NPASS Compound

Structure

NPC19123 OpenBabel06302215312D 32 35 0 0 1 0 0 0 0 0999 V2000 0.0023 -4.8828 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8478 -4.3943 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6936 -4.8823 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8475 -3.4179 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6930 -2.9294 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0017 -2.9299 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0015 -1.9534 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8470 -1.4649 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6927 -1.9529 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8467 -0.4885 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6919 0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6916 0.9773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 0.9769 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8470 1.4653 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8472 2.4428 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6939 2.9313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6942 3.9313 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5403 2.4423 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3864 2.9308 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2322 2.4418 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2319 1.4644 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3858 0.9759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5400 1.4649 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5397 0.4649 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6933 0.9764 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6931 -0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8464 -0.4890 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 0.0003 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0984 2.9415 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8443 -1.4654 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8438 -3.4183 0.0000 O 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 4 1 0 0 0 0 4 5 1 1 0 0 0 4 6 1 0 0 0 0 6 7 1 0 0 0 0 6 32 1 1 0 0 0 7 8 1 0 0 0 0 7 31 1 6 0 0 0 8 9 1 6 0 0 0 10 8 1 6 0 0 0 10 11 1 0 0 0 0 10 28 1 0 0 0 0 11 12 1 0 0 0 0 13 12 1 6 0 0 0 13 14 1 0 0 0 0 13 28 1 0 0 0 0 14 15 1 1 0 0 0 14 25 1 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 16 18 1 0 0 0 0 18 19 1 6 0 0 0 18 23 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 20 30 1 6 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 6 0 0 0 23 25 1 0 0 0 0 25 26 1 6 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	448.36
Volume:	491.143
LogP:	4.54
LogD:	4.643
LogS:	-4.754
# Rotatable Bonds:	5
TPSA:	77.76
# H-Bond Aceptor:	4
# H-Bond Donor:	3
# Rings:	4
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.563
Synthetic Accessibility Score:	4.824
Fsp3:	0.964
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-4.749
MDCK Permeability:	1.595711182744708e-05
Pgp-inhibitor:	0.99
Pgp-substrate:	0.988
Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.942
30% Bioavailability (F30%):	0.83

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.235
Plasma Protein Binding (PPB):	95.38369750976562%
Volume Distribution (VD):	0.925
Pgp-substrate:	1.964221477508545%

ADMET: Metabolism

CYP1A2-inhibitor:	0.058
CYP1A2-substrate:	0.366
CYP2C19-inhibitor:	0.017
CYP2C19-substrate:	0.864
CYP2C9-inhibitor:	0.058
CYP2C9-substrate:	0.071
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.097
CYP3A4-inhibitor:	0.284
CYP3A4-substrate:	0.249

ADMET: Excretion

Clearance (CL):	14.908
Half-life (T1/2):	0.237

ADMET: Toxicity

hERG Blockers:	0.406
Human Hepatotoxicity (H-HT):	0.3
Drug-inuced Liver Injury (DILI):	0.336
AMES Toxicity:	0.015
Rat Oral Acute Toxicity:	0.433
Maximum Recommended Daily Dose:	0.094
Skin Sensitization:	0.623
Carcinogencity:	0.3
Eye Corrosion:	0.168
Eye Irritation:	0.049
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: NPC19123

Natural Product ID:	NPC19123
*Common Name:**	SBSXXCCMIWEPEE-GZKYLSGOSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SBSXXCCMIWEPEE-GZKYLSGOSA-N
Standard InCHI:	InChI=1S/C28H48O4/c1-15(2)16(3)25(31)26(32)17(4)20-7-8-21-19-14-24(30)23-13-18(29)9-11-28(23,6)22(19)10-12-27(20,21)5/h15-23,25-26,29,31-32H,7-14H2,1-6H3/t16-,17-,18-,19-,20+,21-,22-,23+,25+,26+,27+,28+/m0/s1
SMILES:	CC(C)[C@H](C)[C@H]([C@@H]([C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC(=O)[C@H]4C[C@H](CC[C@]4(C)[C@H]3CC[C@]12C)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	13475125
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001445] Bile acids, alcohols and derivatives [CHEMONTID:0002194] Hydroxy bile acids, alcohols and derivatives [CHEMONTID:0001104] Trihydroxy bile acids, alcohols 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
NPO7904	Ganoderma applanatum	Species	Polyporaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/S0031-9422(00)91122-1]
NPO88	Rheum undulatum	Species	Polygonaceae	Eukaryota	rhizome	n.a.	n.a.	PMID[10714491]
NPO7904	Ganoderma applanatum	Species	Polyporaceae	Eukaryota	n.a.	Sri Lankan	n.a.	PMID[16933889]
NPO5105	Lagenaria siceraria	Species	Cucurbitaceae	Eukaryota	n.a.	stem	n.a.	PMID[18310955]
NPO7539	Raphanus sativus	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24176362]
NPO7539	Raphanus sativus	Species	Brassicaceae	Eukaryota	seeds	n.a.	n.a.	PMID[25466198]
NPO1533	Corynespora cassiicola	Species	Corynesporascaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25594263]
NPO1533	Corynespora cassiicola	Species	Corynesporascaceae	Eukaryota	n.a.	Xisha Islands coral reef in the South China Sea	2009-DEC	PMID[25594263]
NPO7904	Ganoderma applanatum	Species	Polyporaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27996259]
NPO7539	Raphanus sativus	Species	Brassicaceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO5105	Lagenaria siceraria	Species	Cucurbitaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO5105	Lagenaria siceraria	Species	Cucurbitaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO7539	Raphanus sativus	Species	Brassicaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO5105	Lagenaria siceraria	Species	Cucurbitaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO7539	Raphanus sativus	Species	Brassicaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO5105	Lagenaria siceraria	Species	Cucurbitaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO7539	Raphanus sativus	Species	Brassicaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO4947	Tagetes minuta	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6454	Delphinium tatsienense	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7539	Raphanus sativus	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7904	Ganoderma applanatum	Species	Polyporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6454	Delphinium tatsienense	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7539	Raphanus sativus	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4947	Tagetes minuta	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5314	Sargassum parvivesiculosum	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7539	Raphanus sativus	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5105	Lagenaria siceraria	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO6454	Delphinium tatsienense	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7904	Ganoderma applanatum	Species	Polyporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO88	Rheum undulatum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO7539	Raphanus sativus	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1533	Corynespora cassiicola	Species	Corynesporascaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4947	Tagetes minuta	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2553	Adenocarpus commutatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO88	Rheum undulatum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7604	Viguiera lanceolata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5403	Fagus menziesii	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16088	Streptomyces scabiei	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO7539	Raphanus sativus	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8197	Scrophularia deserti	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6454	Delphinium tatsienense	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2247	Iphiona scabra	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO421	Polygonum maritimum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23693	Alseodaphne semecarpifolia	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7759	Penicillium nalgiovensis	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7904	Ganoderma applanatum	Species	Polyporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5105	Lagenaria siceraria	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4112	Ficus fistulosa	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3111	Daphnandra micrantha	Species	Atherospermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5260	Osteospermum thodei	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5314	Sargassum parvivesiculosum	Species	Sargassaceae	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 NPC19123 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	314
0.1-0.2	2954
0.2-0.3	12074
0.3-0.4	12216
0.4-0.5	5822
0.5-0.6	5035
0.6-0.7	3235
0.7-0.8	862
0.8-0.85	107
0.85-0.9	52
0.9-0.95	25
0.95-1	1

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 NPC19123 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	357
0.1-0.2	3428
0.2-0.3	3677
0.3-0.4	1056
0.4-0.5	234
0.5-0.6	214
0.6-0.7	141
0.7-0.8	18
0.8-0.85	6
0.85-0.9	15
0.9-0.95	4
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