NPASS Compound

Structure

NPC25601 OpenBabel06302215382D 36 39 0 0 1 0 0 0 0 0999 V2000 1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 3.5000 0.0000 O 0 0 0 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 -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 -1.7321 2.0000 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 -0.8660 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 4.5000 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 -2.5981 4.5000 0.0000 O 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 -4.3301 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 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 -6.0622 0.5000 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 -5.1962 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 0.0000 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 -4.3301 3.5000 0.0000 O 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 0.8660 1.5000 0.0000 O 0 0 0 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 1.7321 0.0000 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 0.8660 -1.5000 0.0000 C 0 0 1 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 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 -0.0000 -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 -1.5000 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 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 4 25 1 0 0 0 0 5 6 1 0 0 0 0 6 22 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 10 1 0 0 0 0 8 9 1 0 0 0 0 10 11 2 0 0 0 0 10 12 1 0 0 0 0 12 13 2 0 0 0 0 12 23 1 0 0 0 0 13 14 1 0 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 23 24 1 0 0 0 0 26 25 1 1 0 0 0 26 27 1 0 0 0 0 26 33 1 0 0 0 0 27 28 1 0 0 0 0 27 36 1 6 0 0 0 28 29 1 0 0 0 0 28 35 1 1 0 0 0 29 30 1 0 0 0 0 29 34 1 6 0 0 0 30 31 1 1 0 0 0 30 33 1 0 0 0 0 31 32 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	720.3
Volume:	699.191
LogP:	3.2
LogD:	1.885
LogS:	-4.316
# Rotatable Bonds:	14
TPSA:	199.65
# H-Bond Aceptor:	15
# H-Bond Donor:	2
# Rings:	6
# Heavy Atoms:	15

MedChem Properties

QED Drug-Likeness Score:	0.278
Synthetic Accessibility Score:	6.479
Fsp3:	0.694
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.359
MDCK Permeability:	0.00010746550105977803
Pgp-inhibitor:	0.754
Pgp-substrate:	0.948
Human Intestinal Absorption (HIA):	0.58
20% Bioavailability (F20%):	0.004
30% Bioavailability (F30%):	0.877

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.04
Plasma Protein Binding (PPB):	63.34507751464844%
Volume Distribution (VD):	1.009
Pgp-substrate:	25.539758682250977%

ADMET: Metabolism

CYP1A2-inhibitor:	0.019
CYP1A2-substrate:	0.035
CYP2C19-inhibitor:	0.016
CYP2C19-substrate:	0.076
CYP2C9-inhibitor:	0.177
CYP2C9-substrate:	0.051
CYP2D6-inhibitor:	0.825
CYP2D6-substrate:	0.056
CYP3A4-inhibitor:	0.422
CYP3A4-substrate:	0.72

ADMET: Excretion

Clearance (CL):	2.466
Half-life (T1/2):	0.336

ADMET: Toxicity

hERG Blockers:	0.1
Human Hepatotoxicity (H-HT):	0.983
Drug-inuced Liver Injury (DILI):	0.926
AMES Toxicity:	0.504
Rat Oral Acute Toxicity:	0.637
Maximum Recommended Daily Dose:	0.91
Skin Sensitization:	0.226
Carcinogencity:	0.057
Eye Corrosion:	0.003
Eye Irritation:	0.012
Respiratory Toxicity:	0.943

Download Data

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

Natural Product: NPC25601

Natural Product ID:	NPC25601
*Common Name:**	FIBYVUGPMHIWTD-RODNGKRTSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	FIBYVUGPMHIWTD-RODNGKRTSA-N
Standard InCHI:	InChI=1S/C23H24O13/c1-32-21-12(35-23-19(31)18(30)15(27)13(7-24)36-23)6-11-14(16(21)28)17(29)22(33-2)20(34-11)8-3-4-9(25)10(26)5-8/h3-6,13,15,18-19,23-28,30-31H,7H2,1-2H3/t13-,15-,18+,19-,23-/m1/s1
SMILES:	COc1c(cc2c(c1O)c(=O)c(c(c1ccc(c(c1)O)O)o2)OC)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101243893
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003533] Flavonoid-7-O-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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO23108	Pinus flexilis	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9834165]
NPO20454	Bidens pilosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[469551]
NPO23440	Aconitum napellus	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23876370]
NPO24718	Streptomyces parvulus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[23423168]
NPO15117	Chromolaena odorata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23186307]
NPO24588	Phellinus igniarius	Species	Hymenochaetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20583752]
NPO23924	Psilotum nudum	Species	Psilotaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20488581]
NPO24811	Cibotium barometz	Species	Cibotiaceae	Eukaryota	rhizomes	n.a.	n.a.	PMID[19739599]
NPO9392	Elaeodendron alluaudianum	Species	Celastraceae	Eukaryota	n.a.	Madagascar Rainforest	n.a.	PMID[19058971]
NPO9392	Elaeodendron alluaudianum	Species	Celastraceae	Eukaryota	n.a.	stem	n.a.	PMID[19058971]

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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
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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

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
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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 NPC25601 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	444
0.1-0.2	1773
0.2-0.3	4156
0.3-0.4	9775
0.4-0.5	8387
0.5-0.6	4259
0.6-0.7	5245
0.7-0.8	5274
0.8-0.85	1537
0.85-0.9	1157
0.9-0.95	503
0.95-1	187

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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 NPC25601 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	395
0.1-0.2	942
0.2-0.3	1978
0.3-0.4	2688
0.4-0.5	1794
0.5-0.6	894
0.6-0.7	301
0.7-0.8	117
0.8-0.85	17
0.85-0.9	14
0.9-0.95	9
0.95-1	1

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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