NPASS Compound

Structure

NPC168569 OpenBabel06302215392D 25 27 0 0 1 0 0 0 0 0999 V2000 -0.8660 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 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 -0.8660 -0.5000 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 -1.7321 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 -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 0.8660 2.5000 0.0000 O 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 1 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 3.4641 0.0000 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 4.3301 -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 2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 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 -2.5981 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -3.5000 0.0000 C 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 25 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 23 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 24 1 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 9 23 1 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 10 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 1 0 0 0 13 22 1 0 0 0 0 14 19 2 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 21 1 0 0 0 0 18 19 1 0 0 0 0 18 20 1 0 0 0 0 22 23 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	340.13
Volume:	351.666
LogP:	4.344
LogD:	3.223
LogS:	-3.66
# Rotatable Bonds:	3
TPSA:	86.99
# H-Bond Aceptor:	5
# H-Bond Donor:	3
# Rings:	3
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.58
Synthetic Accessibility Score:	3.211
Fsp3:	0.25
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.74
MDCK Permeability:	1.5070089830260258e-05
Pgp-inhibitor:	0.055
Pgp-substrate:	0.051
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.454
30% Bioavailability (F30%):	0.828

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.024
Plasma Protein Binding (PPB):	96.62060546875%
Volume Distribution (VD):	0.606
Pgp-substrate:	4.171710014343262%

ADMET: Metabolism

CYP1A2-inhibitor:	0.692
CYP1A2-substrate:	0.44
CYP2C19-inhibitor:	0.874
CYP2C19-substrate:	0.06
CYP2C9-inhibitor:	0.878
CYP2C9-substrate:	0.907
CYP2D6-inhibitor:	0.898
CYP2D6-substrate:	0.545
CYP3A4-inhibitor:	0.38
CYP3A4-substrate:	0.17

ADMET: Excretion

Clearance (CL):	21.52
Half-life (T1/2):	0.69

ADMET: Toxicity

hERG Blockers:	0.028
Human Hepatotoxicity (H-HT):	0.449
Drug-inuced Liver Injury (DILI):	0.791
AMES Toxicity:	0.1
Rat Oral Acute Toxicity:	0.74
Maximum Recommended Daily Dose:	0.54
Skin Sensitization:	0.94
Carcinogencity:	0.471
Eye Corrosion:	0.003
Eye Irritation:	0.897
Respiratory Toxicity:	0.854

Download Data

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

Natural Product: NPC168569

Natural Product ID:	NPC168569
*Common Name:**	ADFZZQAJJGHYDR-IBGZPJMESA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ADFZZQAJJGHYDR-IBGZPJMESA-N
Standard InCHI:	InChI=1S/C20H20O5/c1-11(2)3-5-13-15(21)8-6-14-17(23)10-19(25-20(13)14)12-4-7-16(22)18(24)9-12/h3-4,6-9,19,21-22,24H,5,10H2,1-2H3/t19-/m0/s1
SMILES:	CC(=CCc1c(ccc2C(=O)C[C@@H](c3ccc(c(c3)O)O)Oc12)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	25837768
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0000337] Flavans [CHEMONTID:0003642] 8-prenylated flavans [CHEMONTID:0003508] 8-prenylated flavanones

*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
NPO17812	Jatropha neopauciflora	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17125233]
NPO24286	Micromonospora lupini	Species	Micromonosporaceae	Bacteria	n.a.	n.a.	n.a.	PMID[17475486]
NPO21731	Acanthella cavernosa	Species	Axinellidae	Eukaryota	n.a.	n.a.	n.a.	PMID[2045823]
NPO24286	Micromonospora lupini	Species	Micromonosporaceae	Bacteria	n.a.	n.a.	n.a.	PMID[21226490]
NPO24200	Piper angustifolium	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20119	Aconitum sungpanense	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20119	Aconitum sungpanense	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24200	Piper angustifolium	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20119	Aconitum sungpanense	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20119	Aconitum sungpanense	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14151	Macaca fascicularis	Species	Cercopithecidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23661	Spiraea koreana	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24420	Aria japonica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17812	Jatropha neopauciflora	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24286	Micromonospora lupini	Species	Micromonosporaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO23983	Siphonoglossa buchii	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO23937	0tholaena pallens	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4721	Amphiachyris dracunculoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6174	Croton malambo	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24200	Piper angustifolium	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23806	Polygala triphylla	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17273	Empedobacter haloabium	Species	Flavobacteriaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO21430	Myctophum asperum	Species	Myctophidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21440	Trixis wrightii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21731	Acanthella cavernosa	Species	Axinellidae	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 NPC168569 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	404
0.1-0.2	1542
0.2-0.3	3948
0.3-0.4	9530
0.4-0.5	8645
0.5-0.6	3253
0.6-0.7	4623
0.7-0.8	5377
0.8-0.85	2787
0.85-0.9	1888
0.9-0.95	613
0.95-1	87

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 NPC168569 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	350
0.1-0.2	931
0.2-0.3	1690
0.3-0.4	2582
0.4-0.5	1816
0.5-0.6	1054
0.6-0.7	515
0.7-0.8	147
0.8-0.85	39
0.85-0.9	20
0.9-0.95	4
0.95-1	2

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