NPASS Compound

Structure

NPC258867 OpenBabel06302215412D 34 39 0 0 1 0 0 0 0 0999 V2000 0.8182 -0.8074 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8182 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.5268 0.4091 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5268 1.2273 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.2354 1.6364 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9440 1.2272 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6526 1.6363 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6527 2.4545 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.3613 2.8636 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.3612 2.0698 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0699 2.4545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7785 2.8636 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7785 3.6818 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.0699 4.0909 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.4669 4.7784 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6730 4.7784 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8792 4.7785 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3613 3.6818 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.6527 4.0910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9441 3.6819 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9441 2.8637 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.5691 3.6576 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2355 2.4546 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.2355 3.2485 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5269 2.8637 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8183 2.4547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8182 1.6364 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.1190 2.0402 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1096 1.2274 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.1096 0.4091 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2995 0.5188 0.0000 O 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 -0.4037 -0.6992 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.4660 4.0787 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 6 0 0 0 2 30 1 0 0 0 0 2 32 1 0 0 0 0 2 3 1 0 0 0 0 4 3 1 6 0 0 0 4 5 1 0 0 0 0 4 27 1 0 0 0 0 5 23 1 0 0 0 0 5 6 2 0 0 0 0 6 7 1 0 0 0 0 8 7 1 1 0 0 0 8 9 1 0 0 0 0 8 21 1 0 0 0 0 9 18 1 0 0 0 0 9 10 1 1 0 0 0 9 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 13 34 1 1 0 0 0 14 15 1 6 0 0 0 14 16 1 0 0 0 0 14 18 1 0 0 0 0 16 17 1 0 0 0 0 18 19 1 1 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 1 0 0 0 21 23 1 0 0 0 0 23 24 1 6 0 0 0 23 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 1 0 0 0 27 29 1 0 0 0 0 29 30 1 6 0 0 0 29 31 1 0 0 0 0 31 32 1 0 0 0 0 32 33 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	470.34
Volume:	505.985
LogP:	4.847
LogD:	4.005
LogS:	-4.873
# Rotatable Bonds:	1
TPSA:	66.76
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	6
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.383
Synthetic Accessibility Score:	5.915
Fsp3:	0.9
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:	-5.239
MDCK Permeability:	2.442524055368267e-05
Pgp-inhibitor:	0.767
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.173
30% Bioavailability (F30%):	0.839

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.427
Plasma Protein Binding (PPB):	95.24358367919922%
Volume Distribution (VD):	1.031
Pgp-substrate:	3.9201996326446533%

ADMET: Metabolism

CYP1A2-inhibitor:	0.023
CYP1A2-substrate:	0.202
CYP2C19-inhibitor:	0.033
CYP2C19-substrate:	0.892
CYP2C9-inhibitor:	0.124
CYP2C9-substrate:	0.059
CYP2D6-inhibitor:	0.03
CYP2D6-substrate:	0.125
CYP3A4-inhibitor:	0.792
CYP3A4-substrate:	0.618

ADMET: Excretion

Clearance (CL):	5.747
Half-life (T1/2):	0.265

ADMET: Toxicity

hERG Blockers:	0.536
Human Hepatotoxicity (H-HT):	0.282
Drug-inuced Liver Injury (DILI):	0.041
AMES Toxicity:	0.006
Rat Oral Acute Toxicity:	0.59
Maximum Recommended Daily Dose:	0.931
Skin Sensitization:	0.453
Carcinogencity:	0.183
Eye Corrosion:	0.054
Eye Irritation:	0.025
Respiratory Toxicity:	0.977

Download Data

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

Natural Product: NPC258867

Natural Product ID:	NPC258867
*Common Name:**	AXIVEZBRJDDWRQ-ZRZJEJNWSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	AXIVEZBRJDDWRQ-ZRZJEJNWSA-N
Standard InCHI:	InChI=1S/C30H46O4/c1-25-15-19-18-7-8-21-27(3)11-10-22(32)28(4,17-31)20(27)9-12-30(21,6)29(18,5)14-13-26(19,2)23(16-25)34-24(25)33/h7,19-23,31-32H,8-17H2,1-6H3/t19-,20+,21+,22-,23+,25+,26+,27-,28+,29+,30+/m0/s1
SMILES:	C[C@@]12C[C@H]3C4=CC[C@@H]5[C@@]6(C)CC[C@@H]([C@](C)(CO)[C@@H]6CC[C@@]5(C)[C@]4(C)CC[C@@]3(C)[C@@H](C1)OC2=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	102482971
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
NPO784	Sinapis alba	Species	Brassicaceae	Eukaryota	n.a.	seed	n.a.	DOI[10.1007/s11418-005-0009-z]
NPO1086	Botrytis cinerea	Species	Sclerotiniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10691704]
NPO1086	Botrytis cinerea	Species	Sclerotiniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16378371]
NPO1086	Botrytis cinerea	Species	Sclerotiniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16643065]
NPO8025	Aaptos ciliata	Species	Suberitidae	Eukaryota	n.a.	n.a.	n.a.	PMID[18257536]
NPO5325	Lobophytum durum	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[19177635]
NPO5325	Lobophytum durum	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[19433363]
NPO2765	Oxytropis falcata	Species	Fabaceae	Eukaryota	n.a.	Sunan County, Gansu Province, China	2006-JUN	PMID[20684529]
NPO5608	Croton gratissimus	Species	Euphorbiaceae	Eukaryota	n.a.	stem	n.a.	PMID[22032651]
NPO5608	Croton gratissimus	Species	Euphorbiaceae	Eukaryota	n.a.	leaf	n.a.	PMID[22032651]
NPO2765	Oxytropis falcata	Species	Fabaceae	Eukaryota	whole plant	Guide County, Qinghai Province, China	2008-AUG	PMID[22775441]
NPO8257	Carpha glomerata	Species	Cyperaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30219526]
NPO1086	Botrytis cinerea	Species	Sclerotiniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32705864]
NPO784	Sinapis alba	Species	Brassicaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO784	Sinapis alba	Species	Brassicaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO784	Sinapis alba	Species	Brassicaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO3344	Bryonia alba	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2921	Angelica acutiloba	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1473	Xanthorhiza simplicissima	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7845	Tephrosia elata	Species	Geometridae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6859	Eurycoma harmandiana	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO784	Sinapis alba	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO784	Sinapis alba	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8790	Cyanostegia angustifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3344	Bryonia alba	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2131	Dactylorhiza viridis	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7845	Tephrosia elata	Species	Geometridae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO373	Viburnum erubescens	Species	Adoxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2921	Angelica acutiloba	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1473	Xanthorhiza simplicissima	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6859	Eurycoma harmandiana	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2921	Angelica acutiloba	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7845	Tephrosia elata	Species	Geometridae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO784	Sinapis alba	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO1473	Xanthorhiza simplicissima	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO2921	Angelica acutiloba	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO784	Sinapis alba	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9594	Lysimachia fordiana	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1473	Xanthorhiza simplicissima	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2439	Diplopterygium glaucum	Species	Gleicheniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6859	Eurycoma harmandiana	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3151	Solanum lanceolatum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2131	Dactylorhiza viridis	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9737	Ampelocera edentula	Species	Ulmaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10038.1	Abies pinsapo var. marocana	Varieties	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6065	Brassica carinata	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8257	Carpha glomerata	Species	Cyperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8790	Cyanostegia angustifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5086	Alternaria macrospora	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9867	Ixeris debilis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO784	Sinapis alba	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1086	Botrytis cinerea	Species	Sclerotiniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2765	Oxytropis falcata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8938	Halobacillus litoralis	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO7032	Marasmiellus troyanus	Species	Omphalotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3344	Bryonia alba	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4536	Remirea maritima	Species	Cyperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7845	Tephrosia elata	Species	Geometridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13474	Euphrasia genargentea	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21472	Pterolobium hexapetalum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10132	Schizophyllum lobatum	Species	Schizophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO593	Wikstroemia viridiflora	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8025	Aaptos ciliata	Species	Suberitidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9998	Abies excelsa	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7418	Eucalyptus resinifera	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3838	Chrysosporum ovalisporum	Species	Aphanizomenonaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO5608	Croton gratissimus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1293	Streptomyces matensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO6807	Ranunculus asiaticus	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5857	Achlya heterosexualis	Species	Saprolegniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5325	Lobophytum durum	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4123	Trididemnum cyanophorum	Species	Didemnidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9091	Orthosiphon spicatus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2670	Maytenus chuchuhuasha	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO373	Viburnum erubescens	Species	Adoxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2921	Angelica acutiloba	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4901	Arnica mollis	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

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 NPC258867 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	193
0.1-0.2	1185
0.2-0.3	4757
0.3-0.4	13078
0.4-0.5	9069
0.5-0.6	5650
0.6-0.7	4480
0.7-0.8	3645
0.8-0.85	337
0.85-0.9	201
0.9-0.95	98
0.95-1	4

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 NPC258867 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	157
0.1-0.2	1457
0.2-0.3	3934
0.3-0.4	2397
0.4-0.5	697
0.5-0.6	191
0.6-0.7	191
0.7-0.8	115
0.8-0.85	5
0.85-0.9	6
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