NPASS Compound

Structure

NPC25872 OpenBabel06302216062D 24 26 0 0 1 0 0 0 0 0999 V2000 0.9481 1.5089 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8584 0.5129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6115 -0.1450 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2185 -1.0646 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.2335 -2.0645 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0919 -1.5516 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.9504 -1.0387 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8238 -1.5256 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8387 -2.5255 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.3516 -3.3840 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9803 -3.0384 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.1069 -2.5514 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9952 -4.0383 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 4.8386 -2.5106 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2225 -0.9749 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.4010 -1.7568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4010 -1.7568 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.0245 -0.9749 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.9800 -0.6802 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8019 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9010 0.4339 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.7575 -1.6551 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8349 -2.6577 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 22 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 6 0 0 0 4 6 1 0 0 0 0 4 15 1 0 0 0 0 6 7 1 6 0 0 0 6 12 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 1 0 0 0 9 11 1 0 0 0 0 9 14 1 0 0 0 0 11 12 1 0 0 0 0 11 13 1 6 0 0 0 15 16 1 6 0 0 0 15 22 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 17 24 1 6 0 0 0 18 19 1 6 0 0 0 18 20 1 0 0 0 0 18 23 1 0 0 0 0 20 21 1 0 0 0 0 22 21 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	400.16
Volume:	371.825
LogP:	3.586
LogD:	3.374
LogS:	-3.667
# Rotatable Bonds:	1
TPSA:	60.69
# H-Bond Aceptor:	3
# H-Bond Donor:	3
# Rings:	3
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.463
Synthetic Accessibility Score:	4.898
Fsp3:	0.9
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.735
MDCK Permeability:	1.1563298357941676e-05
Pgp-inhibitor:	0.013
Pgp-substrate:	0.145
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.014
30% Bioavailability (F30%):	0.011

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.679
Plasma Protein Binding (PPB):	78.8786392211914%
Volume Distribution (VD):	0.725
Pgp-substrate:	18.385883331298828%

ADMET: Metabolism

CYP1A2-inhibitor:	0.026
CYP1A2-substrate:	0.591
CYP2C19-inhibitor:	0.055
CYP2C19-substrate:	0.823
CYP2C9-inhibitor:	0.172
CYP2C9-substrate:	0.091
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.096
CYP3A4-inhibitor:	0.566
CYP3A4-substrate:	0.685

ADMET: Excretion

Clearance (CL):	9.058
Half-life (T1/2):	0.268

ADMET: Toxicity

hERG Blockers:	0.035
Human Hepatotoxicity (H-HT):	0.354
Drug-inuced Liver Injury (DILI):	0.095
AMES Toxicity:	0.012
Rat Oral Acute Toxicity:	0.491
Maximum Recommended Daily Dose:	0.454
Skin Sensitization:	0.308
Carcinogencity:	0.507
Eye Corrosion:	0.393
Eye Irritation:	0.061
Respiratory Toxicity:	0.972

Download Data

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

Natural Product: NPC25872

Natural Product ID:	NPC25872
*Common Name:**	JPCOLXANIJAXTB-IHRHECOVSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JPCOLXANIJAXTB-IHRHECOVSA-N
Standard InCHI:	InChI=1S/C20H33BrO3/c1-12-11-18(2,13-5-7-19(3,23)16(21)9-13)15-10-17(22)20(4,24)8-6-14(12)15/h13-17,22-24H,1,5-11H2,2-4H3/t13-,14-,15-,16-,17+,18+,19+,20+/m1/s1
SMILES:	C=C1C[C@@](C)([C@@H]2CC[C@@](C)([C@@H](C2)Br)O)[C@@H]2C[C@@H]([C@](C)(CC[C@H]12)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11143863
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000129] Alcohols and polyols [CHEMONTID:0001661] Secondary alcohols [CHEMONTID:0002647] Cyclohexanols

*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
NPO8821	Delphinium dictyocarpum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8821	Delphinium dictyocarpum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2491	Laurencia obtusa	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO666	Cymbidium aloifolium	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5527	Ligularia atroviolacea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10341	Pseudogymnoascus pannorum	Species	Pseudeurotiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2491	Laurencia obtusa	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8821	Delphinium dictyocarpum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1054	Peucedanum graveolens	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18938	Ladeania juncea	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15600	Trifolium pannonicum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13493	Mauremys reevesii	Species	Geoemydidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2329	Scutellaria glabra	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1221	Juniperus serawschanica	Species	Cupressaceae	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 NPC25872 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	165
0.1-0.2	2746
0.2-0.3	16644
0.3-0.4	10337
0.4-0.5	8297
0.5-0.6	3915
0.6-0.7	569
0.7-0.8	23
0.8-0.85	1
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 NPC25872 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	176
0.1-0.2	3391
0.2-0.3	4161
0.3-0.4	951
0.4-0.5	263
0.5-0.6	181
0.6-0.7	27
0.7-0.8	0
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