NPASS Compound

Structure

NPC130396 OpenBabel06302216022D 23 24 0 0 1 0 0 0 0 0999 V2000 -3.4641 -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 -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 -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 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 2.5000 0.0000 O 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 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 2 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 2.2321 -0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 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 2.5981 1.5000 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 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 21 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 13 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 10 12 1 0 0 0 0 13 14 2 0 0 0 0 14 21 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 16 22 1 1 0 0 0 17 18 1 0 0 0 0 17 19 1 0 0 0 0 17 20 1 0 0 0 0 20 21 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	316.17
Volume:	339.409
LogP:	4.417
LogD:	2.322
LogS:	-3.114
# Rotatable Bonds:	4
TPSA:	66.76
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	2
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.66
Synthetic Accessibility Score:	3.442
Fsp3:	0.421
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:	-4.869
MDCK Permeability:	1.1010261914634611e-05
Pgp-inhibitor:	0.004
Pgp-substrate:	0.912
Human Intestinal Absorption (HIA):	0.011
20% Bioavailability (F20%):	0.1
30% Bioavailability (F30%):	0.125

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.076
Plasma Protein Binding (PPB):	94.9349136352539%
Volume Distribution (VD):	0.346
Pgp-substrate:	5.338583469390869%

ADMET: Metabolism

CYP1A2-inhibitor:	0.161
CYP1A2-substrate:	0.083
CYP2C19-inhibitor:	0.024
CYP2C19-substrate:	0.062
CYP2C9-inhibitor:	0.108
CYP2C9-substrate:	0.785
CYP2D6-inhibitor:	0.286
CYP2D6-substrate:	0.147
CYP3A4-inhibitor:	0.028
CYP3A4-substrate:	0.105

ADMET: Excretion

Clearance (CL):	5.039
Half-life (T1/2):	0.248

ADMET: Toxicity

hERG Blockers:	0.019
Human Hepatotoxicity (H-HT):	0.956
Drug-inuced Liver Injury (DILI):	0.659
AMES Toxicity:	0.006
Rat Oral Acute Toxicity:	0.228
Maximum Recommended Daily Dose:	0.942
Skin Sensitization:	0.383
Carcinogencity:	0.281
Eye Corrosion:	0.003
Eye Irritation:	0.035
Respiratory Toxicity:	0.374

Download Data

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

Natural Product: NPC130396

Natural Product ID:	NPC130396
*Common Name:**	LFVIFYAUZBCUOY-IQIBNGDESA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	LFVIFYAUZBCUOY-IQIBNGDESA-N
Standard InCHI:	InChI=1S/C19H24O4/c1-12(2)5-7-14-9-13(6-8-17(21)22)10-15-11-16(20)19(3,4)23-18(14)15/h5-6,8-10,16,20H,7,11H2,1-4H3,(H,21,22)/b8-6+/t16-/m1/s1
SMILES:	CC(=CCc1cc(/C=C/C(=O)O)cc2C[C@H](C(C)(C)Oc12)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000123] Benzopyrans [CHEMONTID:0003410] 1-benzopyrans [CHEMONTID:0003522] 2,2-dimethyl-1-benzopyrans

*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
NPO12006	Apis mellifera	Species	Apidae	Eukaryota	n.a.	n.a.	n.a.	PMID[17548953]
NPO13379	Schizanthus tricolor	Species	Solanaceae	Eukaryota	Aerial parts	n.a.	n.a.	PMID[20166702]
NPO11266	Garcinia cambogia	Species	Clusiaceae	Eukaryota	n.a.	exocarp	n.a.	PMID[21114277]
NPO13379	Schizanthus tricolor	Species	Solanaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[21171571]
NPO12006	Apis mellifera	Species	Apidae	Eukaryota	n.a.	n.a.	n.a.	PMID[24675423]
NPO12006	Apis mellifera	Species	Apidae	Eukaryota	n.a.	Bako, Ethiopia		PMID[24926420]
NPO12006	Apis mellifera	Species	Apidae	Eukaryota	n.a.	Enemore, Ethiopia		PMID[24926420]
NPO12006	Apis mellifera	Species	Apidae	Eukaryota	n.a.	Gedo, Ethiopia		PMID[24926420]
NPO12006	Apis mellifera	Species	Apidae	Eukaryota	n.a.	Holleta, Ethiopia		PMID[24926420]
NPO3013	Clathria basilana	Species	Microcionidae	Eukaryota	n.a.	n.a.	n.a.	PMID[29094598]
NPO13473	Anodendron affine	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12006	Apis mellifera	Species	Apidae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11842	Petasites laevigatus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7541	Ormosia hosiei	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11266	Garcinia cambogia	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11842	Petasites laevigatus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11266	Garcinia cambogia	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7541	Ormosia hosiei	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13473	Anodendron affine	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7541	Ormosia hosiei	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12006	Apis mellifera	Species	Apidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14470	Polypodium decumanum	Species	Polypodiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14169	Acrocarpia paniculata	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13178	Ornithoglossum viride	Species	Colchicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13876	Cedrela salvadorensis	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13473	Anodendron affine	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9569	Licaria chrysophylla	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13379	Schizanthus tricolor	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11266	Garcinia cambogia	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7541	Ormosia hosiei	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5280	Rubia tetragona	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13669	Hertia cheirifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12006	Apis mellifera	Species	Apidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14369	Pocillopora eydouxi	Species	Pocilloporidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4700	Pertusaria truncata	Species	Pertusariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12521	Sphaeranthus confertifolius	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3013	Clathria basilana	Species	Microcionidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11842	Petasites laevigatus	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 NPC130396 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	252
0.1-0.2	1184
0.2-0.3	3406
0.3-0.4	8147
0.4-0.5	10662
0.5-0.6	4127
0.6-0.7	10556
0.7-0.8	4201
0.8-0.85	144
0.85-0.9	15
0.9-0.95	2
0.95-1	1

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 NPC130396 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	217
0.1-0.2	813
0.2-0.3	1643
0.3-0.4	2501
0.4-0.5	1970
0.5-0.6	1156
0.6-0.7	685
0.7-0.8	157
0.8-0.85	8
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