NPASS Compound

Structure

NPC472995 OpenBabel07101719252D 41 41 0 0 1 0 0 0 0 0999 V2000 -0.0000 6.0000 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 3.4641 -3.0000 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 5.1962 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 4.0000 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 0.8660 -3.5000 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 -1.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 5.5000 0.0000 C 0 0 0 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 2.5981 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 4.0000 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 4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 4.5000 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 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 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -0.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 3.4641 1.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 1 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 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 1 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 1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1962 0.0000 0.0000 O 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 2.5981 -0.5000 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 3.4641 3.0000 0.0000 O 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 -0.5000 -0.8660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.5000 0.0000 O 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 0.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 11 1 0 0 0 0 2 12 1 0 0 0 0 3 13 1 0 0 0 0 4 16 2 0 0 0 0 5 16 1 0 0 0 0 6 17 1 0 0 0 0 7 18 1 0 0 0 0 8 19 1 0 0 0 0 9 20 2 0 0 0 0 11 17 1 0 0 0 0 12 18 2 0 0 0 0 13 19 2 0 0 0 0 14 17 2 0 0 0 0 14 23 1 0 0 0 0 15 21 1 0 0 0 0 15 22 1 0 0 0 0 16 21 1 0 0 0 0 18 29 1 0 0 0 0 19 30 1 0 0 0 0 20 22 1 0 0 0 0 21 32 1 0 0 0 0 22 39 1 0 0 0 0 23 33 2 0 0 0 0 23 40 1 0 0 0 0 24 20 1 1 0 0 0 24 25 1 0 0 0 0 24 26 1 0 0 0 0 25 28 1 0 0 0 0 25 34 1 6 0 0 0 26 27 1 0 0 0 0 26 40 1 6 0 0 0 27 31 1 6 0 0 0 27 35 1 0 0 0 0 28 31 1 6 0 0 0 28 41 1 0 0 0 0 29 36 2 0 0 0 0 29 39 1 0 0 0 0 30 37 2 0 0 0 0 30 41 1 0 0 0 0 31 10 1 6 0 0 0 31 38 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	578.31
Volume:	602.986
LogP:	2.348
LogD:	1.268
LogS:	-3.112
# Rotatable Bonds:	15
TPSA:	159.82
# H-Bond Aceptor:	10
# H-Bond Donor:	4
# Rings:	1
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.117
Synthetic Accessibility Score:	5.522
Fsp3:	0.581
Lipinski Rule-of-5:	Accepted
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:	-4.775
MDCK Permeability:	3.249424844398163e-05
Pgp-inhibitor:	0.996
Pgp-substrate:	0.962
Human Intestinal Absorption (HIA):	0.866
20% Bioavailability (F20%):	0.01
30% Bioavailability (F30%):	0.971

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.061
Plasma Protein Binding (PPB):	74.08634185791016%
Volume Distribution (VD):	1.628
Pgp-substrate:	14.638914108276367%

ADMET: Metabolism

CYP1A2-inhibitor:	0.143
CYP1A2-substrate:	0.242
CYP2C19-inhibitor:	0.406
CYP2C19-substrate:	0.665
CYP2C9-inhibitor:	0.916
CYP2C9-substrate:	0.092
CYP2D6-inhibitor:	0.114
CYP2D6-substrate:	0.046
CYP3A4-inhibitor:	0.818
CYP3A4-substrate:	0.296

ADMET: Excretion

Clearance (CL):	4.168
Half-life (T1/2):	0.564

ADMET: Toxicity

hERG Blockers:	0.019
Human Hepatotoxicity (H-HT):	0.974
Drug-inuced Liver Injury (DILI):	0.388
AMES Toxicity:	0.01
Rat Oral Acute Toxicity:	0.24
Maximum Recommended Daily Dose:	0.847
Skin Sensitization:	0.19
Carcinogencity:	0.036
Eye Corrosion:	0.003
Eye Irritation:	0.014
Respiratory Toxicity:	0.928

Download Data

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

Natural Product: NPC472995

Natural Product ID:	NPC472995
*Common Name:**	NYAOMORZVGLFQV-NKWFWLRYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	NYAOMORZVGLFQV-NKWFWLRYSA-N
Standard InCHI:	InChI=1S/C31H46O10/c1-11-17(6)14-23(33)40-26-24(20(9)22(15-21(32)16(4)5)39-29(36)18(7)12-2)25(34)28(31(10,38)27(26)35)41-30(37)19(8)13-3/h12-14,21-22,24-28,32,34-35,38H,4,9,11,15H2,1-3,5-8,10H3/b17-14+,18-12-,19-13-/t21?,22?,24-,25-,26+,27+,28-,31-/m0/s1
SMILES:	CC/C(=C/C(=O)O[C@@H]1[C@@H](C(=C)C(OC(=O)/C(=CC)/C)CC(C(=C)C)O)[C@H](O)[C@@H]([C@@]([C@@H]1O)(C)O)OC(=O)/C(=CC)/C)/C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL3597518
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001550] Sesquiterpenoids

*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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO32699	parasenecio rubescens	Species	Asteraceae	Eukaryota	Whole Plant	n.a.	n.a.	PMID[26200396]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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	3
Others	2

Activity Type	# Activity
Cell Line	3
Organism	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT319	Cell Line	B16	Mus musculus	IC50	=	39690.0	nM	PMID[468509]
NPT65	Cell Line	HepG2	Homo sapiens	IC50	=	71500.0	nM	PMID[468509]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	=	78900.0	nM	PMID[468509]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	IZ	=	9.0	mm	PMID[468509]
NPT19	Organism	Escherichia coli	Escherichia coli	IZ	=	8.0	mm	PMID[468509]

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☑ 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 NPC472995 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	193
0.1-0.2	1325
0.2-0.3	4152
0.3-0.4	6351
0.4-0.5	15145
0.5-0.6	9020
0.6-0.7	5315
0.7-0.8	1151
0.8-0.85	32
0.85-0.9	7
0.9-0.95	5
0.95-1	1

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Similarity Score	Similarity Level	Natural Product ID
0.9451	High Similarity	NPC469583
0.9348	High Similarity	NPC472997
0.9348	High Similarity	NPC472996
0.9247	High Similarity	NPC472998
0.8713	High Similarity	NPC475586

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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 NPC472995 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	172
0.1-0.2	1675
0.2-0.3	3604
0.3-0.4	2342
0.4-0.5	963
0.5-0.6	305
0.6-0.7	81
0.7-0.8	5
0.8-0.85	2
0.85-0.9	1
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8958	High Similarity	NPD5344	Discontinued
0.8469	Intermediate Similarity	NPD6648	Approved
0.8211	Intermediate Similarity	NPD7838	Discovery
0.8021	Intermediate Similarity	NPD6698	Approved
0.8021	Intermediate Similarity	NPD46	Approved

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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