NPASS Compound

Structure

NPC227509 OpenBabel06302215222D 36 41 0 0 0 0 0 0 0 0999 V2000 -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 O 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 -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 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 -1.7321 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 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 -0.8660 5.5000 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 -0.0000 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 -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 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 3.4641 3.0000 0.0000 C 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 4.3301 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 2.5981 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 -0.8660 -0.5000 0.0000 O 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 2.5981 -0.5000 0.0000 O 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 -1.7321 7.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 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 16 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 36 1 0 0 0 0 6 15 2 0 0 0 0 6 7 1 0 0 0 0 7 12 2 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 10 35 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 2 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 17 30 2 0 0 0 0 17 18 1 0 0 0 0 18 27 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 26 2 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 23 24 1 0 0 0 0 23 34 1 0 0 0 0 24 25 2 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 2 0 0 0 0 28 33 1 0 0 0 0 29 30 1 0 0 0 0 30 31 1 0 0 0 0 31 32 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	226.07
Volume:	228.854
LogP:	2.549
LogD:	2.374
LogS:	-3.639
# Rotatable Bonds:	2
TPSA:	54.98
# H-Bond Aceptor:	4
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.683
Synthetic Accessibility Score:	2.542
Fsp3:	0.077
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	2
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.901
MDCK Permeability:	8.991549293568823e-06
Pgp-inhibitor:	0.0
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.007
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.184

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.947
Plasma Protein Binding (PPB):	86.3133773803711%
Volume Distribution (VD):	1.086
Pgp-substrate:	11.402259826660156%

ADMET: Metabolism

CYP1A2-inhibitor:	0.992
CYP1A2-substrate:	0.949
CYP2C19-inhibitor:	0.471
CYP2C19-substrate:	0.375
CYP2C9-inhibitor:	0.396
CYP2C9-substrate:	0.894
CYP2D6-inhibitor:	0.669
CYP2D6-substrate:	0.794
CYP3A4-inhibitor:	0.551
CYP3A4-substrate:	0.302

ADMET: Excretion

Clearance (CL):	4.78
Half-life (T1/2):	0.545

ADMET: Toxicity

hERG Blockers:	0.029
Human Hepatotoxicity (H-HT):	0.664
Drug-inuced Liver Injury (DILI):	0.886
AMES Toxicity:	0.263
Rat Oral Acute Toxicity:	0.895
Maximum Recommended Daily Dose:	0.66
Skin Sensitization:	0.83
Carcinogencity:	0.734
Eye Corrosion:	0.409
Eye Irritation:	0.972
Respiratory Toxicity:	0.982

Download Data

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

Natural Product: NPC227509

Natural Product ID:	NPC227509
*Common Name:**	RBVCTUJCRSUBKB-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	RBVCTUJCRSUBKB-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C30H22O6/c1-35-25-13-23(33)27-19-9-5-17(31)11-15(19)3-7-21(27)29(25)30-22-8-4-16-12-18(32)6-10-20(16)28(22)24(34)14-26(30)36-2/h3-14,31-34H,1-2H3
SMILES:	COc1cc(c2c3ccc(cc3ccc2c1c1c2ccc3cc(ccc3c2c(cc1OC)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000025] Phenanthrenes and derivatives [CHEMONTID:0003007] Phenanthrols

*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]
NPO10780	Bletilla striata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15686910]
NPO10780	Bletilla striata	Species	Orchidaceae	Eukaryota	Fibrous Roots	n.a.	n.a.	PMID[25760525]
NPO10780	Bletilla striata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31415170]
NPO11893	Telesto riisei	Species	Telestidae	Eukaryota	n.a.	n.a.	n.a.	PMID[7857405]
NPO13319	Isodon lungshengensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10780	Bletilla striata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10780	Bletilla striata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13319	Isodon lungshengensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10780	Bletilla striata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO10780	Bletilla striata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO8734	Centaurea pabotii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10780	Bletilla striata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7186	Hypogymnia enteromorpha	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11893	Telesto riisei	Species	Telestidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12597	Eria barbata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26125	Pseudomonas corrugata	Species	Pseudomonadaceae	Bacteria	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]
NPO3644	Climacoptera lanata	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13913	Ravensara aromatica	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6224	Grindelia boliviana	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]
NPO445	Desmarestia aculeata	Species	Desmarestiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12919	Clibadium glabrescens	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]
NPO13319	Isodon lungshengensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14509	Stevia seleriana	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 NPC227509 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	564
0.1-0.2	2097
0.2-0.3	5494
0.3-0.4	12586
0.4-0.5	4787
0.5-0.6	4488
0.6-0.7	8426
0.7-0.8	3617
0.8-0.85	447
0.85-0.9	122
0.9-0.95	41
0.95-1	28

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 NPC227509 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	472
0.1-0.2	1032
0.2-0.3	1616
0.3-0.4	2809
0.4-0.5	1672
0.5-0.6	984
0.6-0.7	479
0.7-0.8	81
0.8-0.85	3
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