NPASS Compound

Structure

NPC295146 OpenBabel06302215582D 42 47 0 0 1 0 0 0 0 0999 V2000 -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 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 1 0 0 0 0 0 0 0 0 0 3.4641 0.0000 0.0000 C 0 0 1 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 5.1962 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 6.0622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -2.0000 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 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -2.0000 0.0000 O 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 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 0.8660 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 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 3.4641 -2.0000 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 2.5981 -3.5000 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 0.8660 -3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 -3.5000 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 -1.7321 -5.0000 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 -3.5000 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 -3.4641 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -3.5000 0.0000 O 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 4.3301 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 39 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 3 42 1 0 0 0 0 4 17 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 6 41 1 6 0 0 0 7 8 1 1 0 0 0 7 16 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 15 1 0 0 0 0 12 13 1 0 0 0 0 12 14 1 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 18 39 1 0 0 0 0 19 18 1 6 0 0 0 19 20 1 0 0 0 0 19 36 1 0 0 0 0 20 25 2 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 23 38 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 6 0 0 0 27 36 1 0 0 0 0 28 33 2 0 0 0 0 28 29 1 0 0 0 0 29 30 2 0 0 0 0 30 31 1 0 0 0 0 31 32 2 0 0 0 0 31 35 1 0 0 0 0 32 33 1 0 0 0 0 32 34 1 0 0 0 0 36 37 1 1 0 0 0 39 40 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	161.07
Volume:	153.217
LogP:	-3.119
LogD:	-0.423
LogS:	-1.061
# Rotatable Bonds:	5
TPSA:	86.63
# H-Bond Aceptor:	5
# H-Bond Donor:	3
# Rings:	0
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.507
Synthetic Accessibility Score:	2.415
Fsp3:	0.667
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.098
MDCK Permeability:	0.001889214850962162
Pgp-inhibitor:	0.0
Pgp-substrate:	0.006
Human Intestinal Absorption (HIA):	0.583
20% Bioavailability (F20%):	0.006
30% Bioavailability (F30%):	0.005

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.472
Plasma Protein Binding (PPB):	12.768697738647461%
Volume Distribution (VD):	0.512
Pgp-substrate:	86.64620208740234%

ADMET: Metabolism

CYP1A2-inhibitor:	0.004
CYP1A2-substrate:	0.044
CYP2C19-inhibitor:	0.029
CYP2C19-substrate:	0.042
CYP2C9-inhibitor:	0.009
CYP2C9-substrate:	0.581
CYP2D6-inhibitor:	0.014
CYP2D6-substrate:	0.156
CYP3A4-inhibitor:	0.008
CYP3A4-substrate:	0.004

ADMET: Excretion

Clearance (CL):	2.864
Half-life (T1/2):	0.738

ADMET: Toxicity

hERG Blockers:	0.014
Human Hepatotoxicity (H-HT):	0.098
Drug-inuced Liver Injury (DILI):	0.038
AMES Toxicity:	0.012
Rat Oral Acute Toxicity:	0.011
Maximum Recommended Daily Dose:	0.032
Skin Sensitization:	0.182
Carcinogencity:	0.074
Eye Corrosion:	0.003
Eye Irritation:	0.073
Respiratory Toxicity:	0.123

Download Data

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

Natural Product: NPC295146

Natural Product ID:	NPC295146
*Common Name:**	IZNXKUAZOWJYDK-VRBHQIMASA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	IZNXKUAZOWJYDK-VRBHQIMASA-N
Standard InCHI:	InChI=1S/C31H28O11/c1-12-26(38)17-11-22(37)29(13-2-6-18(33)20(35)8-13)42-31(17)25(27(12)39)24-16-5-4-15(32)10-23(16)41-30(28(24)40)14-3-7-19(34)21(36)9-14/h2-10,22,24,28-30,32-40H,11H2,1H3/t22-,24-,28-,29+,30+/m0/s1
SMILES:	Cc1c(c2C[C@@H]([C@@H](c3ccc(c(c3)O)O)Oc2c([C@@H]2c3ccc(cc3O[C@H](c3ccc(c(c3)O)O)[C@H]2O)O)c1O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001586] Biflavonoids and polyflavonoids

*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
NPO6062	Acacia mearnsii	Species	Fabaceae	Eukaryota	n.a.	bark	n.a.	PMID[21192716]
NPO13726	Agrobacterium tumefaciens	Species	Rhizobiaceae	Bacteria	n.a.	n.a.	n.a.	PMID[22466953]
NPO13726	Agrobacterium tumefaciens	Species	Rhizobiaceae	Bacteria	n.a.	n.a.	n.a.	PMID[24450804]
NPO14381	Swertia pseudochinensis	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6062	Acacia mearnsii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9357	Mitragyna inermis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27620.1	Pteris cretica var. nervosa	Varieties	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25181	Cyperus papyrus	Species	Cyperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14381	Swertia pseudochinensis	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9357	Mitragyna inermis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27620.1	Pteris cretica var. nervosa	Varieties	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25479	Sabal blackburniana	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6062	Acacia mearnsii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22798	Pseudofumaria lutea	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25181	Cyperus papyrus	Species	Cyperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14381	Swertia pseudochinensis	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14381	Swertia pseudochinensis	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO13685	Scrophularia umbrosa	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12716	Stocksia brahuica	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO13987	Solanum sublobatum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22798	Pseudofumaria lutea	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5383	Othonna dentata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12213	Perriera orientalis	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14381	Swertia pseudochinensis	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27620.1	Pteris cretica var. nervosa	Varieties	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13600	Ichthyothere latifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8181	Hypoxylon tinctor	Species	Xylariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3075	Dimorphotheca aurantiaca	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12021	Artemisia incanescens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29152	Caloboletus calopus	Species	Boletaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10325	Boletus pini	Species	Boletaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9620	Rhodococcus fascians	Species	0cardiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO25181	Cyperus papyrus	Species	Cyperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6062	Acacia mearnsii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6599	Neorautanenia ficifolia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26723	Lachnophyllum gossypinum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9357	Mitragyna inermis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9017	Fagus grandifolia	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25479	Sabal blackburniana	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8628	Strychnos erichsonii	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13726	Agrobacterium tumefaciens	Species	Rhizobiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO12564	Sinularia facile	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13790	Abedus herberti	Species	Belostomatidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14078	Paramecium tetraurelia	Species	Parameciidae	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 NPC295146 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	487
0.1-0.2	1680
0.2-0.3	4535
0.3-0.4	11290
0.4-0.5	6940
0.5-0.6	4125
0.6-0.7	6295
0.7-0.8	5765
0.8-0.85	913
0.85-0.9	502
0.9-0.95	134
0.95-1	31

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 NPC295146 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	411
0.1-0.2	894
0.2-0.3	1951
0.3-0.4	2704
0.4-0.5	1584
0.5-0.6	872
0.6-0.7	597
0.7-0.8	125
0.8-0.85	7
0.85-0.9	3
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