NPASS Compound

Structure

NPC127654 OpenBabel06302215172D 23 22 0 0 0 0 0 0 0 0999 V2000 -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 -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 -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 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.3923 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.2583 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.1244 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.9904 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.3923 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 0.0000 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 -2.5981 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 O 0 5 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 23 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 6 7 2 0 0 0 0 6 20 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 2 0 0 0 0 10 19 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 2 0 0 0 0 14 18 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 M CHG 1 22 -1 M END $$$$

Physi-Chem Properties

Molecular Weight:	320.24
Volume:	367.665
LogP:	4.93
LogD:	3.796
LogS:	-3.852
# Rotatable Bonds:	11
TPSA:	57.53
# H-Bond Aceptor:	3
# H-Bond Donor:	2
# Rings:	0
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.407
Synthetic Accessibility Score:	3.109
Fsp3:	0.55
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:	-5.059
MDCK Permeability:	3.2785603252705187e-05
Pgp-inhibitor:	0.331
Pgp-substrate:	0.006
Human Intestinal Absorption (HIA):	0.212
20% Bioavailability (F20%):	0.145
30% Bioavailability (F30%):	0.028

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.24
Plasma Protein Binding (PPB):	95.44928741455078%
Volume Distribution (VD):	0.477
Pgp-substrate:	3.6339328289031982%

ADMET: Metabolism

CYP1A2-inhibitor:	0.172
CYP1A2-substrate:	0.143
CYP2C19-inhibitor:	0.032
CYP2C19-substrate:	0.062
CYP2C9-inhibitor:	0.276
CYP2C9-substrate:	0.915
CYP2D6-inhibitor:	0.305
CYP2D6-substrate:	0.222
CYP3A4-inhibitor:	0.025
CYP3A4-substrate:	0.092

ADMET: Excretion

Clearance (CL):	3.068
Half-life (T1/2):	0.812

ADMET: Toxicity

hERG Blockers:	0.008
Human Hepatotoxicity (H-HT):	0.935
Drug-inuced Liver Injury (DILI):	0.005
AMES Toxicity:	0.0
Rat Oral Acute Toxicity:	0.003
Maximum Recommended Daily Dose:	0.226
Skin Sensitization:	0.981
Carcinogencity:	0.023
Eye Corrosion:	0.045
Eye Irritation:	0.949
Respiratory Toxicity:	0.028

Download Data

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

Natural Product: NPC127654

Natural Product ID:	NPC127654
*Common Name:**	USXGDFAHMRCBBX-PFZXPCEQSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	USXGDFAHMRCBBX-PFZXPCEQSA-N
Standard InCHI:	InChI=1S/C20H32O3/c1-16(2)8-5-12-19(20(22)23)13-7-11-17(3)9-6-10-18(4)14-15-21/h8-9,13-14,21H,5-7,10-12,15H2,1-4H3,(H,22,23)/p-1/b17-9+,18-14+,19-13+
SMILES:	CC(=CCC/C(=CCC/C(=C/CC/C(=C/CO)/C)/C)/C(=O)[O-])C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11186287
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0001357] Acyclic diterpenoids

*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
NPO23728	Favolaschia tonkinensis	Species	Favolaschiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20329738]
NPO17318	Streptomyces cyaneus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[21462031]
NPO15612	Glaucium oxylobum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15612	Glaucium oxylobum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15612	Glaucium oxylobum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO17158	Trichocereus bridgesii	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17318	Streptomyces cyaneus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO5124	Aconitum ibukiense	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23636	Liparis condylobulbon	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24166	Spongia lamellosa	Species	Spongiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23446	Rumex pulcher	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23728	Favolaschia tonkinensis	Species	Favolaschiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12311	Graphis handelii	Species	Graphidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17500	Candelaria vitellina	Species	Candelariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14653	Haliotis diversicolor	Species	Haliotidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23174	Tortrix viridana	Species	Tortricidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14339	Fevillea trilobata	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23590	Woodsia scopulina	Species	Woodsiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25141	Mycetinis alliaceus	Species	Omphalotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24081	Conocephalum supradecompositum	Species	Conocephalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15612	Glaucium oxylobum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17251	Aniba firmula	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3705	Anacardium humile	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23401	Castilleja integra	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13361	Clerodendrum tomentosum	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

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 NPC127654 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	133
0.1-0.2	3599
0.2-0.3	16487
0.3-0.4	12988
0.4-0.5	6070
0.5-0.6	2551
0.6-0.7	758
0.7-0.8	107
0.8-0.85	4
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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 NPC127654 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	112
0.1-0.2	3454
0.2-0.3	4013
0.3-0.4	1177
0.4-0.5	298
0.5-0.6	66
0.6-0.7	23
0.7-0.8	7
0.8-0.85	0
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