NPASS Compound

Structure

NPC490061 OpenBabel06302216222D 30 32 0 0 1 0 0 0 0 0999 V2000 -4.4823 4.1723 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7913 3.2213 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -5.7695 3.0134 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4386 3.7565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1296 4.7076 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -6.7987 5.4507 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1515 4.9155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2004 4.6065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9435 3.9373 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8424 5.8666 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1222 2.4781 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -3.1277 2.5827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7210 1.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 C 0 0 3 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 -5.1962 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -5.3246 1.6045 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 C 0 0 3 0 0 0 0 0 0 0 0 0 0.0000 -3.0000 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 -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 C 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 2 11 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 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 7 10 1 0 0 0 0 11 19 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 19 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 15 21 2 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 21 22 1 0 0 0 0 22 23 2 0 0 0 0 23 29 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 25 27 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	416.33
Volume:	468.34
LogP:	4.042
LogD:	3.97
LogS:	-4.788
# Rotatable Bonds:	6
TPSA:	60.69
# H-Bond Aceptor:	3
# H-Bond Donor:	3
# Rings:	3
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.52
Synthetic Accessibility Score:	4.585
Fsp3:	0.778
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:	-4.768
MDCK Permeability:	2.970273453684058e-05
Pgp-inhibitor:	0.701
Pgp-substrate:	0.004
Human Intestinal Absorption (HIA):	0.007
20% Bioavailability (F20%):	0.009
30% Bioavailability (F30%):	0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.439
Plasma Protein Binding (PPB):	95.54338836669922%
Volume Distribution (VD):	1.293
Pgp-substrate:	2.089824676513672%

ADMET: Metabolism

CYP1A2-inhibitor:	0.063
CYP1A2-substrate:	0.198
CYP2C19-inhibitor:	0.048
CYP2C19-substrate:	0.512
CYP2C9-inhibitor:	0.263
CYP2C9-substrate:	0.063
CYP2D6-inhibitor:	0.01
CYP2D6-substrate:	0.13
CYP3A4-inhibitor:	0.209
CYP3A4-substrate:	0.423

ADMET: Excretion

Clearance (CL):	10.018
Half-life (T1/2):	0.098

ADMET: Toxicity

hERG Blockers:	0.051
Human Hepatotoxicity (H-HT):	0.824
Drug-inuced Liver Injury (DILI):	0.04
AMES Toxicity:	0.031
Rat Oral Acute Toxicity:	0.827
Maximum Recommended Daily Dose:	0.95
Skin Sensitization:	0.656
Carcinogencity:	0.105
Eye Corrosion:	0.003
Eye Irritation:	0.007
Respiratory Toxicity:	0.961

Download Data

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

Natural Product: NPC490061

Natural Product ID:	NPC490061
*Common Name:**	24,25-Dihydroxyvitamin D3
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	FCKJYANJHNLEEP-NGHQTVFFSA-N
Standard InCHI:	InChI=1S/C27H44O3/c1-18-8-12-22(28)17-21(18)11-10-20-7-6-16-27(5)23(13-14-24(20)27)19(2)9-15-25(29)26(3,4)30/h10-11,19,22-25,28-30H,1,6-9,12-17H2,2-5H3/b20-10-,21-11+
SMILES:	CC(CCC(O)C(C)(C)O)C1CCC2C(CCCC12C)=C/C=C1CC(O)CCC1=C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001460] Vitamin D 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
NPO27293	Sus scrofa	Species	Suidae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO27293	Sus scrofa	Species	Suidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27293	Sus scrofa	Species	Suidae	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
NPO27293	NPC490061	Raw	n.a.	0.00051	n.a.	n.a.	mg/100g	Database [DTU]
NPO27293	NPC490061	n.a.	n.a.	0.00075	n.a.	n.a.	mg/100g	Database [DTU]

☑ 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 NPC490061 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

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 NPC490061 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

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