NPASS Compound

Structure

NPC2121 OpenBabel06302215392D 41 46 0 0 1 0 0 0 0 0999 V2000 1.2316 2.1876 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1502 2.1973 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6179 1.4066 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1670 0.6062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2483 0.5965 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7806 1.3872 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0101 0.9195 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8103 1.3708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6114 0.9020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6014 -0.0175 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7900 -0.4793 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7799 -1.4043 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5701 -1.8675 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3868 -1.4219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3969 -0.4969 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1969 -0.0350 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2070 0.8845 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4171 1.3532 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4631 5.0265 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5448 5.0380 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.0956 5.8390 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.1773 5.8505 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.2918 5.0610 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.1574 4.2599 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.3118 3.4704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2301 3.4819 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0757 4.2484 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2102 5.0725 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2719 6.6515 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5647 6.6285 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0080 1.3337 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7975 0.8646 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5986 1.3138 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6101 2.2322 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8205 2.7013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0195 2.2521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8320 3.6196 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.4111 2.6814 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5560 -2.7875 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 O 0 3 0 0 0 0 0 0 0 0 0 0 3.5365 1.4163 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 3 41 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 40 2 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 9 18 1 0 0 0 0 9 10 1 0 0 0 0 10 15 2 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 11 40 1 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 13 39 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 31 1 0 0 0 0 18 19 1 0 0 0 0 20 19 1 1 0 0 0 20 21 1 0 0 0 0 20 27 1 0 0 0 0 21 22 1 0 0 0 0 21 30 1 6 0 0 0 22 23 1 0 0 0 0 22 29 1 1 0 0 0 23 24 1 0 0 0 0 23 28 1 6 0 0 0 24 25 1 1 0 0 0 24 27 1 0 0 0 0 25 26 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 34 38 1 0 0 0 0 35 36 1 0 0 0 0 35 37 1 0 0 0 0 M CHG 1 40 1 M END $$$$

Physi-Chem Properties

Molecular Weight:	565.13
Volume:	533.965
LogP:	2.657
LogD:	1.882
LogS:	-4.712
# Rotatable Bonds:	5
TPSA:	203.08
# H-Bond Aceptor:	12
# H-Bond Donor:	8
# Rings:	6
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.122
Synthetic Accessibility Score:	4.812
Fsp3:	0.207
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.206
MDCK Permeability:	7.98526616563322e-06
Pgp-inhibitor:	0.176
Pgp-substrate:	0.886
Human Intestinal Absorption (HIA):	0.725
20% Bioavailability (F20%):	0.213
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.007
Plasma Protein Binding (PPB):	91.26801300048828%
Volume Distribution (VD):	0.619
Pgp-substrate:	9.539786338806152%

ADMET: Metabolism

CYP1A2-inhibitor:	0.475
CYP1A2-substrate:	0.037
CYP2C19-inhibitor:	0.037
CYP2C19-substrate:	0.046
CYP2C9-inhibitor:	0.09
CYP2C9-substrate:	0.125
CYP2D6-inhibitor:	0.291
CYP2D6-substrate:	0.19
CYP3A4-inhibitor:	0.127
CYP3A4-substrate:	0.016

ADMET: Excretion

Clearance (CL):	5.706
Half-life (T1/2):	0.71

ADMET: Toxicity

hERG Blockers:	0.216
Human Hepatotoxicity (H-HT):	0.084
Drug-inuced Liver Injury (DILI):	0.977
AMES Toxicity:	0.775
Rat Oral Acute Toxicity:	0.076
Maximum Recommended Daily Dose:	0.026
Skin Sensitization:	0.908
Carcinogencity:	0.167
Eye Corrosion:	0.003
Eye Irritation:	0.678
Respiratory Toxicity:	0.023

Download Data

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

Natural Product: NPC2121

Natural Product ID:	NPC2121
*Common Name:**	KXIWBEACJPYXIM-VMQCTCBBSA-O
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	KXIWBEACJPYXIM-VMQCTCBBSA-O
Standard InCHI:	InChI=1S/C29H24O12/c30-11-22-24(35)25(36)26(37)29(40-22)41-28-16-10-19(12-1-4-14(31)5-2-12)38-20-8-15(32)9-21(23(16)20)39-27(28)13-3-6-17(33)18(34)7-13/h1-10,22,24-26,29-30,35-37H,11H2,(H3-,31,32,33,34)/p+1/t22-,24-,25+,26-,29+/m1/s1
SMILES:	c1cc(ccc1c1cc2c3c(cc(cc3OC(=C2O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O)O)c2ccc(c(c2)O)O)O)[o+]1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101198724
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0001361] Anthocyanins [CHEMONTID:0002996] Anthocyanidin-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
NPO1751	Ribes nigrum	Species	n.a.	n.a.	Fruit	n.a.	n.a.	DOI[10.1016/S0963-9969(99)00095-2]
NPO14178	Leonurus persicus	Species	Lamiaceae	Eukaryota	Aerial parts	n.a.	n.a.	PMID[10395493]
NPO15442	Magnolia sieboldii	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11534769]
NPO1751	Ribes nigrum	Species	n.a.	n.a.	n.a.	fruit	n.a.	PMID[16417304]
NPO14284	Delphinium shawurense	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20351801]
NPO15442	Magnolia sieboldii	Species	Magnoliaceae	Eukaryota	stem bark	n.a.	n.a.	PMID[8988596]
NPO1751	Ribes nigrum	Species	n.a.	n.a.	Seed	n.a.	n.a.	Database[FooDB]
NPO1751	Ribes nigrum	Species	n.a.	n.a.	Seed Essent. Oil	n.a.	n.a.	Database[FooDB]
NPO1751	Ribes nigrum	Species	n.a.	n.a.	Fruits	n.a.		Database[FooDB]
NPO1751	Ribes nigrum	Species	n.a.	n.a.		n.a.	n.a.	Database[FooDB]
NPO1751	Ribes nigrum	Species	n.a.	n.a.	Bulb	n.a.	n.a.	Database[FooDB]
NPO1751	Ribes nigrum	Species	n.a.	n.a.	Fruit	n.a.	n.a.	Database[FooDB]
NPO1751	Ribes nigrum	Species	n.a.	n.a.	Fruit Juice	n.a.	n.a.	Database[FooDB]
NPO1751	Ribes nigrum	Species	n.a.	n.a.	Leaf	n.a.	n.a.	Database[FooDB]
NPO15442	Magnolia sieboldii	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16741	Codonopsis pilosula	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14178	Leonurus persicus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15442	Magnolia sieboldii	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16741	Codonopsis pilosula	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1751	Ribes nigrum	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO2458	Aconitum violaceum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14673	Lathyrus nissolia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14178	Leonurus persicus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16741	Codonopsis pilosula	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16741	Codonopsis pilosula	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO14043	Caulerpa serrulata	Species	Caulerpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13160	Garcinia xipshuanbannaensis	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10887	Pseudeurotium zonatum	Species	Pseudeurotiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16741	Codonopsis pilosula	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6347	Iryanthera paraensis	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12756	Roboastra tigris	Species	Polyceridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15253	Helichrysum graveolens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14673	Lathyrus nissolia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11912	Peltogyne porphyrocardia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14178	Leonurus persicus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11128	Ratibida mexicana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14284	Delphinium shawurense	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13311	Agelas linnaei	Species	Agelasidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9860.1	Pinus brutia var. eldarica	Varieties	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10191	Ormosia balansae	Species	Limoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28601	Aspergillus falconensis	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15626	Alternaria japonica	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12982	Dysidea amblia	Species	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1751	Ribes nigrum	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO7713	Euplotes raikovi	Species	Euplotidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3949	Ceramium rubrum	Species	Ceramiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO965	Bleekeria vitiensis	Species	Plesiopidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13477	Cyberlindnera jadinii	Species	Phaffomycetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2458	Aconitum violaceum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3244	Ascidia ahodori	Species	Ascidiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4512	Fagraea gracilipes	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15442	Magnolia sieboldii	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15160	Gutierrezia lucida	Species	Asteraceae	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 NPC2121 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	458
0.1-0.2	1775
0.2-0.3	3855
0.3-0.4	9324
0.4-0.5	8869
0.5-0.6	4284
0.6-0.7	5178
0.7-0.8	5436
0.8-0.85	2171
0.85-0.9	801
0.9-0.95	512
0.95-1	34

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 NPC2121 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	411
0.1-0.2	928
0.2-0.3	1852
0.3-0.4	2708
0.4-0.5	1842
0.5-0.6	915
0.6-0.7	314
0.7-0.8	136
0.8-0.85	26
0.85-0.9	10
0.9-0.95	8
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