NPASS Compound

Structure

NPC209644 OpenBabel06302215472D 36 43 0 0 1 0 0 0 0 0999 V2000 2.2302 0.6025 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2995 0.6027 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.4755 1.0787 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0003 1.9027 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.4760 2.7267 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3000 2.2507 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4757 1.7752 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4754 0.8236 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2993 0.3475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1236 0.8230 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.9474 0.3470 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7716 0.8225 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5954 0.3465 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5951 -0.6050 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4190 -1.0810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2431 -0.6055 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.7809 -0.1068 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7264 0.6245 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 7.5505 1.1000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1205 1.0379 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4196 0.8220 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.2434 0.3459 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7.0676 0.8214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0679 1.7729 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2441 2.2489 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4199 1.7734 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.7710 -1.0804 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.9471 -0.6044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1239 1.7746 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 0.9515 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.4753 0.1272 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8240 1.4272 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6480 0.9515 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6480 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8240 -0.4757 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 6 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 32 1 0 0 0 0 5 6 1 0 0 0 0 6 29 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 30 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 6 0 0 0 10 29 1 0 0 0 0 11 28 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 21 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 14 27 2 0 0 0 0 16 15 1 6 0 0 0 16 17 1 0 0 0 0 16 22 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 1 0 0 0 18 20 1 0 0 0 0 21 20 1 6 0 0 0 21 26 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 1 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 27 28 1 0 0 0 0 30 36 1 0 0 0 0 30 31 1 6 0 0 0 30 32 1 0 0 0 0 32 33 1 1 0 0 0 33 34 1 0 0 0 0 34 35 1 0 0 0 0 35 36 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	486.37
Volume:	527.018
LogP:	6.303
LogD:	4.512
LogS:	-4.47
# Rotatable Bonds:	1
TPSA:	49.31
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	8
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.515
Synthetic Accessibility Score:	6.655
Fsp3:	0.812
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-5.646
MDCK Permeability:	3.278135636719526e-06
Pgp-inhibitor:	0.006
Pgp-substrate:	0.997
Human Intestinal Absorption (HIA):	0.675
20% Bioavailability (F20%):	0.998
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.278
Plasma Protein Binding (PPB):	73.70600891113281%
Volume Distribution (VD):	1.276
Pgp-substrate:	28.40192985534668%

ADMET: Metabolism

CYP1A2-inhibitor:	0.023
CYP1A2-substrate:	0.277
CYP2C19-inhibitor:	0.15
CYP2C19-substrate:	0.888
CYP2C9-inhibitor:	0.18
CYP2C9-substrate:	0.253
CYP2D6-inhibitor:	0.645
CYP2D6-substrate:	0.892
CYP3A4-inhibitor:	0.889
CYP3A4-substrate:	0.642

ADMET: Excretion

Clearance (CL):	12.062
Half-life (T1/2):	0.019

ADMET: Toxicity

hERG Blockers:	0.839
Human Hepatotoxicity (H-HT):	0.635
Drug-inuced Liver Injury (DILI):	0.725
AMES Toxicity:	0.199
Rat Oral Acute Toxicity:	0.606
Maximum Recommended Daily Dose:	0.994
Skin Sensitization:	0.954
Carcinogencity:	0.212
Eye Corrosion:	0.003
Eye Irritation:	0.006
Respiratory Toxicity:	0.84

Download Data

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

Natural Product: NPC209644

Natural Product ID:	NPC209644
*Common Name:**	JOBCREJXGBQGLZ-KTEXCLGESA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JOBCREJXGBQGLZ-KTEXCLGESA-N
Standard InCHI:	InChI=1S/C32H46N4/c1-19-12-22-15-30-26(31(16-19)24(22)5-3-9-34-31)7-8-28(36-30)23-13-27-29(33-18-23)14-21-11-20(2)17-32(27)25(21)6-4-10-35-32/h13,18-22,24-25,28,34-36H,3-12,14-17H2,1-2H3/t19-,20-,21+,22+,24-,25-,28-,31-,32-/m0/s1
SMILES:	C[C@H]1C[C@@H]2CC3=C(CC[C@@H](c4cc5c(C[C@H]6C[C@H](C)C[C@@]75[C@H]6CCCN7)nc4)N3)[C@]3(C1)[C@H]2CCCN3
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001550] Sesquiterpenoids

*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
NPO19825	Litsea japonica	Species	Lauraceae	Eukaryota	leaves	n.a.	n.a.	PMID[14575444]
NPO16934	Nephthea chabrolii	Species	Nephtheidae	Eukaryota	n.a.	Formosan soft coral	n.a.	PMID[16309317]
NPO7688	Artemisia selengensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[Article]
NPO19076	Gaillardia pulchella	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19364	Aconitum chasmanthum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19076	Gaillardia pulchella	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19364	Aconitum chasmanthum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19076	Gaillardia pulchella	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18499	Podium complanatum	Species	Sphecidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11060	Doris luteorosea	Species	Dorididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17577	Azalea ovata	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO9799	Hebeloma longicaudum	Species	Cortinariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19234	Hymenopappus newberryi	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19298	Gerbera crocea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17341	Gambeya africana	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO7688	Artemisia selengensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17887	Penstemon centranthifolius	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19696	Othonna quercifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18023	Vitex quinata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21360	Cordia corymbosa	Species	Cordiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19076	Gaillardia pulchella	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19869	Fusicolla aquaeductuum	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19565	Crocus chrysanthus	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15450	Minuria leptophylla	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19364	Aconitum chasmanthum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16934	Nephthea chabrolii	Species	Nephtheidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18518	Haematomma nemetzii	Species	Haematommataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19825	Litsea japonica	Species	Lauraceae	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 NPC209644 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	992
0.1-0.2	7401
0.2-0.3	23239
0.3-0.4	6048
0.4-0.5	2620
0.5-0.6	1760
0.6-0.7	587
0.7-0.8	44
0.8-0.85	2
0.85-0.9	0
0.9-0.95	1
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 NPC209644 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	435
0.1-0.2	636
0.2-0.3	1372
0.3-0.4	2401
0.4-0.5	2530
0.5-0.6	1382
0.6-0.7	358
0.7-0.8	36
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