NPASS Compound

Structure

NPC291289 OpenBabel06302215572D 45 44 0 0 0 0 0 0 0 0999 V2000 19.0526 -8.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 18.1865 -7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 18.1865 -6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 17.3205 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 17.3205 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 16.4545 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 16.4545 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 15.5885 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 15.5885 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 14.7224 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 14.7224 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.8564 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.8564 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 12.9904 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 12.1244 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.1244 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 12.1244 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.9904 -3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.1244 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.1244 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.9904 -6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.9904 -7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.8564 -8.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.8564 -9.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 14.7224 -9.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 14.7224 -10.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 15.5885 -11.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -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 2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 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 1 2 1 0 0 0 0 2 3 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 7 8 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 12 1 0 0 0 0 12 13 2 0 0 0 0 12 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 32 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 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 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 30 31 1 0 0 0 0 32 33 1 0 0 0 0 33 34 2 0 0 0 0 33 35 1 0 0 0 0 35 36 1 0 0 0 0 36 37 1 0 0 0 0 37 38 1 0 0 0 0 38 39 1 0 0 0 0 39 40 1 0 0 0 0 40 41 1 0 0 0 0 41 42 1 0 0 0 0 42 43 1 0 0 0 0 43 44 1 0 0 0 0 44 45 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	638.55
Volume:	727.932
LogP:	12.643
LogD:	5.505
LogS:	-6.795
# Rotatable Bonds:	38
TPSA:	78.9
# H-Bond Aceptor:	6
# H-Bond Donor:	0
# Rings:	0
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.039
Synthetic Accessibility Score:	2.338
Fsp3:	0.923
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.979
MDCK Permeability:	3.2942746202024864e-06
Pgp-inhibitor:	0.0
Pgp-substrate:	0.017
Human Intestinal Absorption (HIA):	0.002
20% Bioavailability (F20%):	0.999
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.003
Plasma Protein Binding (PPB):	97.68248748779297%
Volume Distribution (VD):	1.986
Pgp-substrate:	0.8702353835105896%

ADMET: Metabolism

CYP1A2-inhibitor:	0.026
CYP1A2-substrate:	0.123
CYP2C19-inhibitor:	0.119
CYP2C19-substrate:	0.036
CYP2C9-inhibitor:	0.027
CYP2C9-substrate:	0.935
CYP2D6-inhibitor:	0.241
CYP2D6-substrate:	0.002
CYP3A4-inhibitor:	0.209
CYP3A4-substrate:	0.028

ADMET: Excretion

Clearance (CL):	4.876
Half-life (T1/2):	0.109

ADMET: Toxicity

hERG Blockers:	0.32
Human Hepatotoxicity (H-HT):	0.009
Drug-inuced Liver Injury (DILI):	0.256
AMES Toxicity:	0.007
Rat Oral Acute Toxicity:	0.007
Maximum Recommended Daily Dose:	0.01
Skin Sensitization:	0.984
Carcinogencity:	0.06
Eye Corrosion:	0.971
Eye Irritation:	0.878
Respiratory Toxicity:	0.329

Download Data

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

Natural Product: NPC291289

Natural Product ID:	NPC291289
*Common Name:**	VMPHSYLJUKZBJJ-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	VMPHSYLJUKZBJJ-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C39H74O6/c1-4-7-10-13-16-19-22-25-28-31-37(40)43-34-36(45-39(42)33-30-27-24-21-18-15-12-9-6-3)35-44-38(41)32-29-26-23-20-17-14-11-8-5-2/h36H,4-35H2,1-3H3
SMILES:	CCCCCCCCCCCC(=O)OCC(COC(=O)CCCCCCCCCCC)OC(=O)CCCCCCCCCCC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10851
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000175] Glycerolipids [CHEMONTID:0003815] Triradylcglycerols [CHEMONTID:0001135] Triacylglycerols

*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
NPO15351	Streptomyces prunicolor	Species	Streptomycetaceae	Bacteria	n.a.	mycelium	n.a.	DOI[10.1021/np50098a008]
NPO6541	Scrophularia buergeriana	Species	Scrophulariaceae	Eukaryota	roots	n.a.	n.a.	PMID[12444706]
NPO11898	Lobophora variegata	Species	Dictyotaceae	Eukaryota	n.a.	at depths of 630 m at El Mdano (Tenerife, Canary Islands)	n.a.	PMID[26126835]
NPO5247	Elaphoglossum lindbergii	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26689830]
NPO6541	Scrophularia buergeriana	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12853	Leucocarpus perfoliatus	Species	Phrymaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12633	Rapanea neurophylla	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10530	Aconitum subcuneatum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10530	Aconitum subcuneatum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12853	Leucocarpus perfoliatus	Species	Phrymaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12633	Rapanea neurophylla	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6541	Scrophularia buergeriana	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11206	Trifolium hybridum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10530	Aconitum subcuneatum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO6541	Scrophularia buergeriana	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO6541	Scrophularia buergeriana	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1044	Caiman crocodilus	Species	Alligatoridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10530	Aconitum subcuneatum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11898	Lobophora variegata	Species	Dictyotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1116	Periconia atropurpurea	Species	Periconiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5714	Rogeria adenophylla	Species	Pedaliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11527	Ibacus peronii	Species	Scyllaridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5247	Elaphoglossum lindbergii	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15351	Streptomyces prunicolor	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO12633	Rapanea neurophylla	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9363	Ferula ammoniacum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2996	Pistacia atlantica	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6541	Scrophularia buergeriana	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7560	Tachardia acaciae	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO2207	Sphaerella rubella	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO9606	Castanea dentata	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11206	Trifolium hybridum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12146	Stemodia maritima	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23883	Penicillium abidjanum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12853	Leucocarpus perfoliatus	Species	Phrymaceae	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 NPC291289 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	914
0.1-0.2	7865
0.2-0.3	18240
0.3-0.4	10407
0.4-0.5	4208
0.5-0.6	812
0.6-0.7	171
0.7-0.8	58
0.8-0.85	13
0.85-0.9	8
0.9-0.95	0
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 NPC291289 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	1320
0.1-0.2	4801
0.2-0.3	1969
0.3-0.4	699
0.4-0.5	275
0.5-0.6	67
0.6-0.7	12
0.7-0.8	3
0.8-0.85	0
0.85-0.9	3
0.9-0.95	0
0.95-1	1

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