NPASS Compound

Structure

NPC270592 OpenBabel06302215312D 45 49 0 0 1 0 0 0 0 0999 V2000 11.2583 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -1.0000 0.0000 C 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 9.5263 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 0.5000 0.0000 O 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 6.9282 -4.0000 0.0000 O 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 5.1962 -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 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 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 1 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 0.8660 -2.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 C 0 0 1 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 O 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 -0.0000 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.0000 0.0000 O 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 0.8660 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 C 0 0 1 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 -1.7321 -1.0000 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 -0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -4.0000 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 8 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 10 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 10 20 1 0 0 0 0 10 11 2 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 19 2 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 15 45 1 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 21 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 22 21 1 6 0 0 0 22 23 1 0 0 0 0 22 29 1 0 0 0 0 23 24 1 0 0 0 0 23 32 1 1 0 0 0 24 25 1 0 0 0 0 24 31 1 6 0 0 0 25 26 1 0 0 0 0 25 30 1 1 0 0 0 26 27 1 6 0 0 0 26 29 1 0 0 0 0 27 28 1 0 0 0 0 33 32 1 6 0 0 0 33 34 1 0 0 0 0 33 41 1 0 0 0 0 34 35 1 0 0 0 0 34 44 1 1 0 0 0 35 36 1 0 0 0 0 35 43 1 6 0 0 0 36 37 1 0 0 0 0 36 42 1 1 0 0 0 37 38 1 6 0 0 0 37 41 1 0 0 0 0 38 39 2 0 0 0 0 38 40 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	638.15
Volume:	575.767
LogP:	0.234
LogD:	-0.191
LogS:	-2.64
# Rotatable Bonds:	8
TPSA:	275.5
# H-Bond Aceptor:	17
# H-Bond Donor:	9
# Rings:	5
# Heavy Atoms:	17

MedChem Properties

QED Drug-Likeness Score:	0.129
Synthetic Accessibility Score:	4.742
Fsp3:	0.429
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.718
MDCK Permeability:	5.699008397641592e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.989
Human Intestinal Absorption (HIA):	0.931
20% Bioavailability (F20%):	0.026
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.088
Plasma Protein Binding (PPB):	75.60442352294922%
Volume Distribution (VD):	0.569
Pgp-substrate:	17.8306884765625%

ADMET: Metabolism

CYP1A2-inhibitor:	0.034
CYP1A2-substrate:	0.039
CYP2C19-inhibitor:	0.029
CYP2C19-substrate:	0.046
CYP2C9-inhibitor:	0.003
CYP2C9-substrate:	0.106
CYP2D6-inhibitor:	0.021
CYP2D6-substrate:	0.125
CYP3A4-inhibitor:	0.021
CYP3A4-substrate:	0.002

ADMET: Excretion

Clearance (CL):	1.309
Half-life (T1/2):	0.857

ADMET: Toxicity

hERG Blockers:	0.245
Human Hepatotoxicity (H-HT):	0.158
Drug-inuced Liver Injury (DILI):	0.973
AMES Toxicity:	0.359
Rat Oral Acute Toxicity:	0.007
Maximum Recommended Daily Dose:	0.002
Skin Sensitization:	0.081
Carcinogencity:	0.121
Eye Corrosion:	0.003
Eye Irritation:	0.022
Respiratory Toxicity:	0.021

Download Data

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

Natural Product: NPC270592

Natural Product ID:	NPC270592
*Common Name:**	PNHGTHGNROOTDD-NDAVQDCPSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PNHGTHGNROOTDD-NDAVQDCPSA-N
Standard InCHI:	InChI=1S/C28H30O17/c1-40-15-4-9(2-3-11(15)30)14-7-13(32)18-12(31)5-10(6-16(18)42-14)41-28-25(21(35)19(33)17(8-29)43-28)45-27-23(37)20(34)22(36)24(44-27)26(38)39/h2-7,17,19-25,27-31,33-37H,8H2,1H3,(H,38,39)/t17-,19-,20+,21+,22+,23-,24+,25-,27+,28-/m1/s1
SMILES:	COc1cc(ccc1O)c1cc(=O)c2c(cc(cc2o1)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](C(=O)O)O1)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	44139739
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003533] Flavonoid-7-O-glycosides

*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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO21355	Elsholtzia ciliata	Species	Lamiaceae	Eukaryota	Aerial Parts	n.a.	n.a.	PMID[32991171]
NPO20197	Boletinus asiaticus	Species	Gyrodontaceae	Eukaryota	Fruiting Bodies	n.a.	n.a.	PMID[31244141]
NPO20864	Stratiotes aloides	Species	Hydrocharitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20560646]
NPO21283	Stahlianthus campanulatus	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18215	Ficus benjamina	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21355	Elsholtzia ciliata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20197	Boletinus asiaticus	Species	Gyrodontaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20864	Stratiotes aloides	Species	Hydrocharitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20731	Pometia ridleyi	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19308	Ficus formosa	Species	Ficidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
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☑ 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

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
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☑ 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 NPC270592 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

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Similarity Score	Similarity Level	Natural Product ID
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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 NPC270592 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
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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