NPASS Compound

Structure

NPC219113 OpenBabel06302215592D 27 32 0 0 1 0 0 0 0 0999 V2000 -4.2072 -3.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3412 -3.1691 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.4752 -3.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6092 -3.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6092 -2.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7431 -1.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7431 -0.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6092 -0.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4752 -0.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4752 -1.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3412 -2.1691 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2072 -1.6691 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1208 -2.0759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4298 -3.0269 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4080 -3.2348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0771 -2.4917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7681 -1.5406 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7899 -1.3327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2899 -0.4667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6967 0.4468 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3118 -0.6746 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.5771 -0.9528 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.3861 -1.5406 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.0771 -2.4917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4013 0.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4067 0.9135 0.0000 C 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 1 2 1 0 0 0 0 2 11 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 10 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 7 27 1 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 8 25 1 0 0 0 0 9 10 1 0 0 0 0 11 10 1 6 0 0 0 11 12 1 0 0 0 0 12 13 1 6 0 0 0 12 21 1 0 0 0 0 13 18 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 15 16 1 0 0 0 0 16 24 1 0 0 0 0 16 17 2 0 0 0 0 17 18 1 0 0 0 0 17 22 1 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 19 21 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	367.11
Volume:	348.42
LogP:	2.6
LogD:	2.716
LogS:	-4.545
# Rotatable Bonds:	1
TPSA:	66.46
# H-Bond Aceptor:	7
# H-Bond Donor:	0
# Rings:	6
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.718
Synthetic Accessibility Score:	3.599
Fsp3:	0.35
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.972
MDCK Permeability:	4.99762172694318e-05
Pgp-inhibitor:	0.042
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.001
20% Bioavailability (F20%):	0.136
30% Bioavailability (F30%):	0.023

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.955
Plasma Protein Binding (PPB):	92.23001861572266%
Volume Distribution (VD):	2.364
Pgp-substrate:	3.4547765254974365%

ADMET: Metabolism

CYP1A2-inhibitor:	0.922
CYP1A2-substrate:	0.692
CYP2C19-inhibitor:	0.968
CYP2C19-substrate:	0.823
CYP2C9-inhibitor:	0.733
CYP2C9-substrate:	0.868
CYP2D6-inhibitor:	0.976
CYP2D6-substrate:	0.913
CYP3A4-inhibitor:	0.966
CYP3A4-substrate:	0.692

ADMET: Excretion

Clearance (CL):	17.139
Half-life (T1/2):	0.076

ADMET: Toxicity

hERG Blockers:	0.112
Human Hepatotoxicity (H-HT):	0.188
Drug-inuced Liver Injury (DILI):	0.577
AMES Toxicity:	0.601
Rat Oral Acute Toxicity:	0.528
Maximum Recommended Daily Dose:	0.907
Skin Sensitization:	0.083
Carcinogencity:	0.881
Eye Corrosion:	0.003
Eye Irritation:	0.015
Respiratory Toxicity:	0.839

Download Data

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

Natural Product: NPC219113

Natural Product ID:	NPC219113
*Common Name:**	IYGYMKDQCDOMRE-ROUUACIJSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	IYGYMKDQCDOMRE-ROUUACIJSA-N
Standard InCHI:	InChI=1S/C20H17NO6/c1-21-5-4-10-6-14-15(25-8-24-14)7-12(10)17(21)18-11-2-3-13-19(26-9-23-13)16(11)20(22)27-18/h2-3,6-7,17-18H,4-5,8-9H2,1H3/t17-,18-/m0/s1
SMILES:	CN1CCc2cc3c(cc2[C@H]1[C@@H]1c2ccc4c(c2C(=O)O1)OCO4)OCO3
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	120734
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0002188] Phthalide isoquinolines

*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
NPO7961	Bursatella leachii	Species	Aplysiidae	Eukaryota	n.a.	New Zealand	n.a.	PMID[11975522]
NPO7961	Bursatella leachii	Species	Aplysiidae	Eukaryota	n.a.	Thai sea	n.a.	PMID[15974628]
NPO9444	Chaetomium cochliodes	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16989540]
NPO6328	Corydalis incisa	Species	Papaveraceae	Eukaryota	n.a.	aerial part	n.a.	PMID[17366734]
NPO2700	Kopsia arborea	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17665953]
NPO2700	Kopsia arborea	Species	Apocynaceae	Eukaryota	n.a.	Yunnan, China	n.a.	PMID[19133778]
NPO15890	Cimicifuga foetida	Species	Ranunculaceae	Eukaryota	Roots	n.a.	n.a.	PMID[20121210]
NPO5305	Corydalis mucronifera	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29400966]
NPO2700	Kopsia arborea	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31241923]
NPO14045	Corydalis decumbens	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31599578]
NPO9444	Chaetomium cochliodes	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32115958]
NPO3106	Sabia schumanniana	Species	Sabiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12071	Erythrophleum guineense	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5305	Corydalis mucronifera	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14045	Corydalis decumbens	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6637	Corydalis repens	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8522	Dicentra cucullaria	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6328	Corydalis incisa	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8522	Dicentra cucullaria	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3106	Sabia schumanniana	Species	Sabiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14045	Corydalis decumbens	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5305	Corydalis mucronifera	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6637	Corydalis repens	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6328	Corydalis incisa	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21520	Corydalis thalictrifolia	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12071	Erythrophleum guineense	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7291	Adlumia cirrhosa	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15890	Cimicifuga foetida	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8522	Dicentra cucullaria	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO6328	Corydalis incisa	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3106	Sabia schumanniana	Species	Sabiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14045	Corydalis decumbens	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12071	Erythrophleum guineense	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7291	Adlumia cirrhosa	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21520	Corydalis thalictrifolia	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5305	Corydalis mucronifera	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15890	Cimicifuga foetida	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO14045	Corydalis decumbens	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO7961	Bursatella leachii	Species	Aplysiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8522	Dicentra cucullaria	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3106	Sabia schumanniana	Species	Sabiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15890	Cimicifuga foetida	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6637	Corydalis repens	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12071	Erythrophleum guineense	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21520	Corydalis thalictrifolia	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9444	Chaetomium cochliodes	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6328	Corydalis incisa	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14045	Corydalis decumbens	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5305	Corydalis mucronifera	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2700	Kopsia arborea	Species	Apocynaceae	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

Activity Type	# Activity
IC50	1

Activity Type	# Activity
Individual Protein	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT204	Individual Protein	Acetylcholinesterase	Homo sapiens	IC50	>	100000.0	nM	PMID[29400966]

☑ 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 NPC219113 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	323
0.1-0.2	1466
0.2-0.3	4857
0.3-0.4	11543
0.4-0.5	5647
0.5-0.6	8799
0.6-0.7	9132
0.7-0.8	853
0.8-0.85	41
0.85-0.9	19
0.9-0.95	1
0.95-1	16

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 NPC219113 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	209
0.1-0.2	653
0.2-0.3	1129
0.3-0.4	2175
0.4-0.5	2459
0.5-0.6	1756
0.6-0.7	667
0.7-0.8	97
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	3

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