NPASS Compound

Structure

NPC130928 OpenBabel06302215232D 24 25 0 0 0 0 0 0 0 0999 V2000 1.7321 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 2.5981 1.5000 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 1.7321 -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 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 3.0000 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 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 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 -2.5981 0.5000 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 -1.7321 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 2.0000 0.0000 O 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 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 24 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 10 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 23 1 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 9 15 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 11 13 1 0 0 0 0 13 14 2 0 0 0 0 13 19 1 0 0 0 0 14 15 1 0 0 0 0 14 17 1 0 0 0 0 15 16 2 0 0 0 0 17 18 1 0 0 0 0 19 20 2 0 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	331.14
Volume:	339.264
LogP:	3.511
LogD:	2.037
LogS:	-3.36
# Rotatable Bonds:	5
TPSA:	77.76
# H-Bond Aceptor:	6
# H-Bond Donor:	1
# Rings:	2
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.688
Synthetic Accessibility Score:	2.813
Fsp3:	0.333
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.627
MDCK Permeability:	1.6215912182815373e-05
Pgp-inhibitor:	0.032
Pgp-substrate:	0.025
Human Intestinal Absorption (HIA):	0.097
20% Bioavailability (F20%):	0.008
30% Bioavailability (F30%):	0.096

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.357
Plasma Protein Binding (PPB):	88.03800201416016%
Volume Distribution (VD):	0.733
Pgp-substrate:	7.1138105392456055%

ADMET: Metabolism

CYP1A2-inhibitor:	0.849
CYP1A2-substrate:	0.927
CYP2C19-inhibitor:	0.893
CYP2C19-substrate:	0.737
CYP2C9-inhibitor:	0.86
CYP2C9-substrate:	0.906
CYP2D6-inhibitor:	0.344
CYP2D6-substrate:	0.491
CYP3A4-inhibitor:	0.368
CYP3A4-substrate:	0.185

ADMET: Excretion

Clearance (CL):	8.231
Half-life (T1/2):	0.483

ADMET: Toxicity

hERG Blockers:	0.012
Human Hepatotoxicity (H-HT):	0.408
Drug-inuced Liver Injury (DILI):	0.167
AMES Toxicity:	0.143
Rat Oral Acute Toxicity:	0.149
Maximum Recommended Daily Dose:	0.298
Skin Sensitization:	0.149
Carcinogencity:	0.146
Eye Corrosion:	0.003
Eye Irritation:	0.14
Respiratory Toxicity:	0.288

Download Data

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

Natural Product: NPC130928

Natural Product ID:	NPC130928
*Common Name:**	SFAKUCXCZOCMOD-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SFAKUCXCZOCMOD-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C18H21NO5/c1-10(2)6-7-11-13(20)9-8-12-14(11)19(3)15(18(22)24-5)17(23-4)16(12)21/h6,8-9,20H,7H2,1-5H3
SMILES:	CC(=CCc1c(ccc2c1n(C)c(c(c2=O)OC)C(=O)OC)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10806393
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001253] Quinolines and derivatives [CHEMONTID:0000056] Quinolones and derivatives [CHEMONTID:0001716] Hydroquinolones

*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
NPO17467	Aframomum aulacocarpos	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7964787]
NPO766	Chlorophora excelsa	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[HerDing]
NPO15788	Galium aparine	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15788	Galium aparine	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO766	Chlorophora excelsa	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO15788	Galium aparine	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15431	Luidia clathrata	Species	Luidiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18017	Stapelia grandiflora	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14083	Cinnamomum oliveri	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15223	Trema humbertii	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10512	Yersinia pseudotuberculosis	Species	Yersiniaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO15788	Galium aparine	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15938	Cephalotaxus mannii	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO766	Chlorophora excelsa	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO17938	Plectranthus albidus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11806	Gardenia gordonii	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18331	Agnorhiza ovata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17467	Aframomum aulacocarpos	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13387	Senecio sundbergii	Species	Asteraceae	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 NPC130928 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	412
0.1-0.2	2775
0.2-0.3	10877
0.3-0.4	6233
0.4-0.5	10372
0.5-0.6	10217
0.6-0.7	1507
0.7-0.8	272
0.8-0.85	30
0.85-0.9	2
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 NPC130928 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	255
0.1-0.2	675
0.2-0.3	988
0.3-0.4	1673
0.4-0.5	2824
0.5-0.6	2095
0.6-0.7	561
0.7-0.8	76
0.8-0.85	2
0.85-0.9	1
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