NPASS Compound

Structure

NPC29288 OpenBabel06302215422D 40 45 0 0 1 0 0 0 0 0999 V2000 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 O 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 2.5981 -1.5000 0.0000 C 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 3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -4.5000 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 0.9889 0.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3956 1.5827 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3902 1.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0593 2.2213 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 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 5.1962 2.0000 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 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0132 0.1910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.6010 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0132 1.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 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 -0.8660 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 2 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 -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 O 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 1.5000 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 -3.4641 -1.0000 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 C 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 8 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 18 1 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 11 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 11 12 2 0 0 0 0 11 28 1 0 0 0 0 12 17 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 15 17 1 0 0 0 0 17 18 2 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 27 1 0 0 0 0 22 23 2 0 0 0 0 23 24 1 0 0 0 0 23 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 29 28 1 1 0 0 0 29 30 1 0 0 0 0 29 34 1 0 0 0 0 30 31 1 0 0 0 0 30 39 1 6 0 0 0 31 32 1 0 0 0 0 31 37 1 1 0 0 0 32 33 1 0 0 0 0 32 35 1 6 0 0 0 33 34 1 0 0 0 0 35 36 1 0 0 0 0 37 38 1 0 0 0 0 39 40 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	554.18
Volume:	531.766
LogP:	3.651
LogD:	2.997
LogS:	-5.717
# Rotatable Bonds:	8
TPSA:	109.37
# H-Bond Aceptor:	11
# H-Bond Donor:	0
# Rings:	6
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.38
Synthetic Accessibility Score:	4.17
Fsp3:	0.414
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.023
MDCK Permeability:	5.968032928649336e-05
Pgp-inhibitor:	0.988
Pgp-substrate:	0.043
Human Intestinal Absorption (HIA):	0.002
20% Bioavailability (F20%):	0.001
30% Bioavailability (F30%):	0.01

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.134
Plasma Protein Binding (PPB):	82.87683868408203%
Volume Distribution (VD):	0.669
Pgp-substrate:	2.014522075653076%

ADMET: Metabolism

CYP1A2-inhibitor:	0.099
CYP1A2-substrate:	0.987
CYP2C19-inhibitor:	0.029
CYP2C19-substrate:	0.533
CYP2C9-inhibitor:	0.051
CYP2C9-substrate:	0.556
CYP2D6-inhibitor:	0.467
CYP2D6-substrate:	0.898
CYP3A4-inhibitor:	0.787
CYP3A4-substrate:	0.67

ADMET: Excretion

Clearance (CL):	11.882
Half-life (T1/2):	0.089

ADMET: Toxicity

hERG Blockers:	0.447
Human Hepatotoxicity (H-HT):	0.207
Drug-inuced Liver Injury (DILI):	0.949
AMES Toxicity:	0.888
Rat Oral Acute Toxicity:	0.04
Maximum Recommended Daily Dose:	0.136
Skin Sensitization:	0.357
Carcinogencity:	0.494
Eye Corrosion:	0.003
Eye Irritation:	0.049
Respiratory Toxicity:	0.464

Download Data

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

Natural Product: NPC29288

Natural Product ID:	NPC29288
*Common Name:**	LZXXMGFJLMMPML-YXPSQANSSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	LZXXMGFJLMMPML-YXPSQANSSA-N
Standard InCHI:	InChI=1S/C29H30O11/c1-31-19-9-15-16(10-20(19)32-2)25(40-29-27(35-5)26(34-4)22(33-3)12-37-29)17-11-36-28(30)24(17)23(15)14-6-7-18-21(8-14)39-13-38-18/h6-10,22,26-27,29H,11-13H2,1-5H3/t22-,26+,27-,29+/m1/s1
SMILES:	COc1cc2c(cc1OC)c(c1COC(=O)c1c2c1ccc2c(c1)OCO2)O[C@H]1[C@@H]([C@H]([C@@H](CO1)OC)OC)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	60200398
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0001511] Lignan glycosides

*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
NPO24195	Stylissa carteri	Species	Axinellidae	Eukaryota	n.a.	n.a.	n.a.	PMID[15043426]
NPO28817	Plakortis zyggompha	Species	Plakinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[15844945]
NPO28401	Phyllanthus taxodiifolius	Species	Phyllanthaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[16450297]
NPO4806	Clausena wallichii	Species	Rutaceae	Eukaryota	Roots	n.a.	n.a.	PMID[22482432]
NPO28817	Plakortis zyggompha	Species	Plakinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[26859086]
NPO24195	Stylissa carteri	Species	Axinellidae	Eukaryota	n.a.	indopacific	n.a.	PMID[9917317]
NPO29265	Melodinus balansae	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27538	Hemsleya macrosperma	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29265	Melodinus balansae	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27538	Hemsleya macrosperma	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29091	Delisea fimbriata	Species	Bonnemaisoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28713	Psoroma allorhizum	Species	Pannariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28817	Plakortis zyggompha	Species	Plakinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28401	Phyllanthus taxodiifolius	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29088	Nerine masonorum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6047	Dictyota spiralis	Species	Dictyotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28054	Uvaria rugosa	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24195	Stylissa carteri	Species	Axinellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29136	Heckeria umbellata	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO19527	Citropsis gabunensis	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29244	Parmelia flavescentireagens	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25690	Doronicum pardalianches	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27998	Millettia puguensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28848	Selinum decipiens	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4806	Clausena wallichii	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28592	Streptomyces catenulae	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO27538	Hemsleya macrosperma	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29265	Melodinus balansae	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28953	Guatteria scandens	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23970	Heliomeris obscura	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29163	Guettarda trimera	Species	Rubiaceae	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
Others	2

Activity Type	# Activity
Cell Line	3
Others	3

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT139	Cell Line	HT-29	Homo sapiens	IC50	=	18.0	nM	PMID[558791]
NPT377	Cell Line	OVCAR-3	Homo sapiens	IC50	=	7600.0	nM	PMID[558791]
NPT111	Cell Line	K562	Homo sapiens	IC50	=	470.0	nM	PMID[558791]
NPT2	Others	Unspecified		Ratio IC50	>	400.0	n.a.	PMID[558791]
NPT2	Others	Unspecified		IC50	=	430.0	nM	PMID[558791]
NPT2	Others	Unspecified		Ratio IC50	=	0.91	n.a.	PMID[558791]

☑ 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 NPC29288 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	452
0.1-0.2	1740
0.2-0.3	3652
0.3-0.4	9257
0.4-0.5	9360
0.5-0.6	4044
0.6-0.7	7512
0.7-0.8	6277
0.8-0.85	342
0.85-0.9	36
0.9-0.95	11
0.95-1	14

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 NPC29288 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	373
0.1-0.2	940
0.2-0.3	1641
0.3-0.4	2708
0.4-0.5	1982
0.5-0.6	935
0.6-0.7	452
0.7-0.8	109
0.8-0.85	10
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