NPASS Compound

Structure

NPC270750 OpenBabel06302215242D 28 29 0 0 1 0 0 0 0 0999 V2000 5.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4641 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4641 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 -0.0000 0.0000 N 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 -0.7071 0.7071 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.0000 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.8660 -1.5000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 2.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7071 -1.7071 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.6730 -1.4483 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3801 -2.1554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3461 -1.8966 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0532 -2.6037 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0191 -2.3449 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.7262 -3.0520 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4674 -4.0179 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.6921 -2.7932 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2779 -1.3789 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.9319 -0.4824 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 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 17 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 11 1 0 0 0 0 8 9 2 0 0 0 0 8 10 1 0 0 0 0 11 15 1 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 12 14 1 0 0 0 0 14 15 1 0 0 0 0 14 18 1 1 0 0 0 15 16 1 6 0 0 0 16 17 1 0 0 0 0 18 19 2 3 0 0 0 19 20 1 0 0 0 0 19 28 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 23 27 1 6 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	415.1
Volume:	374.182
LogP:	-3.24
LogD:	-0.829
LogS:	-1.724
# Rotatable Bonds:	10
TPSA:	176.33
# H-Bond Aceptor:	11
# H-Bond Donor:	5
# Rings:	2
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.215
Synthetic Accessibility Score:	4.29
Fsp3:	0.562
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.306
MDCK Permeability:	2.7098500140709803e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.96
Human Intestinal Absorption (HIA):	0.905
20% Bioavailability (F20%):	0.005
30% Bioavailability (F30%):	0.012

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.09
Plasma Protein Binding (PPB):	23.036102294921875%
Volume Distribution (VD):	0.418
Pgp-substrate:	76.69737243652344%

ADMET: Metabolism

CYP1A2-inhibitor:	0.001
CYP1A2-substrate:	0.011
CYP2C19-inhibitor:	0.052
CYP2C19-substrate:	0.039
CYP2C9-inhibitor:	0.041
CYP2C9-substrate:	0.506
CYP2D6-inhibitor:	0.308
CYP2D6-substrate:	0.068
CYP3A4-inhibitor:	0.033
CYP3A4-substrate:	0.008

ADMET: Excretion

Clearance (CL):	2.464
Half-life (T1/2):	0.949

ADMET: Toxicity

hERG Blockers:	0.003
Human Hepatotoxicity (H-HT):	0.053
Drug-inuced Liver Injury (DILI):	0.561
AMES Toxicity:	0.007
Rat Oral Acute Toxicity:	0.019
Maximum Recommended Daily Dose:	0.005
Skin Sensitization:	0.345
Carcinogencity:	0.034
Eye Corrosion:	0.003
Eye Irritation:	0.028
Respiratory Toxicity:	0.335

Download Data

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

Natural Product: NPC270750

Natural Product ID:	NPC270750
*Common Name:**	HOKIDJSKDBPKTQ-OLUVUFQESA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HOKIDJSKDBPKTQ-OLUVUFQESA-N
Standard InCHI:	InChI=1S/C16H21N3O8S/c1-7(20)27-5-8-6-28-14-11(13(22)19(14)12(8)16(25)26)18-10(21)4-2-3-9(17)15(23)24/h9,11,14H,2-6,17H2,1H3,(H,18,21)(H,23,24)(H,25,26)/t9-,11+,14-/m1/s1
SMILES:	CC(=O)OCC1=C(C(=O)O)N2C(=O)[C@@H]([C@H]2SC1)N=C(CCC[C@H](C(=O)O)N)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0000013] Amino acids, peptides, and analogues [CHEMONTID:0000347] Amino acids and derivatives [CHEMONTID:0000060] Alpha amino acids and derivatives [CHEMONTID:0001189] N-acyl-alpha amino acids and derivatives

*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
NPO17755	Inula helenium	Species	Asteraceae	Eukaryota	n.a.	root	n.a.	PMID[10364842]
NPO17755	Inula helenium	Species	Asteraceae	Eukaryota	n.a.	root	n.a.	PMID[12392098]
NPO16914	Abacopteris penangiana	n.a.	n.a.	n.a.	n.a.	rhizome	n.a.	PMID[16499328]
NPO16914	Abacopteris penangiana	n.a.	n.a.	n.a.	Rhizomes	n.a.	n.a.	PMID[16499328]
NPO16914	Abacopteris penangiana	n.a.	n.a.	n.a.	aerial parts	Jiangxi Province, China	2004-JUN	PMID[17922550]
NPO21717	Acremonium chrysogenum	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	PMID[23089729]
NPO17755	Inula helenium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23501116]
NPO17755	Inula helenium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24996657]
NPO17755	Inula helenium	Species	Asteraceae	Eukaryota	n.a.	root	n.a.	PMID[25767328]
NPO1816	Pterogorgia citrina	Species	Gorgoniidae	Eukaryota	n.a.	Caribbean	n.a.	PMID[7911157]
NPO17755	Inula helenium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12178	Pinellia pedatisecta	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12178	Pinellia pedatisecta	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17755	Inula helenium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17598	Maytenus mossambicensis	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12178	Pinellia pedatisecta	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO17755	Inula helenium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO17755	Inula helenium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16689	Corydalis clavicula	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10736	Teucrium kotschyanum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21717	Acremonium chrysogenum	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17137	Nymania capensis	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16208	Viguiera pinnatiloba	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1816	Pterogorgia citrina	Species	Gorgoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16914	Abacopteris penangiana	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO814	Acipenser sturio	Species	Acipenseridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22249	Senecio leptolobus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3210	Polyporus arcularius	Species	Polyporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21752.1	Bauhinia forficata subsp. pruinosa	Subspecies	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO309	Phyla canescens	Species	Verbenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16559	Darwinia grandiflora	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15728	Prunus nipponica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17598	Maytenus mossambicensis	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12178	Pinellia pedatisecta	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14792	Abies grandis	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12400	Cereus gummosus	Species	Sagartiidae	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 NPC270750 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	160
0.1-0.2	7286
0.2-0.3	27284
0.3-0.4	6559
0.4-0.5	1211
0.5-0.6	182
0.6-0.7	12
0.7-0.8	1
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	1

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 NPC270750 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	75
0.1-0.2	1021
0.2-0.3	5156
0.3-0.4	2320
0.4-0.5	402
0.5-0.6	147
0.6-0.7	25
0.7-0.8	3
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