NPASS Compound

Structure

NPC10041 OpenBabel06302215272D 43 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 0.8660 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 2 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 1 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 2 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 -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 2 0 0 0 0 0 0 0 0 0 -2.5981 -2.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4641 -3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3301 -2.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 C 0 0 1 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 -5.1962 -1.0000 0.0000 O 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 -4.3301 0.5000 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 -4.3301 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 -4.3301 3.5000 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 -5.1962 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 1.5000 0.0000 O 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 -6.9282 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 0.5000 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 -8.6603 -1.0000 0.0000 C 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 -6.9282 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 -1.5000 0.0000 O 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 -2.5981 1.5000 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 -3.4641 -4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 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 0.8660 -2.5000 0.0000 O 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 2.5981 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 40 1 0 0 0 0 3 4 1 0 0 0 0 3 43 1 1 0 0 0 4 5 1 0 0 0 0 4 42 1 6 0 0 0 5 6 1 0 0 0 0 5 41 1 6 0 0 0 6 7 1 6 0 0 0 6 40 1 0 0 0 0 7 8 1 0 0 0 0 9 8 1 6 0 0 0 9 10 1 0 0 0 0 9 14 1 0 0 0 0 10 11 1 0 0 0 0 10 39 1 1 0 0 0 11 12 1 0 0 0 0 11 38 1 6 0 0 0 12 13 1 0 0 0 0 12 37 1 1 0 0 0 13 14 1 0 0 0 0 13 15 1 6 0 0 0 15 16 1 0 0 0 0 16 26 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 19 24 2 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 36 1 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 22 35 1 0 0 0 0 23 24 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 32 2 0 0 0 0 27 28 1 0 0 0 0 28 29 2 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 30 34 1 0 0 0 0 31 32 1 0 0 0 0 31 33 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	610.15
Volume:	552.318
LogP:	-0.204
LogD:	-0.212
LogS:	-4.201
# Rotatable Bonds:	6
TPSA:	269.43
# H-Bond Aceptor:	16
# H-Bond Donor:	10
# Rings:	5
# Heavy Atoms:	16

MedChem Properties

QED Drug-Likeness Score:	0.14
Synthetic Accessibility Score:	4.783
Fsp3:	0.444
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.458
MDCK Permeability:	1.4711304174852557e-05
Pgp-inhibitor:	0.009
Pgp-substrate:	0.929
Human Intestinal Absorption (HIA):	0.776
20% Bioavailability (F20%):	0.015
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.048
Plasma Protein Binding (PPB):	87.88590240478516%
Volume Distribution (VD):	0.682
Pgp-substrate:	15.740488052368164%

ADMET: Metabolism

CYP1A2-inhibitor:	0.083
CYP1A2-substrate:	0.052
CYP2C19-inhibitor:	0.031
CYP2C19-substrate:	0.047
CYP2C9-inhibitor:	0.019
CYP2C9-substrate:	0.134
CYP2D6-inhibitor:	0.072
CYP2D6-substrate:	0.134
CYP3A4-inhibitor:	0.033
CYP3A4-substrate:	0.004

ADMET: Excretion

Clearance (CL):	1.955
Half-life (T1/2):	0.827

ADMET: Toxicity

hERG Blockers:	0.376
Human Hepatotoxicity (H-HT):	0.098
Drug-inuced Liver Injury (DILI):	0.98
AMES Toxicity:	0.832
Rat Oral Acute Toxicity:	0.029
Maximum Recommended Daily Dose:	0.005
Skin Sensitization:	0.869
Carcinogencity:	0.116
Eye Corrosion:	0.003
Eye Irritation:	0.745
Respiratory Toxicity:	0.019

Download Data

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

Natural Product: NPC10041

Natural Product ID:	NPC10041
*Common Name:**	IKGXIBQEEMLURG-UZPWRIRZSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	IKGXIBQEEMLURG-UZPWRIRZSA-N
Standard InCHI:	InChI=1S/C27H30O16/c1-8-17(32)20(35)22(37)26(40-8)39-7-15-18(33)21(36)23(38)27(42-15)43-25-19(34)16-13(31)5-10(28)6-14(16)41-24(25)9-2-3-11(29)12(30)4-9/h2-6,8,15,17-18,20-23,26-33,35-38H,7H2,1H3/t8-,15+,17+,18+,20-,21-,22-,23+,26+,27-/m0/s1
SMILES:	C[C@H]1[C@H]([C@@H]([C@@H]([C@H](OC[C@@H]2[C@H]([C@@H]([C@H]([C@@H](O2)Oc2c(=O)c3c(cc(cc3oc2c2ccc(c(c2)O)O)O)O)O)O)O)O1)O)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:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003531] Flavonoid-3-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

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO3031	Sabal causiarum	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11508	Polygala reinii	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11036	Piper taboganum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14581	Rubia schumanniana	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13884	Microglossa pyrrhopappa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10163	Oreoherzogia fallax	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11975	Antillogorgia elisabethae	Species	Gorgoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1402	Adenocarpus foliolosus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14173	Ipomoea reptans	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7550	Chromolaena arnottiana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11508	Polygala reinii	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13484	Vidalia volubilis	Species	Tephritidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29061	Anthoxanthum nitens	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6564	Betula exilis	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22285	Clethra macrophylla	Species	Clethraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13183	Cereus dumortieri	Species	Sagartiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3031	Sabal causiarum	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19055	Plenodomus tracheiphilus	Species	Leptosphaeriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10309	Ichthyothere terminalis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14374	Retama duriaei	Species	Fabaceae	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 NPC10041 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	460
0.1-0.2	1842
0.2-0.3	4252
0.3-0.4	9791
0.4-0.5	8319
0.5-0.6	4578
0.6-0.7	5577
0.7-0.8	5191
0.8-0.85	1537
0.85-0.9	565
0.9-0.95	424
0.95-1	161

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 NPC10041 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	404
0.1-0.2	953
0.2-0.3	1998
0.3-0.4	2741
0.4-0.5	1793
0.5-0.6	852
0.6-0.7	273
0.7-0.8	104
0.8-0.85	18
0.85-0.9	6
0.9-0.95	2
0.95-1	6

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