NPASS Compound

Structure

NPC480563 OpenBabel06302216122D 36 40 0 0 1 0 0 0 0 0999 V2000 -3.2502 0.4280 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3282 0.6750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0811 1.5970 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6532 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6532 -0.9545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8272 -1.4321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.9545 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8272 -1.4321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6544 -0.9546 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6544 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8272 0.4775 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8272 1.4327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6544 1.9102 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4816 1.4326 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3082 1.9102 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4590 2.4008 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3085 2.8648 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1354 3.3419 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9620 2.8643 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.9617 1.9097 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9515 1.9094 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4563 1.0523 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1348 1.4326 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.1348 0.4775 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3082 -0.0001 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4816 0.4775 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4816 -0.5032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8193 3.3590 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.3077 -0.9546 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1092 -1.8882 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2155 -0.6596 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.9091 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8720 -2.2973 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7723 -2.4701 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6443 -2.0819 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 4 2 1 1 0 0 0 4 5 1 0 0 0 0 4 29 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 29 1 0 0 0 0 7 8 1 0 0 0 0 7 33 1 6 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 26 1 0 0 0 0 10 11 1 0 0 0 0 10 30 1 1 0 0 0 11 12 1 1 0 0 0 11 29 1 0 0 0 0 12 13 1 0 0 0 0 14 13 1 6 0 0 0 14 15 1 0 0 0 0 14 26 1 0 0 0 0 15 23 1 0 0 0 0 15 16 1 6 0 0 0 15 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 19 28 1 6 0 0 0 20 21 1 0 0 0 0 20 22 1 0 0 0 0 20 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 1 0 0 0 0 30 31 2 0 0 0 0 30 32 1 0 0 0 0 33 34 2 0 0 0 0 33 35 1 0 0 0 0 35 36 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	500.35
Volume:	537.991
LogP:	5.226
LogD:	4.679
LogS:	-4.399
# Rotatable Bonds:	4
TPSA:	83.83
# H-Bond Aceptor:	5
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.354
Synthetic Accessibility Score:	4.917
Fsp3:	0.871
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
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:	-5.481
MDCK Permeability:	1.82891762960935e-05
Pgp-inhibitor:	0.024
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.062
30% Bioavailability (F30%):	0.926

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.046
Plasma Protein Binding (PPB):	85.58971405029297%
Volume Distribution (VD):	0.498
Pgp-substrate:	7.961366176605225%

ADMET: Metabolism

CYP1A2-inhibitor:	0.012
CYP1A2-substrate:	0.514
CYP2C19-inhibitor:	0.022
CYP2C19-substrate:	0.903
CYP2C9-inhibitor:	0.225
CYP2C9-substrate:	0.488
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.361
CYP3A4-inhibitor:	0.409
CYP3A4-substrate:	0.242

ADMET: Excretion

Clearance (CL):	3.215
Half-life (T1/2):	0.306

ADMET: Toxicity

hERG Blockers:	0.04
Human Hepatotoxicity (H-HT):	0.364
Drug-inuced Liver Injury (DILI):	0.014
AMES Toxicity:	0.003
Rat Oral Acute Toxicity:	0.567
Maximum Recommended Daily Dose:	0.944
Skin Sensitization:	0.129
Carcinogencity:	0.019
Eye Corrosion:	0.011
Eye Irritation:	0.035
Respiratory Toxicity:	0.952

Download Data

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

Natural Product: NPC480563

Natural Product ID:	NPC480563
*Common Name:**	RCOMNCICXWMEBP-BDCFQSRGSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	RCOMNCICXWMEBP-BDCFQSRGSA-N
Standard InCHI:	InChI=1S/C31H48O5/c1-18(2)19-10-15-30(26(35)36-7)16-17-31(25(33)34)20(24(19)30)8-9-22-28(5)13-12-23(32)27(3,4)21(28)11-14-29(22,31)6/h19-24,32H,1,8-17H2,2-7H3,(H,33,34)/t19-,20+,21-,22+,23-,24+,28-,29+,30-,31+/m0/s1
SMILES:	C=C(C)[C@@H]1CC[C@@]2(CC[C@@]3([C@H](CC[C@@H]4[C@@]5(C)CC[C@@H](C(C)(C)[C@@H]5CC[C@@]34C)O)[C@@H]12)C(=O)O)C(=O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	132487945
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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
NPO3447	Beaumontia murtonii	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28598616]
NPO40841	Eugenia operculata	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[28598616]
NPO40939	Syzygium corticosum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30057155]
NPO3447	Beaumontia murtonii	Species	Apocynaceae	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	5

Activity Type	# Activity
Cell Line	3
Individual Protein	1
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT139	Cell Line	HT-29	Homo sapiens	IC50	>	10000.0	nM	PMID[30057155]
NPT82	Cell Line	MDA-MB-231	Homo sapiens	IC50	>	10000.0	nM	PMID[30057155]
NPT2	Others	Unspecified		IC50	=	19500.0	nM	PMID[28598616]
NPT721	Individual Protein	Nuclear factor NF-kappa-B p65 subunit	Homo sapiens	IC50	=	1500.0	nM	PMID[30057155]

☑ 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 NPC480563 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	192
0.1-0.2	1586
0.2-0.3	6322
0.3-0.4	15784
0.4-0.5	6235
0.5-0.6	4852
0.6-0.7	4555
0.7-0.8	2610
0.8-0.85	425
0.85-0.9	84
0.9-0.95	33
0.95-1	19

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 NPC480563 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	170
0.1-0.2	1976
0.2-0.3	4111
0.3-0.4	1957
0.4-0.5	482
0.5-0.6	154
0.6-0.7	188
0.7-0.8	101
0.8-0.85	8
0.85-0.9	1
0.9-0.95	1
0.95-1	1

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