NPASS Compound

Structure

NPC152440 OpenBabel06302215082D 47 51 0 0 1 0 0 0 0 0999 V2000 2.8863 1.6532 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2845 0.8986 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3300 1.0424 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6372 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8012 -0.4826 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9653 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.1293 -0.4827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1293 -1.4480 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9653 -1.9306 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7823 -2.4022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8012 -1.4479 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.6372 -1.9305 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4732 -1.4479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4732 -0.4826 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3092 -1.9305 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3092 -2.8958 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1451 -3.3784 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9811 -2.8958 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9811 -1.9305 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1451 -2.5378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9653 -2.8958 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.1294 -3.3785 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7066 -2.8959 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7066 -1.9306 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.1749 -1.1196 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6431 -1.9306 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5176 -3.3642 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3287 -2.8959 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1398 -3.3642 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3287 -1.9594 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1294 -4.3150 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6817 -4.7833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4928 -4.3151 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6816 -5.7199 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7764 -3.3641 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7764 -4.3007 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9654 -4.7689 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5875 -4.7689 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3986 -4.3006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2097 -4.7689 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2097 -5.7054 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3986 -6.1737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5875 -5.7055 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3533 -0.6120 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 -0.4753 0.8232 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9506 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 4 1 0 0 0 0 5 4 1 6 0 0 0 5 6 1 0 0 0 0 5 11 1 0 0 0 0 6 7 1 1 0 0 0 6 45 1 0 0 0 0 8 7 1 1 0 0 0 8 24 1 0 0 0 0 8 9 1 0 0 0 0 8 44 1 0 0 0 0 9 10 1 1 0 0 0 9 11 1 0 0 0 0 9 21 1 0 0 0 0 11 12 1 6 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 13 15 1 0 0 0 0 15 20 2 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 21 22 1 0 0 0 0 21 35 1 1 0 0 0 22 23 1 0 0 0 0 22 31 1 6 0 0 0 23 24 1 0 0 0 0 23 27 1 6 0 0 0 24 25 1 1 0 0 0 24 26 1 0 0 0 0 27 28 1 0 0 0 0 28 29 2 0 0 0 0 28 30 1 0 0 0 0 31 32 1 0 0 0 0 32 33 2 0 0 0 0 32 34 1 0 0 0 0 35 36 1 0 0 0 0 36 37 2 0 0 0 0 36 38 1 0 0 0 0 38 43 2 0 0 0 0 38 39 1 0 0 0 0 39 40 2 0 0 0 0 40 41 1 0 0 0 0 41 42 2 0 0 0 0 42 43 1 0 0 0 0 44 45 1 0 0 0 0 45 46 1 0 0 0 0 45 47 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	652.25
Volume:	647.615
LogP:	4.066
LogD:	2.323
LogS:	-4.025
# Rotatable Bonds:	12
TPSA:	160.96
# H-Bond Aceptor:	12
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.343
Synthetic Accessibility Score:	5.897
Fsp3:	0.514
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:	-5.258
MDCK Permeability:	3.8196503737708554e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.068
20% Bioavailability (F20%):	0.939
30% Bioavailability (F30%):	0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.176
Plasma Protein Binding (PPB):	80.1255111694336%
Volume Distribution (VD):	1.963
Pgp-substrate:	12.902608871459961%

ADMET: Metabolism

CYP1A2-inhibitor:	0.144
CYP1A2-substrate:	0.031
CYP2C19-inhibitor:	0.041
CYP2C19-substrate:	0.064
CYP2C9-inhibitor:	0.623
CYP2C9-substrate:	0.027
CYP2D6-inhibitor:	0.99
CYP2D6-substrate:	0.071
CYP3A4-inhibitor:	0.698
CYP3A4-substrate:	0.439

ADMET: Excretion

Clearance (CL):	5.416
Half-life (T1/2):	0.702

ADMET: Toxicity

hERG Blockers:	0.343
Human Hepatotoxicity (H-HT):	0.761
Drug-inuced Liver Injury (DILI):	0.972
AMES Toxicity:	0.016
Rat Oral Acute Toxicity:	0.027
Maximum Recommended Daily Dose:	0.005
Skin Sensitization:	0.142
Carcinogencity:	0.082
Eye Corrosion:	0.003
Eye Irritation:	0.021
Respiratory Toxicity:	0.036

Download Data

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

Natural Product: NPC152440

Natural Product ID:	NPC152440
*Common Name:**	NDGYPTLRFYJRBP-SJXUQEJZSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	NDGYPTLRFYJRBP-SJXUQEJZSA-N
Standard InCHI:	InChI=1S/C35H40O12/c1-19(36)42-25-24-18-35(47-32(24,4)5)33(6,27(25)45-30(39)22-14-10-8-11-15-22)28(46-31(40)23-16-12-9-13-17-23)26(43-20(2)37)29(34(35,7)41)44-21(3)38/h8-17,24-29,41H,18H2,1-7H3/t24-,25-,26-,27-,28-,29-,33+,34-,35+/m0/s1
SMILES:	CC(=O)O[C@H]1[C@@H]2C[C@]3([C@](C)([C@H]1OC(=O)c1ccccc1)[C@H]([C@@H]([C@@H]([C@]3(C)O)OC(=O)C)OC(=O)C)OC(=O)c1ccccc1)OC2(C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	76323428
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0002995] Pentacarboxylic 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
NPO3859	Maytenus magellanica	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11741484]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15679323]
NPO4368	Magnolia officinalis	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1659613]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	roots	n.a.	n.a.	PMID[16643052]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	Roots; Stems; Tubers	n.a.	n.a.	PMID[16872143]
NPO4368	Magnolia officinalis	Species	Magnoliaceae	Eukaryota	stem bark	n.a.	n.a.	PMID[17918910]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	roots	n.a.	n.a.	PMID[18452334]
NPO8299	Sorocea muriculata	Species	Moraceae	Eukaryota	n.a.	root	n.a.	PMID[18847244]
NPO4368	Magnolia officinalis	Species	Magnoliaceae	Eukaryota	Stems; Barks	n.a.	n.a.	PMID[19086868]
NPO26437	Maytenus jelskii	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20146433]
NPO26437	Maytenus jelskii	Species	Celastraceae	Eukaryota	fruits	n.a.	n.a.	PMID[21856049]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[21902195]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	n.a.	tuberous root	n.a.	PMID[21902195]
NPO4368	Magnolia officinalis	Species	Magnoliaceae	Eukaryota	n.a.	bark	n.a.	PMID[23823874]
NPO26437	Maytenus jelskii	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27541714]
NPO4368	Magnolia officinalis	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28485933]
NPO3599	Rheum maximowiczii	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO473	Artemisia maritima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4368	Magnolia officinalis	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3107	Bupleurum falcatum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21651	Cheilocostus speciosus	Species	Costaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4368	Magnolia officinalis	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3107	Bupleurum falcatum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO473	Artemisia maritima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3599	Rheum maximowiczii	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO473	Artemisia maritima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3107	Bupleurum falcatum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4368	Magnolia officinalis	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4368	Magnolia officinalis	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO3107	Bupleurum falcatum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO8299	Sorocea muriculata	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19620	Stemona tuberosa	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4368	Magnolia officinalis	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13443	Doris montereyensis	Species	Dorididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5157	Penstemon nitidus	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2479	Dorstenia drakena	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4827	Glycyrrhiza macedonica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3859	Maytenus magellanica	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO473	Artemisia maritima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8419	Lepechinia glomerata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1521	Curcuma oligantha	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3107	Bupleurum falcatum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO787	Lentinus degener	Species	Lentinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6325	Senecio nebrodensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21651	Cheilocostus speciosus	Species	Costaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7948	Galium sinaicum	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5329	Aspilia bishoplecta	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26437	Maytenus jelskii	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25504	Streptomyces rutgersensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO5501	Pulicaria angustifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3439	Streptomyces koyangensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO3021	Arcicella aquatica	Species	Cytophagaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO2887	Ottonia ovata	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO3599	Rheum maximowiczii	Species	Polygonaceae	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
Others	2

Activity Type	# Activity
Others	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified		Activity	=	79.3	%	PMID[27541714]
NPT2	Others	Unspecified		Activity	>	60.0	%	PMID[27541714]

☑ 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 NPC152440 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

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 NPC152440 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

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