NPASS Compound

Structure

NPC144462 OpenBabel06302215202D 41 46 0 0 1 0 0 0 0 0999 V2000 -0.8404 4.0766 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8771 3.4780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8771 2.2809 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8404 1.6823 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8404 0.4852 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6808 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6808 -0.9704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5212 -1.4556 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3616 -0.9704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3616 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9602 1.0367 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5587 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5212 0.4852 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8404 -1.4556 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.9704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8404 -1.4556 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8404 -2.6527 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6808 -0.9704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0373 -1.4619 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0373 -0.6129 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.4540 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0579 0.6638 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.0430 1.6954 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6093 2.7092 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8045 2.4929 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3842 1.6954 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0663 0.7150 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.6394 1.0108 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6023 1.6547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1413 2.0087 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7175 1.7189 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1043 2.6526 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6433 3.0067 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5281 2.9424 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3832 0.1533 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3774 -0.1216 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6808 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8404 0.4852 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 -0.8404 -2.6527 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9139 4.0766 0.0000 C 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 41 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 39 2 0 0 0 0 5 6 1 0 0 0 0 6 13 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 14 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 10 12 1 0 0 0 0 10 13 1 0 0 0 0 14 15 2 0 0 0 0 14 40 1 0 0 0 0 15 39 1 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 16 18 1 0 0 0 0 18 19 2 0 0 0 0 20 19 1 1 0 0 0 20 21 1 0 0 0 0 20 35 1 0 0 0 0 22 21 1 6 0 0 0 22 23 1 0 0 0 0 22 37 1 0 0 0 0 23 24 1 0 0 0 0 23 25 1 0 0 0 0 23 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 1 0 0 0 27 35 1 0 0 0 0 27 37 1 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 30 32 1 0 0 0 0 32 33 2 0 0 0 0 32 34 1 0 0 0 0 35 36 2 0 0 0 0 37 18 1 1 0 0 0 37 38 1 0 0 0 0 38 39 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	560.24
Volume:	571.942
LogP:	6.464
LogD:	3.477
LogS:	-3.157
# Rotatable Bonds:	5
TPSA:	119.36
# H-Bond Aceptor:	8
# H-Bond Donor:	2
# Rings:	7
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.462
Synthetic Accessibility Score:	6.741
Fsp3:	0.485
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:	-4.965
MDCK Permeability:	1.670349774940405e-05
Pgp-inhibitor:	0.232
Pgp-substrate:	0.006
Human Intestinal Absorption (HIA):	0.454
20% Bioavailability (F20%):	0.368
30% Bioavailability (F30%):	0.53

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.214
Plasma Protein Binding (PPB):	98.1952133178711%
Volume Distribution (VD):	1.358
Pgp-substrate:	3.3381195068359375%

ADMET: Metabolism

CYP1A2-inhibitor:	0.052
CYP1A2-substrate:	0.423
CYP2C19-inhibitor:	0.019
CYP2C19-substrate:	0.56
CYP2C9-inhibitor:	0.298
CYP2C9-substrate:	0.189
CYP2D6-inhibitor:	0.095
CYP2D6-substrate:	0.076
CYP3A4-inhibitor:	0.412
CYP3A4-substrate:	0.592

ADMET: Excretion

Clearance (CL):	1.218
Half-life (T1/2):	0.12

ADMET: Toxicity

hERG Blockers:	0.025
Human Hepatotoxicity (H-HT):	0.891
Drug-inuced Liver Injury (DILI):	0.944
AMES Toxicity:	0.006
Rat Oral Acute Toxicity:	0.987
Maximum Recommended Daily Dose:	0.927
Skin Sensitization:	0.187
Carcinogencity:	0.899
Eye Corrosion:	0.003
Eye Irritation:	0.009
Respiratory Toxicity:	0.962

Download Data

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

Natural Product: NPC144462

Natural Product ID:	NPC144462
*Common Name:**	COVMVPHACFXMAX-NLAWGVGUSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	COVMVPHACFXMAX-NLAWGVGUSA-N
Standard InCHI:	InChI=1S/C33H36O8/c1-16(2)8-9-20-26-19(11-12-30(4,5)39-26)24(34)23-25(35)21-14-18-15-22-31(6,7)41-32(28(18)36,13-10-17(3)29(37)38)33(21,22)40-27(20)23/h8,10-12,14,18,22,34H,9,13,15H2,1-7H3,(H,37,38)/b17-10-/t18-,22+,32+,33-/m0/s1
SMILES:	CC(=CCc1c2c(C=CC(C)(C)O2)c(c2C(=O)C3=C[C@H]4C[C@@H]5C(C)(C)O[C@](C/C=C(/C)C(=O)O)(C4=O)[C@]35Oc12)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	102533562
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000123] Benzopyrans [CHEMONTID:0003410] 1-benzopyrans [CHEMONTID:0002817] Dibenzopyrans [CHEMONTID:0000200] Xanthenes [CHEMONTID:0000204] Xanthones [CHEMONTID:0003521] Pyranoxanthones

*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
NPO3806	Garcinia morella	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/S0040-4039(00)90246-6]
NPO17342	Microcosmus vulgaris	Species	Pyuridae	Eukaryota	n.a.	n.a.	n.a.	PMID[10785429]
NPO6617	Chirita eburnea	Species	Gesneriaceae	Eukaryota	whole plant	Guangxi Province, China	2002-AUG	PMID[15921435]
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	n.a.	fruit	n.a.	PMID[17117343]
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	n.a.	latex	n.a.	PMID[17117343]
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	resin	n.a.	n.a.	PMID[19072548]
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21486005]
NPO19429	Millettia auriculata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20295	Eclipta prostrata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3806	Garcinia morella	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14692	Salix babylonica	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19508	Toxicodendron radicans	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14692	Salix babylonica	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6202	Aglaomorpha coronans	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19429	Millettia auriculata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20295	Eclipta prostrata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5523	Picria felterrae	Species	Linderniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3806	Garcinia morella	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14692	Salix babylonica	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20295	Eclipta prostrata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3806	Garcinia morella	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO20295	Eclipta prostrata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO20810	Lobaria adusta	Species	Lobariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6202	Aglaomorpha coronans	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5660	Scleropyrum maingayi	Species	Cervantesiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19300	Scleroderma tinctorium	Species	Sclerodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22632	Pteris glauca	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3806	Garcinia morella	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19429	Millettia auriculata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20295	Eclipta prostrata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19760	Fragaria chiloensis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18834	Scrophularia glabrata	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13703	Croton discolor	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1917	Prosopis nigra	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17093	Callitriche stagnalis	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4723	Phanerochaete velutina	Species	Phanerochaetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28098	Rhizomnium pseudopunctatum	Species	Mniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO64	Lysidice brevicalyx	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19508	Toxicodendron radicans	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18593	Wrightia coccinea	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15765	Vernonanthura discolor	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17342	Microcosmus vulgaris	Species	Pyuridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4477	Fasciola hepatica	Species	Fasciolidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5523	Picria felterrae	Species	Linderniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6617	Chirita eburnea	Species	Gesneriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11950	Ruscus hypoglossum	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14692	Salix babylonica	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 NPC144462 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	397
0.1-0.2	1580
0.2-0.3	3220
0.3-0.4	7095
0.4-0.5	10680
0.5-0.6	6226
0.6-0.7	5820
0.7-0.8	7268
0.8-0.85	330
0.85-0.9	32
0.9-0.95	29
0.95-1	20

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 NPC144462 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	343
0.1-0.2	963
0.2-0.3	1856
0.3-0.4	2673
0.4-0.5	1983
0.5-0.6	902
0.6-0.7	284
0.7-0.8	142
0.8-0.85	4
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