NPASS Compound

Structure

NPC481824 OpenBabel06302215382D 38 43 0 0 1 0 0 0 0 0999 V2000 -0.6340 -0.6340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 -0.1340 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.3660 -0.6340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2321 -0.1340 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.1831 -0.4430 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7709 0.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1831 1.1750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2321 0.8660 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 -2.3660 1.3660 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.3660 2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2321 2.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2321 3.8660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0981 2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9641 2.8660 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.8301 2.3660 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.6962 2.8660 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.5622 2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6962 3.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8301 4.3660 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.6222 5.3442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6277 5.4487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2210 4.5352 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9641 3.8660 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 -6.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8301 0.6340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3301 -0.2321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3301 -0.2321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8301 0.6340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3301 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 0.8660 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.5000 0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 1.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 0.0000 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 -1.0000 1.7321 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 31 1 0 0 0 0 4 3 1 1 0 0 0 4 5 1 0 0 0 0 4 8 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 1 0 0 0 9 31 1 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 14 13 1 1 0 0 0 14 15 1 0 0 0 0 14 23 1 0 0 0 0 15 16 1 0 0 0 0 15 24 1 0 0 0 0 15 30 1 1 0 0 0 16 17 1 1 0 0 0 16 18 1 0 0 0 0 19 18 1 1 0 0 0 19 20 1 0 0 0 0 19 23 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 24 29 2 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 28 29 1 0 0 0 0 31 32 1 0 0 0 0 31 38 1 1 0 0 0 32 37 2 0 0 0 0 32 33 1 0 0 0 0 33 34 2 0 0 0 0 34 35 1 0 0 0 0 35 36 2 0 0 0 0 36 37 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	516.34
Volume:	557.894
LogP:	4.305
LogD:	4.195
LogS:	-4.488
# Rotatable Bonds:	6
TPSA:	64.01
# H-Bond Aceptor:	5
# H-Bond Donor:	2
# Rings:	6
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.574
Synthetic Accessibility Score:	4.912
Fsp3:	0.606
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.783
MDCK Permeability:	2.3515183784184046e-05
Pgp-inhibitor:	0.835
Pgp-substrate:	0.997
Human Intestinal Absorption (HIA):	0.493
20% Bioavailability (F20%):	0.829
30% Bioavailability (F30%):	0.832

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.967
Plasma Protein Binding (PPB):	69.4443130493164%
Volume Distribution (VD):	1.703
Pgp-substrate:	25.56346321105957%

ADMET: Metabolism

CYP1A2-inhibitor:	0.013
CYP1A2-substrate:	0.045
CYP2C19-inhibitor:	0.042
CYP2C19-substrate:	0.894
CYP2C9-inhibitor:	0.015
CYP2C9-substrate:	0.079
CYP2D6-inhibitor:	0.994
CYP2D6-substrate:	0.909
CYP3A4-inhibitor:	0.123
CYP3A4-substrate:	0.907

ADMET: Excretion

Clearance (CL):	5.891
Half-life (T1/2):	0.046

ADMET: Toxicity

hERG Blockers:	0.949
Human Hepatotoxicity (H-HT):	0.996
Drug-inuced Liver Injury (DILI):	0.209
AMES Toxicity:	0.011
Rat Oral Acute Toxicity:	0.001
Maximum Recommended Daily Dose:	0.995
Skin Sensitization:	0.951
Carcinogencity:	0.24
Eye Corrosion:	0.003
Eye Irritation:	0.017
Respiratory Toxicity:	0.916

Download Data

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

Natural Product: NPC481824

Natural Product ID:	NPC481824
*Common Name:**	JPVGVKCBHJUCQQ-GAZPSEQRSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JPVGVKCBHJUCQQ-GAZPSEQRSA-N
Standard InCHI:	InChI=1S/C33H44N2O3/c1-23-19-27-15-9-17-34(27)30(32(23,37)25-11-5-3-6-12-25)21-29(36)22-31-33(38,26-13-7-4-8-14-26)24(2)20-28-16-10-18-35(28)31/h3-8,11-14,23-24,27-28,30-31,37-38H,9-10,15-22H2,1-2H3/t23-,24-,27+,28+,30-,31-,32+,33+/m0/s1
SMILES:	C[C@H]1C[C@H]2CCCN2[C@@H](CC(=O)C[C@H]2[C@@]([C@@H](C)C[C@H]3CCCN23)(c2ccccc2)O)[C@@]1(c1ccccc1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	127031613
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002650] Diarylheptanoids [CHEMONTID:0002651] Linear diarylheptanoids

*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
NPO6381	Dendrobium crepidatum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26710212]
NPO6381	Dendrobium crepidatum	Species	Orchidaceae	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

Activity Type	# Activity
IC50	1

Activity Type	# Activity
Cell Line	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT113	Cell Line	RAW264.7	Mus musculus	IC50	=	3600.0	nM	PMID[26710212]

☑ 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 NPC481824 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	191
0.1-0.2	891
0.2-0.3	2206
0.3-0.4	9842
0.4-0.5	20910
0.5-0.6	7906
0.6-0.7	704
0.7-0.8	42
0.8-0.85	1
0.85-0.9	1
0.9-0.95	0
0.95-1	3

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 NPC481824 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	142
0.1-0.2	463
0.2-0.3	774
0.3-0.4	1496
0.4-0.5	3569
0.5-0.6	2206
0.6-0.7	429
0.7-0.8	71
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