NPASS Compound

Structure

NPC4467 OpenBabel06302216032D 32 35 0 0 1 0 0 0 0 0999 V2000 -1.4775 -2.8795 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1685 -3.8305 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1903 -4.0385 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4788 -3.2953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4570 -3.5032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1261 -2.7601 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.8692 -3.4292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 -1.8090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4049 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 -0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.4593 0.4135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 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 -0.8660 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 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 -3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0981 2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0981 2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 2 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 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7071 0.7071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0772 -2.4511 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8376 -4.5737 0.0000 C 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 32 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 6 7 1 6 0 0 0 6 31 1 0 0 0 0 8 6 1 6 0 0 0 8 9 1 0 0 0 0 8 13 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 29 1 0 0 0 0 11 12 1 1 0 0 0 11 13 1 0 0 0 0 13 14 1 1 0 0 0 14 15 1 0 0 0 0 16 15 1 1 0 0 0 16 17 1 0 0 0 0 16 29 1 0 0 0 0 17 26 1 0 0 0 0 17 18 1 6 0 0 0 17 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 21 23 1 0 0 0 0 23 24 1 0 0 0 0 23 25 1 0 0 0 0 23 26 1 0 0 0 0 26 27 1 6 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	442.38
Volume:	505.518
LogP:	7.011
LogD:	5.507
LogS:	-5.877
# Rotatable Bonds:	4
TPSA:	37.3
# H-Bond Aceptor:	2
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.452
Synthetic Accessibility Score:	4.649
Fsp3:	0.9
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:	-4.954
MDCK Permeability:	1.0704756277846172e-05
Pgp-inhibitor:	0.234
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.984
30% Bioavailability (F30%):	0.977

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.212
Plasma Protein Binding (PPB):	95.12030792236328%
Volume Distribution (VD):	1.096
Pgp-substrate:	1.636434555053711%

ADMET: Metabolism

CYP1A2-inhibitor:	0.066
CYP1A2-substrate:	0.399
CYP2C19-inhibitor:	0.138
CYP2C19-substrate:	0.959
CYP2C9-inhibitor:	0.195
CYP2C9-substrate:	0.696
CYP2D6-inhibitor:	0.062
CYP2D6-substrate:	0.434
CYP3A4-inhibitor:	0.493
CYP3A4-substrate:	0.401

ADMET: Excretion

Clearance (CL):	7.076
Half-life (T1/2):	0.127

ADMET: Toxicity

hERG Blockers:	0.052
Human Hepatotoxicity (H-HT):	0.498
Drug-inuced Liver Injury (DILI):	0.021
AMES Toxicity:	0.002
Rat Oral Acute Toxicity:	0.041
Maximum Recommended Daily Dose:	0.401
Skin Sensitization:	0.927
Carcinogencity:	0.094
Eye Corrosion:	0.726
Eye Irritation:	0.784
Respiratory Toxicity:	0.97

Download Data

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

Natural Product: NPC4467

Natural Product ID:	NPC4467
*Common Name:**	NJICGAVMYWKCMW-HSUNHJJFSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	NJICGAVMYWKCMW-HSUNHJJFSA-N
Standard InCHI:	InChI=1S/C30H50O2/c1-20(2)10-9-16-30(8,32)22-13-18-28(6)21(22)11-12-24-27(5)17-15-25(31)26(3,4)23(27)14-19-29(24,28)7/h10,21-24,32H,9,11-19H2,1-8H3/t21-,22+,23+,24+,27+,28-,29-,30+/m1/s1
SMILES:	CC(=CCC[C@@](C)([C@H]1CC[C@]2(C)[C@@H]1CC[C@H]1[C@@]3(C)CCC(=O)C(C)(C)[C@@H]3CC[C@@]21C)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	12309262
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
NPO4240	Elephantopus tomentosus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10075766]
NPO20523	Bacillus subtilis	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	PMID[11112781]
NPO20523	Bacillus subtilis	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	PMID[153409]
NPO658	Leucopaxillus gentianeus	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15568769]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[16309325]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	Seoul, Korea	2000-Jun	PMID[16643034]
NPO658	Leucopaxillus gentianeus	Species	Tricholomataceae	Eukaryota	fruiting bodies	n.a.	n.a.	PMID[17190463]
NPO28092	Xyris pterygoblephara	Species	Xyridaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17870137]
NPO4240	Elephantopus tomentosus	Species	Asteraceae	Eukaryota	n.a.	stem	n.a.	PMID[18239317]
NPO4240	Elephantopus tomentosus	Species	Asteraceae	Eukaryota	n.a.	root	n.a.	PMID[18239317]
NPO28092	Xyris pterygoblephara	Species	Xyridaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18462007]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	fruit	n.a.	n.a.	PMID[18505286]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	fruit	n.a.	n.a.	PMID[19650637]
NPO20523	Bacillus subtilis	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	PMID[21673922]
NPO20523	Bacillus subtilis	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	PMID[23265519]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	fruits	n.a.	n.a.	PMID[23305920]
NPO20523	Bacillus subtilis	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	PMID[23317005]
NPO20523	Bacillus subtilis	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	PMID[23488669]
NPO20523	Bacillus subtilis	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	PMID[27524650]
NPO20523	Bacillus subtilis	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	PMID[29115831]
NPO21679	Nuphar lutea	Species	Nymphaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31182315]
NPO20523	Bacillus subtilis	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	PMID[31287310]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32141747]
NPO21679	Nuphar lutea	Species	Nymphaeaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO5723	Quercus robur	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO963	Litsea pungens	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4240	Elephantopus tomentosus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4240	Elephantopus tomentosus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO963	Litsea pungens	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19984	Turpinia ternata	Species	Staphyleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10613	Thalictrum longistylum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21679	Nuphar lutea	Species	Nymphaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5723	Quercus robur	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO963	Litsea pungens	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO5723	Quercus robur	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9930	Dendrodoris tuberculosa	Species	Dendrodorididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10613	Thalictrum longistylum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11949	Iris ensata	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12677	Penicillium kapuscinskii	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8808	Artemisia schimperi	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6259	Keiferia lycopersicella	Species	Gelechiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7050	Picea mariana	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12081	Streptomyces xanthochromogenes	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO12893	Dermolepida albohirtum	Species	Scarabaeidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13002	Petasites georgicus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4544	Gomortega keule	Species	Gomortegaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7347	Viguiera oblongifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11558	Atylosia trinervia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO658	Leucopaxillus gentianeus	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21679	Nuphar lutea	Species	Nymphaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO963	Litsea pungens	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20523	Bacillus subtilis	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO4240	Elephantopus tomentosus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8492	Viburnum urceolatum	Species	Adoxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11709	Salvia parryi	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27848	Conoideocrella luteorostrata	Species	Clavicipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12317	Naja kaouthia	Species	Elapidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28092	Xyris pterygoblephara	Species	Xyridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19984	Turpinia ternata	Species	Staphyleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8777	Euryops algoensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1038	Phoenix loureiroi	Species	Arecaceae	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 NPC4467 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	149
0.1-0.2	1225
0.2-0.3	6562
0.3-0.4	16155
0.4-0.5	6684
0.5-0.6	5906
0.6-0.7	4039
0.7-0.8	1730
0.8-0.85	202
0.85-0.9	40
0.9-0.95	4
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 NPC4467 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	148
0.1-0.2	1525
0.2-0.3	4279
0.3-0.4	2193
0.4-0.5	558
0.5-0.6	150
0.6-0.7	137
0.7-0.8	125
0.8-0.85	22
0.85-0.9	11
0.9-0.95	2
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