NPASS Compound

Structure

NPC122415 OpenBabel06302215282D 34 39 0 0 1 0 0 0 0 0999 V2000 -0.8444 -2.1762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.6887 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -2.6637 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9750 -1.6887 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4625 -0.8444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4375 -0.8444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9250 -1.6887 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9000 -1.6887 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3875 -0.8444 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.3625 -0.8444 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.8750 -1.6887 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8500 -1.6887 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8250 -1.6887 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3125 -0.8444 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.8250 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6694 0.4875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8250 0.9750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8500 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.3625 0.8444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3875 0.8444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.9250 1.6887 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9250 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4125 0.8444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4375 0.8444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4625 0.8444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9750 -0.0000 0.0000 C 0 0 1 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 -0.4875 -0.8444 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.4625 -0.8444 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 0.9750 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9750 0.9750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6644 1.6644 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.2875 -0.8444 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 29 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 5 1 0 0 0 0 5 27 1 0 0 0 0 5 6 2 0 0 0 0 6 23 1 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 9 8 1 1 0 0 0 9 10 1 0 0 0 0 9 21 1 0 0 0 0 10 18 1 0 0 0 0 10 11 1 1 0 0 0 10 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 14 34 1 6 0 0 0 15 16 1 0 0 0 0 15 17 1 0 0 0 0 15 18 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 27 26 1 6 0 0 0 27 32 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 28 31 1 1 0 0 0 29 30 1 6 0 0 0 31 32 1 0 0 0 0 32 33 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	468.32
Volume:	503.349
LogP:	5.269
LogD:	4.467
LogS:	-5.423
# Rotatable Bonds:	0
TPSA:	66.76
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	6
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.456
Synthetic Accessibility Score:	5.678
Fsp3:	0.833
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.273
MDCK Permeability:	2.8276897864998318e-05
Pgp-inhibitor:	0.99
Pgp-substrate:	0.006
Human Intestinal Absorption (HIA):	0.008
20% Bioavailability (F20%):	0.958
30% Bioavailability (F30%):	0.964

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.06
Plasma Protein Binding (PPB):	93.10059356689453%
Volume Distribution (VD):	1.15
Pgp-substrate:	5.904553413391113%

ADMET: Metabolism

CYP1A2-inhibitor:	0.011
CYP1A2-substrate:	0.144
CYP2C19-inhibitor:	0.06
CYP2C19-substrate:	0.902
CYP2C9-inhibitor:	0.198
CYP2C9-substrate:	0.09
CYP2D6-inhibitor:	0.013
CYP2D6-substrate:	0.08
CYP3A4-inhibitor:	0.717
CYP3A4-substrate:	0.806

ADMET: Excretion

Clearance (CL):	9.359
Half-life (T1/2):	0.024

ADMET: Toxicity

hERG Blockers:	0.471
Human Hepatotoxicity (H-HT):	0.232
Drug-inuced Liver Injury (DILI):	0.032
AMES Toxicity:	0.024
Rat Oral Acute Toxicity:	0.816
Maximum Recommended Daily Dose:	0.928
Skin Sensitization:	0.059
Carcinogencity:	0.036
Eye Corrosion:	0.003
Eye Irritation:	0.014
Respiratory Toxicity:	0.981

Download Data

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

Natural Product: NPC122415

Natural Product ID:	NPC122415
*Common Name:**	GGPUTPVILFAMBK-WWDUYRIUSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	GGPUTPVILFAMBK-WWDUYRIUSA-N
Standard InCHI:	InChI=1S/C30H44O4/c1-25(2)16-18-17-8-9-20-27(5)12-11-21(31)26(3,4)19(27)10-13-29(20,7)28(17,6)14-15-30(18)23(22(25)32)34-24(30)33/h8-9,19-23,31-32H,10-16H2,1-7H3/t19-,20+,21+,22+,23+,27-,28+,29+,30-/m0/s1
SMILES:	CC1(C)CC2=C3C=C[C@@H]4[C@@]5(C)CC[C@H](C(C)(C)[C@@H]5CC[C@@]4(C)[C@]3(C)CC[C@]32[C@@H]([C@H]1O)OC3=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101967008
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000050] Lactones [CHEMONTID:0001243] Beta propiolactones

*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
NPO25976	Dendronephthya gigantea	Species	Nephtheidae	Eukaryota	n.a.	n.a.	n.a.	PMID[10843584]
NPO27252	Iochroma australe	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12027740]
NPO26782	Dendrilla membranosa	Species	Darwinellidae	Eukaryota	n.a.	antarctic	n.a.	PMID[15270575]
NPO25976	Dendronephthya gigantea	Species	Nephtheidae	Eukaryota	n.a.	n.a.	n.a.	PMID[15497934]
NPO25976	Dendronephthya gigantea	Species	Nephtheidae	Eukaryota	n.a.	n.a.	n.a.	PMID[30407007]
NPO26163	Anisodus tanguticus	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25821	Delphinium cashmerianum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25717	Maytenus hookeri	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26163	Anisodus tanguticus	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2039	Callerya cinerea	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26719	Tetrapanax papyrifer	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29051	Ranunculus acris	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25717	Maytenus hookeri	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25821	Delphinium cashmerianum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25717	Maytenus hookeri	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO25997	Senecio rupestris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14466	Penicillium olsonii	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19823	Vicia benghalensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25952	Lastrea thelypteris	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO26980	Halocarpus biformis	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25926	Tephrosia pumila	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26719	Tetrapanax papyrifer	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25873	Thaminophyllum multiflorum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26109	Pilocarpus spicatus	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26727	Eremocarpus setiger	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO26625	Stichopus chloronotus	Species	Stichopodidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24378	Osmanthus heterophyllus	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26408	Melanophryniscus moreirae	Species	Bufonidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26352	Heuchera cylindrica	Species	Saxifragaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26678	Calea pilosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3346	Piper sanctum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26535	Balanus glandula	Species	Balanidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11845	Petrorhagia dubia	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25849	Streptomyces lomondensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO18292	Guarea trichilioides	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25793	Gremmeniella abietina	Species	Helotiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29051	Ranunculus acris	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26289	Lecidella chodati	Species	Lecanoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26952	Cineraria geifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26053	Pluchea suaveolens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26377	Amelanchier vulgaris	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26453	Prunus lusitanica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25821	Delphinium cashmerianum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27377	Diaporthe helianthi	Species	Diaporthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26186	Stereocaulon leprocauloides	Species	Stereocaulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26563	Alectoria japonica	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26884	Helichrysum davenportii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26026	Vitis silvestris	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25741	Aster ageratoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25976	Dendronephthya gigantea	Species	Nephtheidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13781	Eremostachys moluccelloides	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26430	Aplysina laevis	Species	Aplysinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7214	Bufotes viridis	Species	Bufonidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25717	Maytenus hookeri	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26163	Anisodus tanguticus	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27252	Iochroma australe	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26782	Dendrilla membranosa	Species	Darwinellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26754	Stevia connata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26078	Mussaenda parviflora	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2344	Carlina acanthifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2039	Callerya cinerea	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26244	Panax papyrifer	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO137	Nepeta multifida	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26135	Walsura tubulata	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26213	Tephrosia vogelii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26903	Plectranthus purpuratus	Species	Lamiaceae	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 NPC122415 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	235
0.1-0.2	1246
0.2-0.3	4214
0.3-0.4	9369
0.4-0.5	13616
0.5-0.6	6904
0.6-0.7	5294
0.7-0.8	1668
0.8-0.85	135
0.85-0.9	16
0.9-0.95	0
0.95-1	0

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 NPC122415 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	209
0.1-0.2	1426
0.2-0.3	3594
0.3-0.4	2555
0.4-0.5	892
0.5-0.6	288
0.6-0.7	168
0.7-0.8	18
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