NPASS Compound

Structure

NPC27878 OpenBabel06302215132D 42 46 0 0 0 0 0 0 0 0999 V2000 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 8.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 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 -2.5981 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 5.5000 0.0000 O 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 33 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 42 1 0 0 0 0 6 7 1 0 0 0 0 6 15 2 0 0 0 0 7 8 1 0 0 0 0 8 13 2 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 11 14 1 0 0 0 0 12 13 1 0 0 0 0 15 16 1 0 0 0 0 15 33 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 31 2 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 21 30 2 0 0 0 0 22 23 1 0 0 0 0 23 28 2 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 25 26 1 0 0 0 0 26 27 2 0 0 0 0 26 29 1 0 0 0 0 27 28 1 0 0 0 0 30 31 1 0 0 0 0 30 32 1 0 0 0 0 33 34 1 0 0 0 0 34 35 1 0 0 0 0 35 40 2 0 0 0 0 35 36 1 0 0 0 0 36 37 2 0 0 0 0 37 38 1 0 0 0 0 38 39 2 0 0 0 0 38 41 1 0 0 0 0 39 40 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	562.24
Volume:	601.624
LogP:	6.382
LogD:	4.182
LogS:	-3.022
# Rotatable Bonds:	10
TPSA:	110.38
# H-Bond Aceptor:	6
# H-Bond Donor:	5
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.128
Synthetic Accessibility Score:	2.743
Fsp3:	0.167
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:	-5.986
MDCK Permeability:	1.2007708392047789e-05
Pgp-inhibitor:	0.515
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.918
20% Bioavailability (F20%):	1.0
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.021
Plasma Protein Binding (PPB):	99.9275131225586%
Volume Distribution (VD):	0.344
Pgp-substrate:	1.1663674116134644%

ADMET: Metabolism

CYP1A2-inhibitor:	0.167
CYP1A2-substrate:	0.384
CYP2C19-inhibitor:	0.945
CYP2C19-substrate:	0.059
CYP2C9-inhibitor:	0.506
CYP2C9-substrate:	0.992
CYP2D6-inhibitor:	0.72
CYP2D6-substrate:	0.926
CYP3A4-inhibitor:	0.299
CYP3A4-substrate:	0.911

ADMET: Excretion

Clearance (CL):	11.752
Half-life (T1/2):	0.879

ADMET: Toxicity

hERG Blockers:	0.141
Human Hepatotoxicity (H-HT):	0.205
Drug-inuced Liver Injury (DILI):	0.172
AMES Toxicity:	0.265
Rat Oral Acute Toxicity:	0.466
Maximum Recommended Daily Dose:	0.193
Skin Sensitization:	0.94
Carcinogencity:	0.073
Eye Corrosion:	0.003
Eye Irritation:	0.902
Respiratory Toxicity:	0.019

Download Data

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

Natural Product: NPC27878

Natural Product ID:	NPC27878
*Common Name:**	MQWPGJIAXPPAMS-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	MQWPGJIAXPPAMS-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C36H34O6/c1-42-36-22-35(41)32(19-24-5-13-29(38)14-6-24)31(33(36)20-25-7-15-30(39)16-8-25)17-9-26-2-10-27(34(40)21-26)18-23-3-11-28(37)12-4-23/h2-8,10-16,21-22,37-41H,9,17-20H2,1H3
SMILES:	COc1cc(c(Cc2ccc(cc2)O)c(CCc2ccc(Cc3ccc(cc3)O)c(c2)O)c1Cc1ccc(cc1)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101845673
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002650] Diarylheptanoids [CHEMONTID:0002651] Linear diarylheptanoids [CHEMONTID:0000356] Curcuminoids

*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
NPO13319	Isodon lungshengensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10425112]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1402962]
NPO11479	Sargassum siliquastrum	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15921416]
NPO11479	Sargassum siliquastrum	Species	Sargassaceae	Eukaryota	n.a.	subtidal zone (0-2 m) off the southwestern shore of Jeju Island, Korea	2003-Apr	PMID[18817444]
NPO11479	Sargassum siliquastrum	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19006667]
NPO11479	Sargassum siliquastrum	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21377877]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	Flower Buds	n.a.	n.a.	PMID[26977531]
NPO11479	Sargassum siliquastrum	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28720331]
NPO11893	Telesto riisei	Species	Telestidae	Eukaryota	n.a.	n.a.	n.a.	PMID[7857405]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8904847]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	Bark	n.a.	n.a.	Database[FooDB]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	Essential Oil	n.a.	n.a.	Database[FooDB]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	Stem	n.a.	n.a.	Database[FooDB]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13319	Isodon lungshengensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13319	Isodon lungshengensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15591	Tolpis webbii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13511	Monopteryx inpae	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO445	Desmarestia aculeata	Species	Desmarestiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13319	Isodon lungshengensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12919	Clibadium glabrescens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8734	Centaurea pabotii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16226	Prinsepia utilis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8787	Ariocarpus scapharostrus	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11893	Telesto riisei	Species	Telestidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26125	Pseudomonas corrugata	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO14509	Stevia seleriana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13086	Streptomyces carzinostaticus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO14620	Sedum alfredi	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7186	Hypogymnia enteromorpha	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3644	Climacoptera lanata	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12597	Eria barbata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13913	Ravensara aromatica	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11479	Sargassum siliquastrum	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6224	Grindelia boliviana	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 NPC27878 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	472
0.1-0.2	2032
0.2-0.3	5057
0.3-0.4	12622
0.4-0.5	5111
0.5-0.6	4426
0.6-0.7	8401
0.7-0.8	3808
0.8-0.85	516
0.85-0.9	175
0.9-0.95	45
0.95-1	32

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 NPC27878 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	413
0.1-0.2	1058
0.2-0.3	1520
0.3-0.4	2809
0.4-0.5	1716
0.5-0.6	988
0.6-0.7	546
0.7-0.8	93
0.8-0.85	4
0.85-0.9	3
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