NPASS Compound

Structure

NPC290489 OpenBabel06302216012D 37 37 0 0 0 0 0 0 0 0999 V2000 12.1244 19.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 19.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 19.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 18.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 17.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 16.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 16.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 15.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 14.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 13.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 13.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 12.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 11.5000 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 5.1962 10.0000 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 4.3301 8.5000 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 3.4641 7.0000 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 2.5981 5.5000 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 1.7321 4.0000 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 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 O 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 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 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 -1.7321 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 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 1 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 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 2 0 0 0 0 26 28 1 0 0 0 0 28 29 2 3 0 0 0 29 30 1 0 0 0 0 30 35 2 0 0 0 0 30 31 1 0 0 0 0 31 32 2 0 0 0 0 32 33 1 0 0 0 0 33 34 2 0 0 0 0 33 37 1 0 0 0 0 34 35 1 0 0 0 0 34 36 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	516.42
Volume:	592.746
LogP:	11.474
LogD:	4.404
LogS:	-6.178
# Rotatable Bonds:	26
TPSA:	66.76
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	1
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.059
Synthetic Accessibility Score:	2.44
Fsp3:	0.727
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.382
MDCK Permeability:	8.442336365988012e-06
Pgp-inhibitor:	0.022
Pgp-substrate:	0.14
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	1.0
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.002
Plasma Protein Binding (PPB):	101.85779571533203%
Volume Distribution (VD):	6.435
Pgp-substrate:	0.46756550669670105%

ADMET: Metabolism

CYP1A2-inhibitor:	0.063
CYP1A2-substrate:	0.133
CYP2C19-inhibitor:	0.215
CYP2C19-substrate:	0.046
CYP2C9-inhibitor:	0.037
CYP2C9-substrate:	0.991
CYP2D6-inhibitor:	0.583
CYP2D6-substrate:	0.126
CYP3A4-inhibitor:	0.178
CYP3A4-substrate:	0.026

ADMET: Excretion

Clearance (CL):	5.224
Half-life (T1/2):	0.158

ADMET: Toxicity

hERG Blockers:	0.729
Human Hepatotoxicity (H-HT):	0.015
Drug-inuced Liver Injury (DILI):	0.058
AMES Toxicity:	0.092
Rat Oral Acute Toxicity:	0.019
Maximum Recommended Daily Dose:	0.129
Skin Sensitization:	0.988
Carcinogencity:	0.039
Eye Corrosion:	0.266
Eye Irritation:	0.936
Respiratory Toxicity:	0.512

Download Data

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

Natural Product: NPC290489

Natural Product ID:	NPC290489
*Common Name:**	VMRFEDBTCSVDGN-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	VMRFEDBTCSVDGN-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C33H56O4/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22-23-28-37-33(36)27-25-30-24-26-31(34)32(35)29-30/h24-27,29,34-35H,2-23,28H2,1H3
SMILES:	CCCCCCCCCCCCCCCCCCCCCCCCOC(=O)C=Cc1ccc(c(c1)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	78385378
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000476] Cinnamic acids and derivatives [CHEMONTID:0001391] Hydroxycinnamic acids and derivatives [CHEMONTID:0000059] Coumaric acids and derivatives

*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
NPO529	Thalictrum glaucum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18156	Andrographis lineata	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO529	Thalictrum glaucum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3816	Aspergillus sulphureus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22703	Lithoplocamia lithistoides	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO19115	Hoya australis	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO529	Thalictrum glaucum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18970	Baccharis patagonica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7358	Xanthoparmelia verrucigera	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18156	Andrographis lineata	Species	Acanthaceae	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 NPC290489 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	219
0.1-0.2	1196
0.2-0.3	3833
0.3-0.4	9306
0.4-0.5	9384
0.5-0.6	6460
0.6-0.7	9317
0.7-0.8	2650
0.8-0.85	247
0.85-0.9	51
0.9-0.95	24
0.95-1	10

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 NPC290489 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	189
0.1-0.2	836
0.2-0.3	1657
0.3-0.4	2705
0.4-0.5	1890
0.5-0.6	1194
0.6-0.7	606
0.7-0.8	67
0.8-0.85	6
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