NPASS Compound

Structure

NPC218384 OpenBabel06302215352D 37 41 0 0 1 0 0 0 0 0999 V2000 -0.0000 2.9286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8454 2.4405 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6908 2.9286 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8454 1.4643 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 0.9762 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8454 1.4643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6908 0.9762 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6908 1.9524 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6908 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5362 -0.4881 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3816 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3816 0.9762 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.0724 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5362 1.4643 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5362 2.4405 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3816 2.9286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2270 2.4405 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0724 2.9286 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.0724 3.9048 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9178 4.3929 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4059 5.2383 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4297 5.2383 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7632 3.9048 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7632 2.9286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9178 2.4405 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.9178 1.4643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0724 0.9762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2270 1.4643 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2270 0.4881 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7632 1.9524 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7632 0.9762 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.6087 2.4405 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8454 -0.4881 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3573 -1.3335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3335 -1.3335 0.0000 C 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 -0.8454 -0.4881 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 4 1 0 0 0 0 5 4 1 6 0 0 0 5 6 1 0 0 0 0 5 36 1 0 0 0 0 6 7 1 0 0 0 0 7 14 1 0 0 0 0 7 8 1 1 0 0 0 7 9 1 0 0 0 0 9 10 1 1 0 0 0 9 33 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 28 1 0 0 0 0 12 13 1 1 0 0 0 12 14 1 0 0 0 0 14 15 1 1 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 17 28 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 6 0 0 0 18 25 1 0 0 0 0 19 20 1 0 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 25 30 1 1 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 6 0 0 0 30 31 2 0 0 0 0 30 32 1 0 0 0 0 33 34 1 0 0 0 0 33 35 1 0 0 0 0 33 36 1 0 0 0 0 36 37 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	514.37
Volume:	555.287
LogP:	6.14
LogD:	4.755
LogS:	-4.592
# Rotatable Bonds:	3
TPSA:	83.83
# H-Bond Aceptor:	5
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.314
Synthetic Accessibility Score:	4.85
Fsp3:	0.875
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:	-5.408
MDCK Permeability:	2.2936746972845867e-05
Pgp-inhibitor:	0.015
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.015
20% Bioavailability (F20%):	0.037
30% Bioavailability (F30%):	0.877

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.035
Plasma Protein Binding (PPB):	93.99951934814453%
Volume Distribution (VD):	0.768
Pgp-substrate:	3.794776678085327%

ADMET: Metabolism

CYP1A2-inhibitor:	0.007
CYP1A2-substrate:	0.141
CYP2C19-inhibitor:	0.02
CYP2C19-substrate:	0.845
CYP2C9-inhibitor:	0.224
CYP2C9-substrate:	0.84
CYP2D6-inhibitor:	0.01
CYP2D6-substrate:	0.124
CYP3A4-inhibitor:	0.262
CYP3A4-substrate:	0.369

ADMET: Excretion

Clearance (CL):	1.865
Half-life (T1/2):	0.147

ADMET: Toxicity

hERG Blockers:	0.005
Human Hepatotoxicity (H-HT):	0.29
Drug-inuced Liver Injury (DILI):	0.042
AMES Toxicity:	0.01
Rat Oral Acute Toxicity:	0.635
Maximum Recommended Daily Dose:	0.882
Skin Sensitization:	0.063
Carcinogencity:	0.042
Eye Corrosion:	0.065
Eye Irritation:	0.054
Respiratory Toxicity:	0.975

Download Data

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

Natural Product: NPC218384

Natural Product ID:	NPC218384
*Common Name:**	SLLMHUNWRZOHCM-PROZZQCMSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SLLMHUNWRZOHCM-PROZZQCMSA-N
Standard InCHI:	InChI=1S/C32H50O5/c1-19(33)37-22-18-29(6)23(28(4,5)25(22)34)11-12-31(8)24(29)10-9-20-21-17-27(2,3)13-15-32(21,26(35)36)16-14-30(20,31)7/h9,21-25,34H,10-18H2,1-8H3,(H,35,36)/t21-,22+,23-,24+,25-,29-,30+,31+,32-/m0/s1
SMILES:	CC(=O)O[C@@H]1C[C@@]2(C)[C@@H](CC[C@]3(C)[C@@H]2CC=C2[C@@H]4CC(C)(C)CC[C@@]4(CC[C@@]32C)C(=O)O)C(C)(C)[C@H]1O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	21579254
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
NPO25546	Eucalyptus occidentalis	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15104478]
NPO17475	Thermococcus kodakarensis	Species	Thermococcaceae	Archaea	n.a.	n.a.	n.a.	PMID[24610711]
NPO25342	Veronica virginica	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25546	Eucalyptus occidentalis	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17475	Thermococcus kodakarensis	Species	Thermococcaceae	Archaea	n.a.	n.a.	n.a.	Database[UNPD]
NPO24901	Ochna obtusata	Species	Ochnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16421	Chalciporus piperatus	Species	Boletaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21565	Ceramaster patagonicus	Species	Goniasteridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24432	Oxylobus oaxacanus	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO12229	Woodwardia prolifera	Species	Blechnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1646	Balsamorhiza hookeri	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO901	Flourensia ilicifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17056	Ligularia anoleuca	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11106	0thofagus dombeyi	Species	0thofagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11323	Siphonochilus aethiopicus	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23712	Gardenia lucida	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11612	Protea roupelliae	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12109	Cyathocline lyrata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25204	Millettia thonningii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22860	Veronica orientalis	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24856	Calea subcordata	Species	Asteraceae	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
EC50	9

Activity Type	# Activity
Cell Line	8
CELL-LINE	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1215	Cell Line	8505C	Homo sapiens	EC50	=	8800.0	nM	PMID[490328]
NPT1948	Cell Line	A253 cell line		EC50	=	11000.0	nM	PMID[490328]
NPT179	Cell Line	A2780	Homo sapiens	EC50	=	19900.0	nM	PMID[490328]
NPT81	Cell Line	A549	Homo sapiens	EC50	=	4300.0	nM	PMID[490328]
NPT579	Cell Line	DLD-1	Homo sapiens	EC50	=	23100.0	nM	PMID[490328]
NPT139	Cell Line	HT-29	Homo sapiens	EC50	=	10700.0	nM	PMID[490328]
NPT83	Cell Line	MCF7	Homo sapiens	EC50	=	11500.0	nM	PMID[490328]
NPT886	Cell Line	NIH3T3	Mus musculus	EC50	=	15400.0	nM	PMID[490328]
NPT24664	CELL-LINE	518A2	Homo sapiens	EC50	=	21000.0	nM	PMID[490328]

☑ 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 NPC218384 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	221
0.1-0.2	1337
0.2-0.3	4598
0.3-0.4	12544
0.4-0.5	10388
0.5-0.6	5570
0.6-0.7	5020
0.7-0.8	2226
0.8-0.85	304
0.85-0.9	323
0.9-0.95	147
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 NPC218384 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	194
0.1-0.2	1658
0.2-0.3	3803
0.3-0.4	2316
0.4-0.5	710
0.5-0.6	229
0.6-0.7	202
0.7-0.8	30
0.8-0.85	4
0.85-0.9	3
0.9-0.95	1
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