NPASS Compound

Structure

NPC121126 OpenBabel06302216192D 33 37 0 0 1 0 0 0 0 0999 V2000 -1.7441 0.0472 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7441 1.0069 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5752 1.4868 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4064 1.0069 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4064 0.0472 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5752 -0.4327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5752 -1.4396 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2379 -0.4330 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0696 0.0472 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9011 -1.3928 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7326 -1.8730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7326 -2.8328 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9009 -3.3130 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0697 -2.8332 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0694 -1.8730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2379 -1.3928 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9010 -4.3130 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.5986 -3.3327 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0693 1.0074 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9353 1.5076 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2381 1.4872 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8720 1.5104 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.0069 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8720 1.5104 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7441 1.0069 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7441 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8720 -0.5035 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8720 -1.5104 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7441 -2.0139 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6161 -0.5035 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6161 1.5104 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8720 2.5173 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 22 1 0 0 0 0 3 4 1 0 0 0 0 4 21 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 8 1 0 0 0 0 6 7 1 0 0 0 0 8 16 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 9 19 1 0 0 0 0 10 15 2 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 12 18 1 0 0 0 0 13 14 2 0 0 0 0 13 17 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 19 20 2 0 0 0 0 19 21 1 0 0 0 0 23 22 1 1 0 0 0 23 24 1 0 0 0 0 23 30 1 0 0 0 0 24 25 1 0 0 0 0 24 33 1 6 0 0 0 25 26 1 0 0 0 0 25 32 1 1 0 0 0 26 27 1 0 0 0 0 26 31 1 6 0 0 0 27 28 1 1 0 0 0 27 30 1 0 0 0 0 28 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	462.08
Volume:	413.381
LogP:	0.59
LogD:	0.431
LogS:	-3.967
# Rotatable Bonds:	3
TPSA:	203.42
# H-Bond Aceptor:	12
# H-Bond Donor:	7
# Rings:	5
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.159
Synthetic Accessibility Score:	4.189
Fsp3:	0.286
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.336
MDCK Permeability:	1.1320408702886198e-05
Pgp-inhibitor:	0.002
Pgp-substrate:	0.989
Human Intestinal Absorption (HIA):	0.787
20% Bioavailability (F20%):	0.026
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.016
Plasma Protein Binding (PPB):	81.1207275390625%
Volume Distribution (VD):	0.769
Pgp-substrate:	22.843887329101562%

ADMET: Metabolism

CYP1A2-inhibitor:	0.545
CYP1A2-substrate:	0.096
CYP2C19-inhibitor:	0.02
CYP2C19-substrate:	0.054
CYP2C9-inhibitor:	0.082
CYP2C9-substrate:	0.318
CYP2D6-inhibitor:	0.071
CYP2D6-substrate:	0.177
CYP3A4-inhibitor:	0.043
CYP3A4-substrate:	0.008

ADMET: Excretion

Clearance (CL):	4.921
Half-life (T1/2):	0.816

ADMET: Toxicity

hERG Blockers:	0.041
Human Hepatotoxicity (H-HT):	0.441
Drug-inuced Liver Injury (DILI):	0.988
AMES Toxicity:	0.659
Rat Oral Acute Toxicity:	0.016
Maximum Recommended Daily Dose:	0.033
Skin Sensitization:	0.891
Carcinogencity:	0.06
Eye Corrosion:	0.003
Eye Irritation:	0.394
Respiratory Toxicity:	0.038

Download Data

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

Natural Product: NPC121126

Natural Product ID:	NPC121126
*Common Name:**	HKFFFIWYFPSUML-GUFUGUNKSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HKFFFIWYFPSUML-GUFUGUNKSA-N
Standard InCHI:	InChI=1S/C21H18O12/c22-5-13-16(26)17(27)18(28)21(33-13)30-6-1-10(25)15-12(2-6)32-20(29)14-7-3-8(23)9(24)4-11(7)31-19(14)15/h1-4,13,16-18,21-28H,5H2/t13-,16-,17+,18-,21-/m1/s1
SMILES:	c1c(cc2c(c1O)c1c(c3cc(c(cc3o1)O)O)c(=O)o2)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	6325048
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002506] Isoflavonoids [CHEMONTID:0000354] Coumestans

*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
NPO21382	Eutypa lata	Species	Diatrypaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12608846]
NPO2842	Garcinia lucida	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17880175]
NPO20295	Eclipta prostrata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21507	Ephedra intermedia	Species	Ephedraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21507	Ephedra intermedia	Species	Ephedraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20295	Eclipta prostrata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21507	Ephedra intermedia	Species	Ephedraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20295	Eclipta prostrata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20295	Eclipta prostrata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO21507	Ephedra intermedia	Species	Ephedraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO20233	Marchantia paleacea	Species	Marchantiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18749	Corydalis vernyi	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20982	Morus lactea	Species	Sulidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11034	Mnium pseudopunctatum	Species	Mniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21382	Eutypa lata	Species	Diatrypaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3468	Astragalus floccosifolius	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21251	Tabernaemontana odoratissima	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21507	Ephedra intermedia	Species	Ephedraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19272	Alcyonium fauri	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20648	Streptomyces cellulosae	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO19410	Clutia abyssinica	Species	Peraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20718	Hypericum elegans	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19837	Euonymus latifolius	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20431	Centaurea canariensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20101	Eria acutifolia	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17908	Rhododendron reticulatum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17115	Kielmeyera petiolaris	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2842	Garcinia lucida	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26309	Ahnfeltiopsis flabelliformis	Species	Phyllophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19559	Cetraria pseudocomplicata	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20295	Eclipta prostrata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14172	Rhopaloeides odorabile	Species	Spongiidae	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 NPC121126 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	447
0.1-0.2	1944
0.2-0.3	4147
0.3-0.4	9536
0.4-0.5	8913
0.5-0.6	4439
0.6-0.7	5504
0.7-0.8	5159
0.8-0.85	1756
0.85-0.9	658
0.9-0.95	194
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 NPC121126 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	401
0.1-0.2	943
0.2-0.3	2127
0.3-0.4	2689
0.4-0.5	1801
0.5-0.6	812
0.6-0.7	220
0.7-0.8	124
0.8-0.85	21
0.85-0.9	10
0.9-0.95	2
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