NPASS Compound

Structure

NPC203664 OpenBabel07101719252D 41 44 0 0 1 0 0 0 0 0999 V2000 5.7197 -0.3578 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9777 3.2386 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3304 3.7738 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6468 2.4954 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6394 4.7248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6905 2.0796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2709 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9921 1.7399 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 0.0000 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9995 3.0306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 2.6910 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 6.3378 1.5443 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3596 1.3364 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 4.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.9703 5.4680 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 1.7321 4.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 0.0000 C 0 0 2 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 -0.8660 1.5000 0.0000 C 0 0 2 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 0.8660 2.5000 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 2.3230 0.9968 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 7.0069 0.8012 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2793 6.4190 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 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 1.7321 6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0506 0.3854 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 6.0000 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 2.9921 5.2601 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 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 36 1 0 0 0 0 2 37 1 0 0 0 0 3 5 2 0 0 0 0 3 12 1 0 0 0 0 4 6 2 0 0 0 0 4 12 1 0 0 0 0 5 15 1 0 0 0 0 6 19 1 0 0 0 0 7 12 2 0 0 0 0 7 16 1 0 0 0 0 8 13 2 0 0 0 0 8 17 1 0 0 0 0 9 13 1 0 0 0 0 9 28 1 0 0 0 0 10 29 1 0 0 0 0 11 14 2 0 0 0 0 11 38 1 0 0 0 0 14 25 1 0 0 0 0 15 16 2 0 0 0 0 15 30 1 0 0 0 0 16 36 1 0 0 0 0 17 21 1 0 0 0 0 17 39 1 6 0 0 0 18 10 1 6 0 0 0 18 22 1 0 0 0 0 18 40 1 0 0 0 0 19 31 2 0 0 0 0 19 39 1 0 0 0 0 20 13 1 1 0 0 0 20 21 1 0 0 0 0 20 26 1 0 0 0 0 21 14 1 1 0 0 0 22 23 1 0 0 0 0 22 32 1 1 0 0 0 23 24 1 0 0 0 0 23 33 1 6 0 0 0 24 27 1 0 0 0 0 24 34 1 1 0 0 0 25 35 2 0 0 0 0 25 37 1 0 0 0 0 26 38 1 0 0 0 0 26 41 1 6 0 0 0 27 40 1 0 0 0 0 27 41 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	580.18
Volume:	543.294
LogP:	0.735
LogD:	0.425
LogS:	-1.639
# Rotatable Bonds:	11
TPSA:	210.9
# H-Bond Aceptor:	14
# H-Bond Donor:	6
# Rings:	4
# Heavy Atoms:	14

MedChem Properties

QED Drug-Likeness Score:	0.114
Synthetic Accessibility Score:	4.889
Fsp3:	0.481
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:	-6.29
MDCK Permeability:	8.482298289891332e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	0.557
Human Intestinal Absorption (HIA):	0.867
20% Bioavailability (F20%):	0.125
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.269
Plasma Protein Binding (PPB):	45.038360595703125%
Volume Distribution (VD):	0.411
Pgp-substrate:	25.26434326171875%

ADMET: Metabolism

CYP1A2-inhibitor:	0.032
CYP1A2-substrate:	0.071
CYP2C19-inhibitor:	0.026
CYP2C19-substrate:	0.108
CYP2C9-inhibitor:	0.016
CYP2C9-substrate:	0.066
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.135
CYP3A4-inhibitor:	0.083
CYP3A4-substrate:	0.182

ADMET: Excretion

Clearance (CL):	2.828
Half-life (T1/2):	0.955

ADMET: Toxicity

hERG Blockers:	0.019
Human Hepatotoxicity (H-HT):	0.189
Drug-inuced Liver Injury (DILI):	0.954
AMES Toxicity:	0.193
Rat Oral Acute Toxicity:	0.496
Maximum Recommended Daily Dose:	0.094
Skin Sensitization:	0.349
Carcinogencity:	0.728
Eye Corrosion:	0.003
Eye Irritation:	0.014
Respiratory Toxicity:	0.942

Download Data

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

Natural Product: NPC203664

Natural Product ID:	NPC203664
*Common Name:**	E-6-O-P-Feruloyl Scandoside Methyl Ester
IUPAC Name:	methyl (1S,4aS,5R,7aS)-5-[(E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enoyl]oxy-7-(hydroxymethyl)-1-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-1,4a,5,7a-tetrahydrocyclopenta[c]pyran-4-carboxylate
Synonyms:
Standard InCHIKey:	QHRICBJWYCXFDR-GZJXMKRRSA-N
Standard InCHI:	InChI=1S/C27H32O14/c1-36-16-7-12(3-5-15(16)30)4-6-19(31)39-17-8-13(9-28)20-21(17)14(25(35)37-2)11-38-26(20)41-27-24(34)23(33)22(32)18(10-29)40-27/h3-8,11,17-18,20-24,26-30,32-34H,9-10H2,1-2H3/b6-4+/t17-,18-,20-,21+,22-,23+,24-,26+,27+/m1/s1
SMILES:	COc1cc(ccc1O)/C=C/C(=O)O[C@@H]1C=C(CO)[C@@H]2[C@H]1C(=CO[C@H]2O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)C(=O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL592955
PubChem CID:	46225505
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0004081] Iridoid 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
NPO32921	hedyotis diffusa	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20004577]
NPO32921	hedyotis diffusa	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11170670]

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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	1
Others	5

Activity Type	# Activity
Individual Protein	6

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT279	Individual Protein	Leukocyte elastase	Homo sapiens	Inhibition	=	25.1	%	PMID[501379]
NPT279	Individual Protein	Leukocyte elastase	Homo sapiens	IC50	>	100000.0	nM	PMID[501379]
NPT279	Individual Protein	Leukocyte elastase	Homo sapiens	Inhibition	=	23.6	%	PMID[501379]
NPT279	Individual Protein	Leukocyte elastase	Homo sapiens	Inhibition	=	22.9	%	PMID[501379]
NPT279	Individual Protein	Leukocyte elastase	Homo sapiens	Inhibition	=	23.3	%	PMID[501379]
NPT279	Individual Protein	Leukocyte elastase	Homo sapiens	Inhibition	=	24.7	%	PMID[501379]

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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 NPC203664 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	322
0.1-0.2	1269
0.2-0.3	3168
0.3-0.4	7172
0.4-0.5	10488
0.5-0.6	5813
0.6-0.7	8519
0.7-0.8	5196
0.8-0.85	589
0.85-0.9	145
0.9-0.95	15
0.95-1	1

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Similarity Score	Similarity Level	Natural Product ID
0.9375	High Similarity	NPC475213
0.9375	High Similarity	NPC152796
0.9342	High Similarity	NPC179914
0.9324	High Similarity	NPC69367
0.9216	High Similarity	NPC469384

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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 NPC203664 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	266
0.1-0.2	792
0.2-0.3	1767
0.3-0.4	2737
0.4-0.5	1981
0.5-0.6	1036
0.6-0.7	497
0.7-0.8	68
0.8-0.85	5
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
0.8827	High Similarity	NPD7685	Pre-registration
0.8333	Intermediate Similarity	NPD7266	Discontinued
0.8269	Intermediate Similarity	NPD1653	Approved
0.8176	Intermediate Similarity	NPD8055	Clinical (unspecified phase)
0.8133	Intermediate Similarity	NPD7228	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