NPASS Compound

Structure

NPC275175 OpenBabel06302216202D 31 34 0 0 1 0 0 0 0 0999 V2000 0.8474 -7.3071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0037 -6.8204 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0035 -5.8464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8468 -5.3591 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8465 -4.3851 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6899 -3.8979 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 2.5336 -4.3847 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6896 -2.9239 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 2.5327 -2.4362 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5324 -1.4618 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8448 -1.4622 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8445 -0.4622 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0003 -0.9750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8440 -1.4627 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8437 -2.4371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0008 -2.9244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8451 -2.4366 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8454 -3.4366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6885 -0.9755 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6882 -1.9755 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5322 -1.4632 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3761 -0.9760 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3764 -0.0010 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -2.5328 0.4868 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5330 1.4868 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3988 0.9868 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6888 -0.0005 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.8445 0.4873 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2425 0.4990 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8396 -7.3076 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 31 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 0 0 0 0 6 8 1 0 0 0 0 8 17 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 17 1 0 0 0 0 11 12 1 1 0 0 0 11 13 1 0 0 0 0 13 29 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 14 19 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 6 0 0 0 19 27 1 0 0 0 0 19 20 1 6 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 23 30 1 0 0 0 0 24 25 1 0 0 0 0 24 26 1 0 0 0 0 24 27 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	426.39
Volume:	496.727
LogP:	7.248
LogD:	5.268
LogS:	-6.403
# Rotatable Bonds:	4
TPSA:	20.23
# H-Bond Aceptor:	1
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	1

MedChem Properties

QED Drug-Likeness Score:	0.447
Synthetic Accessibility Score:	4.582
Fsp3:	0.867
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:	-4.849
MDCK Permeability:	9.394335393153597e-06
Pgp-inhibitor:	0.217
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.936
30% Bioavailability (F30%):	0.941

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.332
Plasma Protein Binding (PPB):	97.0927505493164%
Volume Distribution (VD):	3.127
Pgp-substrate:	1.215941071510315%

ADMET: Metabolism

CYP1A2-inhibitor:	0.045
CYP1A2-substrate:	0.446
CYP2C19-inhibitor:	0.109
CYP2C19-substrate:	0.967
CYP2C9-inhibitor:	0.142
CYP2C9-substrate:	0.646
CYP2D6-inhibitor:	0.04
CYP2D6-substrate:	0.431
CYP3A4-inhibitor:	0.48
CYP3A4-substrate:	0.612

ADMET: Excretion

Clearance (CL):	10.788
Half-life (T1/2):	0.009

ADMET: Toxicity

hERG Blockers:	0.033
Human Hepatotoxicity (H-HT):	0.273
Drug-inuced Liver Injury (DILI):	0.056
AMES Toxicity:	0.003
Rat Oral Acute Toxicity:	0.031
Maximum Recommended Daily Dose:	0.472
Skin Sensitization:	0.473
Carcinogencity:	0.02
Eye Corrosion:	0.071
Eye Irritation:	0.354
Respiratory Toxicity:	0.587

Download Data

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

Natural Product: NPC275175

Natural Product ID:	NPC275175
*Common Name:**	CAHGCLMLTWQZNJ-CJCXBBMPSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	CAHGCLMLTWQZNJ-CJCXBBMPSA-N
Standard InCHI:	InChI=1S/C30H50O/c1-20(2)10-9-11-21(3)22-14-18-30(8)24-12-13-25-27(4,5)26(31)16-17-28(25,6)23(24)15-19-29(22,30)7/h10,21-22,25-26,31H,9,11-19H2,1-8H3/t21?,22?,25?,26?,28-,29-,30+/m1/s1
SMILES:	CC(=CCCC(C)C1CC[C@@]2(C)C3=C(CC[C@]12C)[C@@]1(C)CCC(C(C)(C)C1CC3)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	44135612
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
NPO7732	Solanum melongena	Species	Solanaceae	Eukaryota	n.a.	root	n.a.	DOI[10.1271/bbb1961.42.623]
NPO12170	Solanum indicum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11575964]
NPO17823	Lycium chinense	Species	Solanaceae	Eukaryota	fruits	n.a.	n.a.	PMID[12467621]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	fruit	n.a.	PMID[12802735]
NPO17823	Lycium chinense	Species	Solanaceae	Eukaryota	n.a.	root	n.a.	PMID[16212233]
NPO14304.1	Physalis alkekengi var. franchetii	Varieties	Solanaceae	Eukaryota	calyces	Yilan, Heilongjiang Province, China	2004-SEP	PMID[18348534]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	fruit	n.a.	PMID[18384095]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	leaf	n.a.	PMID[22014120]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	fruit	n.a.	PMID[22014120]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	leaf	n.a.	PMID[22014168]
NPO17823	Lycium chinense	Species	Solanaceae	Eukaryota	root bark	n.a.	n.a.	PMID[23282106]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23540838]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24295708]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	leaf	n.a.	PMID[25102361]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	fruit	n.a.	PMID[25306330]
NPO17823	Lycium chinense	Species	Solanaceae	Eukaryota	Root Bark	n.a.	n.a.	PMID[26982999]
NPO1085	Peganum harmala	Species	Nitrariaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[28128938]
NPO7732	Solanum melongena	Species	Solanaceae	Eukaryota	Roots	n.a.	n.a.	PMID[31742403]
NPO1085	Peganum harmala	Species	Nitrariaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6736972]
NPO17823	Lycium chinense	Species	Solanaceae	Eukaryota	fruits	n.a.	n.a.	PMID[9090870]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO7732	Solanum melongena	Species	Solanaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO7732	Solanum melongena	Species	Solanaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO7732	Solanum melongena	Species	Solanaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	Oil	n.a.	n.a.	Database[FooDB]
NPO7732	Solanum melongena	Species	Solanaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO21485	Polygala sibirica	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27456	Euphorbia pulcherrima	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1085	Peganum harmala	Species	Nitrariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4174	Dioscorea deltoidea	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO30509	Solanum indicum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO30073	Costus speciosus	Species	Costaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21462	Lannea grandis	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7732	Solanum melongena	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17823	Lycium chinense	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3354	Fomes officinalis	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14304.1	Physalis alkekengi var. franchetii	Varieties	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO118	Ustilago maydis	Species	Ustilaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7732	Solanum melongena	Species	Solanaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO1085	Peganum harmala	Species	Nitrariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12170	Solanum indicum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17823	Lycium chinense	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21485	Polygala sibirica	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3354	Fomes officinalis	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7732	Solanum melongena	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14304.1	Physalis alkekengi var. franchetii	Varieties	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27456	Euphorbia pulcherrima	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO118	Ustilago maydis	Species	Ustilaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21651	Cheilocostus speciosus	Species	Costaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4174	Dioscorea deltoidea	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21462	Lannea grandis	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7732	Solanum melongena	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO30073	Costus speciosus	Species	Costaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21462	Lannea grandis	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO30509	Solanum indicum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21485	Polygala sibirica	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO17823	Lycium chinense	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO1085	Peganum harmala	Species	Nitrariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21485	Polygala sibirica	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO17823	Lycium chinense	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO27456	Euphorbia pulcherrima	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4174	Dioscorea deltoidea	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21485	Polygala sibirica	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7732	Solanum melongena	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17823	Lycium chinense	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1085	Peganum harmala	Species	Nitrariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21651	Cheilocostus speciosus	Species	Costaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12170	Solanum indicum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3354	Fomes officinalis	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO118	Ustilago maydis	Species	Ustilaginaceae	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 NPC275175 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	152
0.1-0.2	1450
0.2-0.3	8409
0.3-0.4	15641
0.4-0.5	6760
0.5-0.6	5897
0.6-0.7	3171
0.7-0.8	961
0.8-0.85	160
0.85-0.9	61
0.9-0.95	19
0.95-1	16

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 NPC275175 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	155
0.1-0.2	1829
0.2-0.3	4501
0.3-0.4	1940
0.4-0.5	333
0.5-0.6	160
0.6-0.7	169
0.7-0.8	51
0.8-0.85	10
0.85-0.9	2
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