-0.85	8
0.85-0.9	6
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