NPASS Compound

Structure

NPC120020 OpenBabel06302215232D 28 30 0 0 1 0 0 0 0 0999 V2000 -0.8184 1.4118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0587 0.9857 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7973 1.6413 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.7970 0.6654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6415 0.1776 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6413 -0.7973 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.8662 -1.7484 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4853 -1.2851 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.3305 -0.7977 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3308 0.1771 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1750 0.6646 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.0214 0.1758 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1753 1.6404 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3313 2.1282 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3315 3.1031 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4865 3.5910 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.1794 2.6136 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6423 3.1035 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6420 2.1287 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6423 4.0784 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0215 1.1533 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4848 -2.2600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1991 -2.9235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9816 -3.8738 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1308 -2.6366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6555 -0.7385 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 -0.9215 -0.3190 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 27 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 6 0 0 0 3 19 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 1 0 0 0 6 8 1 0 0 0 0 6 26 1 0 0 0 0 8 9 1 0 0 0 0 8 22 1 1 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 6 0 0 0 11 13 1 0 0 0 0 11 21 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 20 1 0 0 0 0 16 17 1 6 0 0 0 16 18 1 0 0 0 0 18 19 1 6 0 0 0 18 20 1 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 23 25 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	392.22
Volume:	405.594
LogP:	2.656
LogD:	1.88
LogS:	-3.567
# Rotatable Bonds:	2
TPSA:	85.36
# H-Bond Aceptor:	6
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.319
Synthetic Accessibility Score:	5.914
Fsp3:	0.727
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	2
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.75
MDCK Permeability:	2.6812340365722775e-05
Pgp-inhibitor:	0.878
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.026
20% Bioavailability (F20%):	0.683
30% Bioavailability (F30%):	0.982

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.518
Plasma Protein Binding (PPB):	79.48958587646484%
Volume Distribution (VD):	0.849
Pgp-substrate:	23.441856384277344%

ADMET: Metabolism

CYP1A2-inhibitor:	0.02
CYP1A2-substrate:	0.196
CYP2C19-inhibitor:	0.122
CYP2C19-substrate:	0.553
CYP2C9-inhibitor:	0.124
CYP2C9-substrate:	0.048
CYP2D6-inhibitor:	0.035
CYP2D6-substrate:	0.063
CYP3A4-inhibitor:	0.879
CYP3A4-substrate:	0.319

ADMET: Excretion

Clearance (CL):	3.736
Half-life (T1/2):	0.456

ADMET: Toxicity

hERG Blockers:	0.156
Human Hepatotoxicity (H-HT):	0.72
Drug-inuced Liver Injury (DILI):	0.365
AMES Toxicity:	0.041
Rat Oral Acute Toxicity:	0.069
Maximum Recommended Daily Dose:	0.967
Skin Sensitization:	0.948
Carcinogencity:	0.691
Eye Corrosion:	0.232
Eye Irritation:	0.366
Respiratory Toxicity:	0.977

Download Data

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

Natural Product: NPC120020

Natural Product ID:	NPC120020
*Common Name:**	SXSOYTHMKCYVOO-KNDSDOTKSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SXSOYTHMKCYVOO-KNDSDOTKSA-N
Standard InCHI:	InChI=1S/C22H32O6/c1-14-16-7-12-22(5,28-19(14)24)17(26-15(2)23)8-11-20(3,25)9-6-10-21(4)18(13-16)27-21/h6,9,16-18,25H,1,7-8,10-13H2,2-5H3/b9-6+/t16-,17-,18+,20-,21+,22-/m1/s1
SMILES:	C=C1[C@@H]2CC[C@](C)([C@@H](CC[C@@](C)(/C=C/C[C@@]3(C)[C@H](C2)O3)O)OC(=O)C)OC1=O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	44518136
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000050] Lactones

*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
NPO3286	Erythrina americana	Species	Fabaceae	Eukaryota	Flowers	Tantempango, Hidalgo, Mexico	2019-May	DOI[10.1007/s11130-020-00822-2]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	seed	n.a.	DOI[10.1016/0031-9422(96)00258-0]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	fruit	n.a.	DOI[10.1016/S1383-5769(99)00023-9]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10086989]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1512598]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[15165151]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	fruit	Indonesia	n.a.	PMID[17896817]
NPO7475	Sinularia querciformis	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[18831569]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	Vietnam	n.a.	PMID[19026551]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	seeds	n.a.	n.a.	PMID[20050684]
NPO10949	Riccardia multifida	Species	Aneuraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21625478]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[22506620]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6481366]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7561896]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3371	Podocarpus nubigenus	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3286	Erythrina americana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3286	Erythrina americana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3371	Podocarpus nubigenus	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3371	Podocarpus nubigenus	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3286	Erythrina americana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9011	Anaptychia neoleucomelaena	Species	Physciaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7724	Heterobasidion annosum	Species	Bondarzewiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4491	Aplophyllum cappadocicum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO10949	Riccardia multifida	Species	Aneuraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10200	Pourouma cecropiifolia	Species	Urticaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6712	Artocarpus scortechinii	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2735	Orthodon hirtus	Species	Cyprinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO232	Cayaponia racemosa	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3048	Laportea moroides	Species	Urticaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5448	Wattakaka volubilis	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3286	Erythrina americana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7475	Sinularia querciformis	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11440	Dictyota menstrualis	Species	Dictyotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3371	Podocarpus nubigenus	Species	Podocarpaceae	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 NPC120020 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	231
0.1-0.2	1379
0.2-0.3	4878
0.3-0.4	9228
0.4-0.5	15705
0.5-0.6	7347
0.6-0.7	3150
0.7-0.8	671
0.8-0.85	90
0.85-0.9	14
0.9-0.95	4
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 NPC120020 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	220
0.1-0.2	1966
0.2-0.3	3662
0.3-0.4	2183
0.4-0.5	846
0.5-0.6	219
0.6-0.7	42
0.7-0.8	11
0.8-0.85	1
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