NPASS Compound

Structure

NPC294629 OpenBabel07101718182D 41 45 0 0 1 0 0 0 0 0999 V2000 1.7321 -4.0000 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 6.9282 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 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 5.1962 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 C 0 0 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 6.9282 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 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 -1.5000 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 -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 3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 C 0 0 2 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 0.0000 2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 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 2.5981 -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 0.8660 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 9.5263 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -2.5000 0.0000 O 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 -0.0000 -3.0000 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 0.0000 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.0000 0.0000 O 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 2.5981 -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 6.0622 0.5000 0.0000 O 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 3 4 2 0 0 0 0 3 10 1 0 0 0 0 4 11 1 0 0 0 0 5 10 2 0 0 0 0 5 12 1 0 0 0 0 6 13 1 0 0 0 0 6 15 2 0 0 0 0 7 14 2 0 0 0 0 7 16 1 0 0 0 0 8 1 1 6 0 0 0 8 20 1 0 0 0 0 8 38 1 0 0 0 0 9 2 1 1 0 0 0 9 19 1 0 0 0 0 9 39 1 0 0 0 0 10 15 1 0 0 0 0 11 12 2 0 0 0 0 11 28 1 0 0 0 0 12 29 1 0 0 0 0 13 17 1 0 0 0 0 13 30 2 0 0 0 0 14 18 1 0 0 0 0 14 31 1 0 0 0 0 15 40 1 0 0 0 0 16 17 2 0 0 0 0 16 40 1 0 0 0 0 17 21 1 0 0 0 0 18 21 2 0 0 0 0 19 22 1 0 0 0 0 19 32 1 6 0 0 0 20 23 1 0 0 0 0 20 33 1 1 0 0 0 21 34 1 0 0 0 0 22 24 1 0 0 0 0 22 35 1 1 0 0 0 23 26 1 0 0 0 0 23 36 2 0 0 0 0 24 27 1 0 0 0 0 24 37 1 1 0 0 0 25 18 1 6 0 0 0 25 26 1 0 0 0 0 25 38 1 0 0 0 0 26 41 1 1 0 0 0 27 39 1 0 0 0 0 27 41 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	576.15
Volume:	532.101
LogP:	1.365
LogD:	-0.092
LogS:	-2.738
# Rotatable Bonds:	4
TPSA:	236.81
# H-Bond Aceptor:	14
# H-Bond Donor:	8
# Rings:	5
# Heavy Atoms:	14

MedChem Properties

QED Drug-Likeness Score:	0.189
Synthetic Accessibility Score:	4.919
Fsp3:	0.407
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.32
MDCK Permeability:	1.2695285477093421e-05
Pgp-inhibitor:	0.051
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.846
20% Bioavailability (F20%):	0.161
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.014
Plasma Protein Binding (PPB):	91.9129409790039%
Volume Distribution (VD):	0.595
Pgp-substrate:	11.85041332244873%

ADMET: Metabolism

CYP1A2-inhibitor:	0.034
CYP1A2-substrate:	0.071
CYP2C19-inhibitor:	0.036
CYP2C19-substrate:	0.054
CYP2C9-inhibitor:	0.055
CYP2C9-substrate:	0.381
CYP2D6-inhibitor:	0.013
CYP2D6-substrate:	0.146
CYP3A4-inhibitor:	0.025
CYP3A4-substrate:	0.01

ADMET: Excretion

Clearance (CL):	1.679
Half-life (T1/2):	0.638

ADMET: Toxicity

hERG Blockers:	0.147
Human Hepatotoxicity (H-HT):	0.345
Drug-inuced Liver Injury (DILI):	0.981
AMES Toxicity:	0.779
Rat Oral Acute Toxicity:	0.066
Maximum Recommended Daily Dose:	0.04
Skin Sensitization:	0.892
Carcinogencity:	0.041
Eye Corrosion:	0.003
Eye Irritation:	0.616
Respiratory Toxicity:	0.341

Download Data

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

Natural Product: NPC294629

Natural Product ID:	NPC294629
*Common Name:**	2''-O-Alpha-Rhamnosyl-6-C-(6-Deoxy-Ribo-Hexos-3-Ulosyl)Luteolin
IUPAC Name:	2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-6-[(2S,3S,5R,6R)-5-hydroxy-6-methyl-4-oxo-3-[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxyoxan-2-yl]chromen-4-one
Synonyms:
Standard InCHIKey:	WGIMZJFXUGTVFX-FLCGOUAWSA-N
Standard InCHI:	InChI=1S/C27H28O14/c1-8-20(33)23(36)26(41-27-24(37)22(35)19(32)9(2)39-27)25(38-8)18-14(31)7-16-17(21(18)34)13(30)6-15(40-16)10-3-4-11(28)12(29)5-10/h3-9,19-20,22,24-29,31-35,37H,1-2H3/t8-,9+,19+,20-,22-,24-,25+,26-,27+/m1/s1
SMILES:	C[C@@H]1[C@H](C(=O)[C@H]([C@H](c2c(cc3c(c(=O)cc(c4ccc(c(c4)O)O)o3)c2O)O)O1)O[C@H]1[C@@H]([C@@H]([C@H]([C@H](C)O1)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1224898
PubChem CID:	49800177
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001615] Flavones

*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
NPO33290	fargesia robusta	Species	Poaceae	Eukaryota	leaves	n.a.	n.a.	PMID[20863141]

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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
Others	2

Activity Type	# Activity
NON-MOLECULAR	1
Others	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT35	Others	n.a.	""	Activity	=	5.7	n.a.	PMID[476687]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Activity	=	0.646	n.a.	PMID[476687]

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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 NPC294629 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	463
0.1-0.2	1852
0.2-0.3	4177
0.3-0.4	9640
0.4-0.5	8467
0.5-0.6	4674
0.6-0.7	5502
0.7-0.8	5154
0.8-0.85	1696
0.85-0.9	584
0.9-0.95	398
0.95-1	90

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Similarity Score	Similarity Level	Natural Product ID
0.9815	High Similarity	NPC150767
0.9815	High Similarity	NPC95866
0.9815	High Similarity	NPC78734
0.9755	High Similarity	NPC134532
0.9755	High Similarity	NPC203259

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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 NPC294629 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	408
0.1-0.2	960
0.2-0.3	1974
0.3-0.4	2733
0.4-0.5	1818
0.5-0.6	856
0.6-0.7	256
0.7-0.8	108
0.8-0.85	23
0.85-0.9	6
0.9-0.95	2
0.95-1	6

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9755	High Similarity	NPD6797	Phase 2
0.9695	High Similarity	NPD7251	Discontinued
0.9518	High Similarity	NPD7808	Phase 3
0.9512	High Similarity	NPD7054	Approved
0.9512	High Similarity	NPD7804	Clinical (unspecified phase)

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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