NPASS Compound

Structure

NPC5503 OpenBabel06302215592D 23 24 0 0 0 0 0 0 0 0999 V2000 2.5981 -2.5000 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 0.8660 -2.5000 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 -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 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 -4.3301 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 0.5000 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 -5.1962 2.0000 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 -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 0.8660 0.5000 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 -0.8660 -2.5000 0.0000 O 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 -4.0000 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 18 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 21 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 8 17 2 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 11 16 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 15 16 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 21 22 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	308.18
Volume:	351.148
LogP:	5.759
LogD:	4.362
LogS:	-6.165
# Rotatable Bonds:	6
TPSA:	18.46
# H-Bond Aceptor:	2
# H-Bond Donor:	0
# Rings:	2
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.526
Synthetic Accessibility Score:	2.196
Fsp3:	0.238
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:	-4.783
MDCK Permeability:	1.7409529391443357e-05
Pgp-inhibitor:	0.993
Pgp-substrate:	0.008
Human Intestinal Absorption (HIA):	0.008
20% Bioavailability (F20%):	0.012
30% Bioavailability (F30%):	0.379

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.089
Plasma Protein Binding (PPB):	92.64179992675781%
Volume Distribution (VD):	2.323
Pgp-substrate:	5.17300271987915%

ADMET: Metabolism

CYP1A2-inhibitor:	0.96
CYP1A2-substrate:	0.903
CYP2C19-inhibitor:	0.967
CYP2C19-substrate:	0.522
CYP2C9-inhibitor:	0.843
CYP2C9-substrate:	0.925
CYP2D6-inhibitor:	0.31
CYP2D6-substrate:	0.874
CYP3A4-inhibitor:	0.665
CYP3A4-substrate:	0.488

ADMET: Excretion

Clearance (CL):	10.861
Half-life (T1/2):	0.194

ADMET: Toxicity

hERG Blockers:	0.484
Human Hepatotoxicity (H-HT):	0.383
Drug-inuced Liver Injury (DILI):	0.842
AMES Toxicity:	0.186
Rat Oral Acute Toxicity:	0.014
Maximum Recommended Daily Dose:	0.066
Skin Sensitization:	0.846
Carcinogencity:	0.158
Eye Corrosion:	0.004
Eye Irritation:	0.176
Respiratory Toxicity:	0.033

Download Data

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

Natural Product: NPC5503

Natural Product ID:	NPC5503
*Common Name:**	NNMRGAKKWWIQTM-VAWYXSNFSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	NNMRGAKKWWIQTM-VAWYXSNFSA-N
Standard InCHI:	InChI=1S/C21H24O2/c1-16(2)10-13-19-20(22-3)14-18(15-21(19)23-4)12-11-17-8-6-5-7-9-17/h5-12,14-15H,13H2,1-4H3/b12-11+
SMILES:	CC(=CCc1c(cc(/C=C/c2ccccc2)cc1OC)OC)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	18546438
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000253] Stilbenes

*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
NPO5702	Brosimum rubescens	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9358642]
NPO2463	Anemone rivularis	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4666	Canarium samoense	Species	Strombidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7481	Callicarpa nudiflora	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9899	Ceanothus americanus	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10268	Tessmannia densiflora	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17250	Schnabelia terniflora	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2985	Illicium parviflorum	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6854	Podocarpus elongatus	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3193	Derris rariflora	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5702	Brosimum rubescens	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7296	Cynometra ananta	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2463	Anemone rivularis	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1497	Capnophyllum peregrinum	Species	Apiaceae	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 NPC5503 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	453
0.1-0.2	1879
0.2-0.3	5329
0.3-0.4	13851
0.4-0.5	3669
0.5-0.6	6183
0.6-0.7	8278
0.7-0.8	2559
0.8-0.85	394
0.85-0.9	80
0.9-0.95	20
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 NPC5503 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	400
0.1-0.2	1051
0.2-0.3	1447
0.3-0.4	2790
0.4-0.5	1743
0.5-0.6	1059
0.6-0.7	549
0.7-0.8	102
0.8-0.85	8
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