NPASS Compound

Structure

NPC204694 OpenBabel06302216142D 42 44 0 0 1 0 0 0 0 0999 V2000 -4.3301 0.5000 0.0000 C 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 -5.1962 2.0000 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 -6.9282 2.0000 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 -8.6603 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.3923 2.0000 0.0000 O 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 -6.0622 3.5000 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 -4.3301 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 0.0000 C 0 0 2 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 -2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 3.5000 0.0000 C 0 0 1 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 -0.0000 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 -0.8660 0.5000 0.0000 O 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 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 0.8660 3.5000 0.0000 O 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 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 12 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 10 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 11 41 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 1 0 0 0 14 17 1 0 0 0 0 15 16 1 0 0 0 0 17 18 1 0 0 0 0 17 40 1 6 0 0 0 18 23 2 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 20 21 1 0 0 0 0 20 38 1 0 0 0 0 21 22 2 0 0 0 0 21 26 1 0 0 0 0 22 23 1 0 0 0 0 22 24 1 0 0 0 0 24 25 1 0 0 0 0 27 26 1 1 0 0 0 27 28 1 0 0 0 0 27 34 1 0 0 0 0 28 29 1 0 0 0 0 28 37 1 6 0 0 0 29 30 1 0 0 0 0 29 36 1 1 0 0 0 30 31 1 0 0 0 0 30 35 1 6 0 0 0 31 32 1 1 0 0 0 31 34 1 0 0 0 0 32 33 1 0 0 0 0 38 39 1 0 0 0 0 41 42 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	598.23
Volume:	571.783
LogP:	-0.36
LogD:	-0.081
LogS:	-2.058
# Rotatable Bonds:	14
TPSA:	206.22
# H-Bond Aceptor:	14
# H-Bond Donor:	7
# Rings:	3
# Heavy Atoms:	14

MedChem Properties

QED Drug-Likeness Score:	0.145
Synthetic Accessibility Score:	4.438
Fsp3:	0.5
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.106
MDCK Permeability:	4.647012610803358e-05
Pgp-inhibitor:	0.152
Pgp-substrate:	0.993
Human Intestinal Absorption (HIA):	0.635
20% Bioavailability (F20%):	0.01
30% Bioavailability (F30%):	0.661

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.305
Plasma Protein Binding (PPB):	39.80576705932617%
Volume Distribution (VD):	0.367
Pgp-substrate:	33.1814079284668%

ADMET: Metabolism

CYP1A2-inhibitor:	0.009
CYP1A2-substrate:	0.346
CYP2C19-inhibitor:	0.005
CYP2C19-substrate:	0.858
CYP2C9-inhibitor:	0.0
CYP2C9-substrate:	0.285
CYP2D6-inhibitor:	0.0
CYP2D6-substrate:	0.225
CYP3A4-inhibitor:	0.01
CYP3A4-substrate:	0.158

ADMET: Excretion

Clearance (CL):	2.934
Half-life (T1/2):	0.77

ADMET: Toxicity

hERG Blockers:	0.439
Human Hepatotoxicity (H-HT):	0.174
Drug-inuced Liver Injury (DILI):	0.174
AMES Toxicity:	0.073
Rat Oral Acute Toxicity:	0.01
Maximum Recommended Daily Dose:	0.023
Skin Sensitization:	0.329
Carcinogencity:	0.015
Eye Corrosion:	0.003
Eye Irritation:	0.009
Respiratory Toxicity:	0.002

Download Data

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

Natural Product: NPC204694

Natural Product ID:	NPC204694
*Common Name:**	UAWIBXORCBDCBZ-DVPXTGAWSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	UAWIBXORCBDCBZ-DVPXTGAWSA-N
Standard InCHI:	InChI=1S/C28H38O14/c1-36-16-8-14(6-5-7-29)9-17(37-2)26(16)40-20(12-30)22(32)15-10-18(38-3)27(19(11-15)39-4)42-28-25(35)24(34)23(33)21(13-31)41-28/h5-6,8-11,20-25,28-35H,7,12-13H2,1-4H3/b6-5+/t20-,21-,22-,23-,24+,25-,28+/m1/s1
SMILES:	COc1cc(/C=C/CO)cc(c1O[C@H](CO)[C@@H](c1cc(c(c(c1)OC)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)OC)O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10077272
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0001511] Lignan 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
NPO8918	Plantago depressa	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26562611]
NPO3477	Plantago asiatica	Species	Plantaginaceae	Eukaryota	n.a.	seed	n.a.	PMID[2610694]
NPO3477	Plantago asiatica	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2488968]
NPO17774	Hemerocallis fulva	Species	Xanthorrhoeaceae	Eukaryota	Flowers	n.a.	n.a.	DOI[10.1016/j.lwt.2014.11.023]
NPO8918	Plantago depressa	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3477	Plantago asiatica	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17774	Hemerocallis fulva	Species	Xanthorrhoeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3477	Plantago asiatica	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO17774	Hemerocallis fulva	Species	Xanthorrhoeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO8918	Plantago depressa	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]

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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

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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 NPC204694 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	402
0.1-0.2	1502
0.2-0.3	4145
0.3-0.4	10533
0.4-0.5	7978
0.5-0.6	4900
0.6-0.7	7289
0.7-0.8	4487
0.8-0.85	997
0.85-0.9	330
0.9-0.95	113
0.95-1	21

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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 NPC204694 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	332
0.1-0.2	835
0.2-0.3	1887
0.3-0.4	2787
0.4-0.5	1674
0.5-0.6	953
0.6-0.7	559
0.7-0.8	115
0.8-0.85	5
0.85-0.9	3
0.9-0.95	0
0.95-1	0

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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