NPASS Compound

Structure

NPC101908 OpenBabel06302215222D 22 22 0 0 1 0 0 0 0 0999 V2000 6.9282 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 4.0000 0.0000 N 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 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 1 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 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -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 -0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 0.0000 O 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 -1.7321 -2.0000 0.0000 O 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 2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 4 2 3 0 0 0 4 5 1 0 0 0 0 4 22 1 0 0 0 0 5 6 2 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 9 21 1 6 0 0 0 10 11 1 0 0 0 0 11 16 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 19 1 0 0 0 0 15 16 1 0 0 0 0 15 17 1 0 0 0 0 17 18 1 0 0 0 0 19 20 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	305.16
Volume:	324.371
LogP:	1.415
LogD:	0.476
LogS:	-1.856
# Rotatable Bonds:	10
TPSA:	64.63
# H-Bond Aceptor:	5
# H-Bond Donor:	1
# Rings:	1
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.711
Synthetic Accessibility Score:	2.243
Fsp3:	0.412
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:	-4.609
MDCK Permeability:	4.2494910303503275e-05
Pgp-inhibitor:	0.731
Pgp-substrate:	0.061
Human Intestinal Absorption (HIA):	0.022
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.009

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.975
Plasma Protein Binding (PPB):	54.29434585571289%
Volume Distribution (VD):	0.766
Pgp-substrate:	24.03243637084961%

ADMET: Metabolism

CYP1A2-inhibitor:	0.136
CYP1A2-substrate:	0.506
CYP2C19-inhibitor:	0.356
CYP2C19-substrate:	0.885
CYP2C9-inhibitor:	0.114
CYP2C9-substrate:	0.754
CYP2D6-inhibitor:	0.035
CYP2D6-substrate:	0.869
CYP3A4-inhibitor:	0.282
CYP3A4-substrate:	0.468

ADMET: Excretion

Clearance (CL):	7.837
Half-life (T1/2):	0.917

ADMET: Toxicity

hERG Blockers:	0.063
Human Hepatotoxicity (H-HT):	0.127
Drug-inuced Liver Injury (DILI):	0.119
AMES Toxicity:	0.042
Rat Oral Acute Toxicity:	0.161
Maximum Recommended Daily Dose:	0.525
Skin Sensitization:	0.669
Carcinogencity:	0.055
Eye Corrosion:	0.005
Eye Irritation:	0.062
Respiratory Toxicity:	0.228

Download Data

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

Natural Product: NPC101908

Natural Product ID:	NPC101908
*Common Name:**	XAJXBWHLLVMCFS-OBUCXMDBSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XAJXBWHLLVMCFS-OBUCXMDBSA-N
Standard InCHI:	InChI=1S/C17H23NO4/c1-4-18-17(20)8-6-5-7-14(19)11-13-9-10-15(21-2)16(12-13)22-3/h5-10,12,14,19H,4,11H2,1-3H3,(H,18,20)/b7-5+,8-6+/t14-/m0/s1
SMILES:	CCN=C(/C=C/C=C/[C@@H](Cc1ccc(c(c1)OC)OC)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	72196849
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0002279] Benzene and substituted derivatives [CHEMONTID:0004113] Methoxybenzenes [CHEMONTID:0004111] Dimethoxybenzenes

*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
NPO6257	Ficus septica	Species	Moraceae	Eukaryota	Stems	Tainan Hsien, Taiwan, Republic of China	2000-JAN	PMID[16038551]
NPO6257	Ficus septica	Species	Moraceae	Eukaryota	leaves	n.a.	n.a.	PMID[19938815]
NPO2618	Curcuma wenyujin	Species	Zingiberaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[23738470]
NPO2618	Curcuma wenyujin	Species	Zingiberaceae	Eukaryota	n.a.	root	n.a.	PMID[23738470]
NPO2618	Curcuma wenyujin	Species	Zingiberaceae	Eukaryota	Rhizomes	n.a.	n.a.	PMID[25275213]
NPO794	Lippia graveolens	Species	Verbenaceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO794	Lippia graveolens	Species	Verbenaceae	Eukaryota	Shoot	n.a.	n.a.	Database[FooDB]
NPO794	Lippia graveolens	Species	Verbenaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO13118	Paeonia officinalis	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6257	Ficus septica	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13118	Paeonia officinalis	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6257	Ficus septica	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2618	Curcuma wenyujin	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO2618	Curcuma wenyujin	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO12080	Metrodorea flavida	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10161	Macaranga pleiostemona	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13118	Paeonia officinalis	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11817	Seiridium cardinale	Species	Sporocadaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1187	Baccharis scandens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO794	Lippia graveolens	Species	Verbenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7346	Ligularia odontomanes	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1863	Alpinia pricei	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8078	Palaquium leiocarpum	Species	Sapotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6257	Ficus septica	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2618	Curcuma wenyujin	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3390	Radermachia sinica	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO474	Beilschmiedia kunstleri	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20070.1	Crinum stuhlmannii subsp. delagoense	Subspecies	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11706	Gordonia terrae	Species	Gordoniaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO12193	Metadina trichotoma	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15978	Nalanthamala diospyri	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12316	Pterospermum lanceolatum	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11948	Ferulago sylvatica	Species	Apiaceae	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	4

Activity Type	# Activity
Cell Line	4

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT165	Cell Line	HeLa	Homo sapiens	IC50	=	14580.0	nM	PMID[478514]
NPT81	Cell Line	A549	Homo sapiens	IC50	=	13830.0	nM	PMID[478514]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	=	12870.0	nM	PMID[478514]
NPT744	Cell Line	IMR-32	Homo sapiens	IC50	=	9430.0	nM	PMID[478514]

☑ 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 NPC101908 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	159
0.1-0.2	1164
0.2-0.3	4979
0.3-0.4	13215
0.4-0.5	5104
0.5-0.6	9075
0.6-0.7	6855
0.7-0.8	1944
0.8-0.85	155
0.85-0.9	41
0.9-0.95	5
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 NPC101908 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	133
0.1-0.2	684
0.2-0.3	1384
0.3-0.4	2478
0.4-0.5	2234
0.5-0.6	1353
0.6-0.7	720
0.7-0.8	151
0.8-0.85	13
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