NPASS Compound

Structure

NPC266573 OpenBabel06302215352D 34 36 0 0 1 0 0 0 0 0999 V2000 4.3301 -7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -7.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -4.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1962 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 C 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 0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 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 6 5 1 1 0 0 0 6 7 1 0 0 0 0 6 14 1 0 0 0 0 7 8 1 0 0 0 0 8 13 2 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 14 15 1 0 0 0 0 15 16 2 3 0 0 0 16 17 1 0 0 0 0 16 34 1 0 0 0 0 17 18 1 1 0 0 0 17 25 1 0 0 0 0 18 19 1 0 0 0 0 19 24 2 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 23 24 1 0 0 0 0 25 26 2 3 0 0 0 26 27 1 0 0 0 0 26 33 1 0 0 0 0 27 32 2 0 0 0 0 27 28 1 0 0 0 0 28 29 2 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 31 32 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	458.22
Volume:	492.692
LogP:	3.816
LogD:	3.66
LogS:	-4.363
# Rotatable Bonds:	14
TPSA:	84.5
# H-Bond Aceptor:	6
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.43
Synthetic Accessibility Score:	2.783
Fsp3:	0.25
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.072
MDCK Permeability:	3.138121610390954e-05
Pgp-inhibitor:	0.993
Pgp-substrate:	0.347
Human Intestinal Absorption (HIA):	0.117
20% Bioavailability (F20%):	0.996
30% Bioavailability (F30%):	0.988

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.074
Plasma Protein Binding (PPB):	97.38642120361328%
Volume Distribution (VD):	0.344
Pgp-substrate:	2.448822259902954%

ADMET: Metabolism

CYP1A2-inhibitor:	0.343
CYP1A2-substrate:	0.042
CYP2C19-inhibitor:	0.926
CYP2C19-substrate:	0.066
CYP2C9-inhibitor:	0.943
CYP2C9-substrate:	0.056
CYP2D6-inhibitor:	0.821
CYP2D6-substrate:	0.308
CYP3A4-inhibitor:	0.931
CYP3A4-substrate:	0.324

ADMET: Excretion

Clearance (CL):	2.485
Half-life (T1/2):	0.685

ADMET: Toxicity

hERG Blockers:	0.556
Human Hepatotoxicity (H-HT):	0.347
Drug-inuced Liver Injury (DILI):	0.892
AMES Toxicity:	0.372
Rat Oral Acute Toxicity:	0.028
Maximum Recommended Daily Dose:	0.261
Skin Sensitization:	0.462
Carcinogencity:	0.594
Eye Corrosion:	0.003
Eye Irritation:	0.011
Respiratory Toxicity:	0.019

Download Data

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

Natural Product: NPC266573

Natural Product ID:	NPC266573
*Common Name:**	AZLMMOOHDUSWNU-RSXGOPAZSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	AZLMMOOHDUSWNU-RSXGOPAZSA-N
Standard InCHI:	InChI=1S/C28H30N2O4/c1-21(31)34-20-24(17-22-11-5-2-6-12-22)19-29-28(33)26(18-23-13-7-3-8-14-23)30-27(32)25-15-9-4-10-16-25/h2-16,24,26H,17-20H2,1H3,(H,29,33)(H,30,32)/t24-,26+/m1/s1
SMILES:	CC(=O)OC[C@H](Cc1ccccc1)CN=C([C@H](Cc1ccccc1)N=C(c1ccccc1)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	5321123
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:0004321] Phenylalanine 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
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	stem	n.a.	DOI[10.1007/s11418-006-0112-9]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	leaf	n.a.	DOI[10.1007/s11418-006-0112-9]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	flower	n.a.	DOI[10.1007/s11418-006-0112-9]
NPO26741	Anemarrhena asphodeloides	Species	Asparagaceae	Eukaryota	rhizomes	n.a.	n.a.	PMID[19757853]
NPO26741	Anemarrhena asphodeloides	Species	Asparagaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[21370894]
NPO8881	Centipeda minima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23189738]
NPO20598	Lythrum salicaria	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24459770]
NPO9124	Inula japonica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27276091]
NPO18676	Clerodendrum trichotomum	Species	Lamiaceae	Eukaryota	Roots	n.a.	n.a.	PMID[29924604]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6387056]
NPO26741	Anemarrhena asphodeloides	Species	Asparagaceae	Eukaryota	Rhizomes	n.a.	n.a.	PMID[8482946]
NPO20116	Ilex cornuta	Species	Aquifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9124	Inula japonica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8881	Centipeda minima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26741	Anemarrhena asphodeloides	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13291	Changium smyrnioides	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20598	Lythrum salicaria	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16963	Fructus leonuri	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[HerDing]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9124	Inula japonica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18030	Herba acalyphae	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO16963	Fructus leonuri	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO16160	Radix aconiti	Species	Lymnaeidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26741	Anemarrhena asphodeloides	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8881	Centipeda minima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20116	Ilex cornuta	Species	Aquifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20598	Lythrum salicaria	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15542	Herba nerviliae	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO13291	Changium smyrnioides	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18676	Clerodendrum trichotomum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11222	Rubus alceifolius	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9124	Inula japonica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8881	Centipeda minima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26741	Anemarrhena asphodeloides	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20116	Ilex cornuta	Species	Aquifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20598	Lythrum salicaria	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20116	Ilex cornuta	Species	Aquifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO8881	Centipeda minima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO13291	Changium smyrnioides	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26741	Anemarrhena asphodeloides	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9124	Inula japonica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO20116	Ilex cornuta	Species	Aquifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18676	Clerodendrum trichotomum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8881	Centipeda minima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11222	Rubus alceifolius	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26741	Anemarrhena asphodeloides	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20598	Lythrum salicaria	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9124	Inula japonica	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 NPC266573 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	99
0.1-0.2	664
0.2-0.3	3244
0.3-0.4	12223
0.4-0.5	15587
0.5-0.6	9443
0.6-0.7	1250
0.7-0.8	179
0.8-0.85	4
0.85-0.9	2
0.9-0.95	1
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 NPC266573 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	87
0.1-0.2	397
0.2-0.3	814
0.3-0.4	1517
0.4-0.5	3078
0.5-0.6	2463
0.6-0.7	723
0.7-0.8	70
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