NPASS Compound

Structure

NPC117570 OpenBabel06302215242D 37 39 0 0 0 0 0 0 0 0999 V2000 -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 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 4.5000 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 -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 -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 -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 -3.4641 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 -1.7321 0.0000 0.0000 O 0 0 0 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 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 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 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -0.0000 0.0000 O 0 0 0 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 6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 7 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 4 36 1 0 0 0 0 5 6 2 0 0 0 0 6 7 1 0 0 0 0 6 35 1 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 8 10 1 0 0 0 0 10 11 1 0 0 0 0 11 17 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 13 15 1 0 0 0 0 15 16 2 0 0 0 0 15 19 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 19 20 2 0 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 22 28 2 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 24 25 1 0 0 0 0 24 26 1 0 0 0 0 26 27 2 0 0 0 0 26 31 1 0 0 0 0 27 28 1 0 0 0 0 27 29 1 0 0 0 0 29 30 1 0 0 0 0 31 32 2 0 0 0 0 31 33 1 0 0 0 0 33 34 1 0 0 0 0 36 37 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	510.15
Volume:	506.143
LogP:	5.474
LogD:	4.112
LogS:	-5.672
# Rotatable Bonds:	10
TPSA:	137.82
# H-Bond Aceptor:	10
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.35
Synthetic Accessibility Score:	2.727
Fsp3:	0.222
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.761
MDCK Permeability:	4.9647085688775405e-05
Pgp-inhibitor:	0.32
Pgp-substrate:	0.052
Human Intestinal Absorption (HIA):	0.67
20% Bioavailability (F20%):	0.16
30% Bioavailability (F30%):	0.832

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.006
Plasma Protein Binding (PPB):	97.97349548339844%
Volume Distribution (VD):	0.456
Pgp-substrate:	4.81226921081543%

ADMET: Metabolism

CYP1A2-inhibitor:	0.708
CYP1A2-substrate:	0.938
CYP2C19-inhibitor:	0.92
CYP2C19-substrate:	0.07
CYP2C9-inhibitor:	0.734
CYP2C9-substrate:	0.921
CYP2D6-inhibitor:	0.179
CYP2D6-substrate:	0.864
CYP3A4-inhibitor:	0.511
CYP3A4-substrate:	0.121

ADMET: Excretion

Clearance (CL):	10.299
Half-life (T1/2):	0.346

ADMET: Toxicity

hERG Blockers:	0.063
Human Hepatotoxicity (H-HT):	0.012
Drug-inuced Liver Injury (DILI):	0.69
AMES Toxicity:	0.078
Rat Oral Acute Toxicity:	0.153
Maximum Recommended Daily Dose:	0.915
Skin Sensitization:	0.81
Carcinogencity:	0.016
Eye Corrosion:	0.003
Eye Irritation:	0.947
Respiratory Toxicity:	0.383

Download Data

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

Natural Product: NPC117570

Natural Product ID:	NPC117570
*Common Name:**	AXWRJPJILHTYGR-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	AXWRJPJILHTYGR-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C27H26O10/c1-13-7-16(33-4)10-19(28)22(13)26(31)36-17-8-14(2)23(20(29)11-17)27(32)37-18-9-15(3)24(25(30)35-6)21(12-18)34-5/h7-12,28-29H,1-6H3
SMILES:	Cc1cc(cc(c1C(=O)Oc1cc(C)c(c(c1)O)C(=O)Oc1cc(C)c(c(c1)OC)C(=O)OC)O)OC
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:0001645] Depsides and depsidones

*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
NPO12665	Eunicella verrucosa	Species	Gorgoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[1687472]
NPO17287	Lagopsis supina	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24707938]
NPO25377	Ocimum gratissimum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29192771]
NPO25377	Ocimum gratissimum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6114991]
NPO12665	Eunicella verrucosa	Species	Gorgoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[7853007]
NPO12930	Apium leptophyllum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25377	Ocimum gratissimum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8013	Corydalis vaginans	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12930	Apium leptophyllum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12930	Apium leptophyllum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26635	Senecio venosus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8013	Corydalis vaginans	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10897	Baccharis ulicina	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4999	Pentzia grandiflora	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9664	Cortinarius cotoneus	Species	Cortinariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19648	Dalbergia nigrescens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12066	Mallotus paniculatus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11732	Lecanora melanocheila	Species	Lecanoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10721	Bombax anceps	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23675	Fumaria microcarpa	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12533	Liatris cylindracea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15716	Trichilia hispida	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12665	Eunicella verrucosa	Species	Gorgoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9674	Trifolium trichocephalum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17287	Lagopsis supina	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6624	Glycine wightii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14771	Piper schmidtii	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12305	Prostanthera sieberi	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25377	Ocimum gratissimum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15799	Phlomis capitata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12930	Apium leptophyllum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17592	Persea borbonia	Species	Lauraceae	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 NPC117570 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	358
0.1-0.2	1636
0.2-0.3	3940
0.3-0.4	9486
0.4-0.5	8868
0.5-0.6	3455
0.6-0.7	5383
0.7-0.8	6137
0.8-0.85	2634
0.85-0.9	745
0.9-0.95	44
0.95-1	11

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 NPC117570 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	317
0.1-0.2	984
0.2-0.3	1625
0.3-0.4	2592
0.4-0.5	1804
0.5-0.6	1163
0.6-0.7	457
0.7-0.8	154
0.8-0.85	42
0.85-0.9	11
0.9-0.95	1
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