NPASS Compound

Structure

NPC104863 OpenBabel06302215582D 50 55 0 0 1 0 0 0 0 0999 V2000 -0.0000 -6.6379 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8212 -7.1121 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8212 -8.0603 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6425 -6.6379 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6425 -5.6897 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.4637 -5.2155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4637 -4.2672 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.2849 -3.7931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2332 -3.7931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7591 -4.6143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2849 -2.8448 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4637 -2.3707 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6425 -2.8448 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6425 -3.7931 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8212 -3.3190 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8212 -4.2672 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 -3.7931 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8212 -4.2672 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7231 -3.9742 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.2805 -4.7414 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7231 -5.5086 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8212 -5.2155 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.4355 -6.0818 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -5.6897 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8212 -5.2155 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8212 -6.1638 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0161 -3.0723 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -2.8448 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2849 -0.9483 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2849 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1062 -1.4224 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1062 -2.3707 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9274 -2.8448 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7486 -2.3707 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7486 -1.4224 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9274 -0.9483 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8212 -2.3707 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8212 -1.4224 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6425 -0.9483 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.9483 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8212 -1.4224 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6425 -0.9483 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6425 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8212 0.4741 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 2.4637 -1.4224 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2849 -0.9483 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1062 -1.4224 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2849 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1062 -2.3707 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 4 1 0 0 0 0 5 4 1 1 0 0 0 5 6 1 0 0 0 0 5 25 1 0 0 0 0 7 6 1 6 0 0 0 7 8 1 0 0 0 0 7 14 1 0 0 0 0 8 9 1 0 0 0 0 8 10 1 0 0 0 0 8 11 1 0 0 0 0 11 12 1 0 0 0 0 11 50 1 1 0 0 0 12 13 1 0 0 0 0 12 46 1 0 0 0 0 13 14 1 0 0 0 0 13 37 1 1 0 0 0 14 15 1 6 0 0 0 14 16 1 0 0 0 0 16 17 1 0 0 0 0 16 25 1 0 0 0 0 17 18 1 0 0 0 0 17 28 1 0 0 0 0 18 19 1 0 0 0 0 18 22 1 0 0 0 0 19 20 1 0 0 0 0 19 27 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 6 0 0 0 22 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 28 29 1 0 0 0 0 29 30 2 0 0 0 0 29 31 1 0 0 0 0 31 36 2 0 0 0 0 31 32 1 0 0 0 0 32 33 2 0 0 0 0 33 34 1 0 0 0 0 34 35 2 0 0 0 0 35 36 1 0 0 0 0 37 38 1 0 0 0 0 38 39 2 0 0 0 0 38 40 1 0 0 0 0 40 45 2 0 0 0 0 40 41 1 0 0 0 0 41 42 2 0 0 0 0 42 43 1 0 0 0 0 43 44 2 0 0 0 0 44 45 1 0 0 0 0 46 47 1 0 0 0 0 47 48 2 0 0 0 0 47 49 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	400.25
Volume:	435.757
LogP:	6.297
LogD:	4.916
LogS:	-5.363
# Rotatable Bonds:	20
TPSA:	34.14
# H-Bond Aceptor:	2
# H-Bond Donor:	0
# Rings:	0
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.12
Synthetic Accessibility Score:	2.84
Fsp3:	0.818
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	2
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.744
MDCK Permeability:	1.346608860330889e-05
Pgp-inhibitor:	0.933
Pgp-substrate:	0.005
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.925
30% Bioavailability (F30%):	0.937

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.162
Plasma Protein Binding (PPB):	97.9696273803711%
Volume Distribution (VD):	1.058
Pgp-substrate:	1.1859312057495117%

ADMET: Metabolism

CYP1A2-inhibitor:	0.28
CYP1A2-substrate:	0.229
CYP2C19-inhibitor:	0.329
CYP2C19-substrate:	0.06
CYP2C9-inhibitor:	0.264
CYP2C9-substrate:	0.93
CYP2D6-inhibitor:	0.041
CYP2D6-substrate:	0.875
CYP3A4-inhibitor:	0.662
CYP3A4-substrate:	0.063

ADMET: Excretion

Clearance (CL):	12.008
Half-life (T1/2):	0.79

ADMET: Toxicity

hERG Blockers:	0.096
Human Hepatotoxicity (H-HT):	0.244
Drug-inuced Liver Injury (DILI):	0.307
AMES Toxicity:	0.075
Rat Oral Acute Toxicity:	0.099
Maximum Recommended Daily Dose:	0.026
Skin Sensitization:	0.921
Carcinogencity:	0.379
Eye Corrosion:	0.197
Eye Irritation:	0.807
Respiratory Toxicity:	0.807

Download Data

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

Natural Product: NPC104863

Natural Product ID:	NPC104863
*Common Name:**	GXKFNMIKBKSMLQ-UFDUEGIDSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	GXKFNMIKBKSMLQ-UFDUEGIDSA-N
Standard InCHI:	InChI=1S/C37H44O13/c1-19(38)46-25-17-24-34(3,4)30(41)28(47-20(2)39)31(49-33(43)22-15-11-8-12-16-22)35(24,5)29-27(48-32(42)21-13-9-7-10-14-21)26-23(40)18-45-36(26,6)50-37(25,29)44/h7-16,23-31,40-41,44H,17-18H2,1-6H3/t23-,24+,25-,26+,27-,28+,29-,30-,31+,35+,36-,37-/m1/s1
SMILES:	CC(=O)O[C@@H]1C[C@H]2C(C)(C)[C@@H]([C@@H]([C@@H]([C@]2(C)[C@H]2[C@@H]([C@@H]3[C@@H](CO[C@]3(C)O[C@]12O)O)OC(=O)c1ccccc1)OC(=O)c1ccccc1)OC(=O)C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001640] Naphthopyrans

*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
NPO2257	Oceanapia phillipensis	Species	Phloeodictyidae	Eukaryota	n.a.	n.a.	n.a.	PMID[10654417]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15516765]
NPO10996	Ferula assa-foetida	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19691312]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20973550]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23700450]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	leaf	n.a.	PMID[23849114]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24310066]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	seed	n.a.	PMID[25433632]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	seed	n.a.	PMID[26860358]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.		PMID[31861466]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	Protoplast	n.a.	n.a.	Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	Shoot	n.a.	n.a.	Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	Petiole	n.a.	n.a.	Database[FooDB]
NPO29219	Primula veris	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5511	Populus tremula	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8981	Senecio integerrimus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	seed	n.a.	Database[MetaboLights]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO8981	Senecio integerrimus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5511	Populus tremula	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29219	Primula veris	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO14887	Handroanthus guayacan	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1638	Ulmus laciniata	Species	Ulmaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10996	Ferula assa-foetida	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29219	Primula veris	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2499	Celmisia petriei	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8981	Senecio integerrimus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11235	Asplenium nidus	Species	Aspleniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14797	Orthosiphon aristatus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5890	Astragalus inopinatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO592	Chroogomphus rutilus	Species	Gomphidiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1408	Cirsium helenioides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10073	Clusia torresii	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2257	Oceanapia phillipensis	Species	Phloeodictyidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5511	Populus tremula	Species	Salicaceae	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 NPC104863 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	306
0.1-0.2	1086
0.2-0.3	2387
0.3-0.4	4575
0.4-0.5	8994
0.5-0.6	12429
0.6-0.7	10533
0.7-0.8	1944
0.8-0.85	211
0.85-0.9	150
0.9-0.95	82
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 NPC104863 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	251
0.1-0.2	689
0.2-0.3	1435
0.3-0.4	2795
0.4-0.5	2476
0.5-0.6	1190
0.6-0.7	268
0.7-0.8	46
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
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