NPASS Compound

Structure

NPC286235 OpenBabel07101718192D 39 43 0 0 1 0 0 0 0 0999 V2000 -4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2494 7.6970 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.7135 4.6970 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 -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 0 0 0 0 0 0 0 0 0 0 -7.2494 5.6970 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1154 4.1970 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 -4.8007 3.8605 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7788 2.3364 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 -7.2494 4.6970 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3007 2.9945 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.2788 3.2024 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 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 -8.1154 6.1970 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.9814 4.6970 0.0000 C 0 0 0 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 -8.9814 5.6970 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 0.0000 2.0000 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 -5.1962 2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.3834 4.1970 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 2.5981 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.8475 6.1970 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 -1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.1154 7.1970 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.8475 4.1970 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.1097 1.5933 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.4698 4.6037 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 -0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 33 1 0 0 0 0 2 34 1 0 0 0 0 3 35 1 0 0 0 0 4 5 2 0 0 0 0 4 12 1 0 0 0 0 5 16 1 0 0 0 0 6 12 2 0 0 0 0 6 17 1 0 0 0 0 7 13 2 0 0 0 0 7 18 1 0 0 0 0 8 13 1 0 0 0 0 8 19 2 0 0 0 0 9 28 1 0 0 0 0 10 37 1 0 0 0 0 11 36 1 0 0 0 0 14 10 1 6 0 0 0 14 15 1 0 0 0 0 14 25 1 0 0 0 0 15 11 1 6 0 0 0 15 26 1 0 0 0 0 16 17 2 0 0 0 0 16 38 1 0 0 0 0 17 33 1 0 0 0 0 18 21 2 0 0 0 0 18 34 1 0 0 0 0 19 21 1 0 0 0 0 19 35 1 0 0 0 0 20 9 1 1 0 0 0 20 22 1 0 0 0 0 20 39 1 0 0 0 0 21 29 1 0 0 0 0 22 23 1 0 0 0 0 22 30 1 6 0 0 0 23 24 1 0 0 0 0 23 31 1 1 0 0 0 24 27 1 0 0 0 0 24 32 1 6 0 0 0 25 12 1 1 0 0 0 25 36 1 0 0 0 0 26 13 1 1 0 0 0 26 37 1 0 0 0 0 27 38 1 1 0 0 0 27 39 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	550.21
Volume:	522.43
LogP:	0.823
LogD:	1.299
LogS:	-3.699
# Rotatable Bonds:	8
TPSA:	165.76
# H-Bond Aceptor:	12
# H-Bond Donor:	5
# Rings:	5
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.312
Synthetic Accessibility Score:	4.53
Fsp3:	0.556
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:	3.094558269367553e-05
Pgp-inhibitor:	0.049
Pgp-substrate:	0.993
Human Intestinal Absorption (HIA):	0.28
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.487

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.163
Plasma Protein Binding (PPB):	46.985923767089844%
Volume Distribution (VD):	0.301
Pgp-substrate:	20.37210464477539%

ADMET: Metabolism

CYP1A2-inhibitor:	0.011
CYP1A2-substrate:	0.819
CYP2C19-inhibitor:	0.008
CYP2C19-substrate:	0.829
CYP2C9-inhibitor:	0.005
CYP2C9-substrate:	0.222
CYP2D6-inhibitor:	0.018
CYP2D6-substrate:	0.315
CYP3A4-inhibitor:	0.051
CYP3A4-substrate:	0.4

ADMET: Excretion

Clearance (CL):	3.248
Half-life (T1/2):	0.558

ADMET: Toxicity

hERG Blockers:	0.639
Human Hepatotoxicity (H-HT):	0.215
Drug-inuced Liver Injury (DILI):	0.279
AMES Toxicity:	0.095
Rat Oral Acute Toxicity:	0.033
Maximum Recommended Daily Dose:	0.087
Skin Sensitization:	0.931
Carcinogencity:	0.071
Eye Corrosion:	0.003
Eye Irritation:	0.018
Respiratory Toxicity:	0.349

Download Data

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

Natural Product: NPC286235

Natural Product ID:	NPC286235
*Common Name:**	Isoeucommin A
IUPAC Name:	(2S,3R,4S,5S,6R)-2-[4-[(3S,3aR,6S,6aR)-6-(4-hydroxy-3,5-dimethoxyphenyl)-1,3,3a,4,6,6a-hexahydrofuro[3,4-c]furan-3-yl]-2-methoxyphenoxy]-6-(hydroxymethyl)oxane-3,4,5-triol
Synonyms:
Standard InCHIKey:	BRLYXYFYCNCKRT-PHMKYDSWSA-N
Standard InCHI:	InChI=1S/C27H34O12/c1-33-17-6-12(4-5-16(17)38-27-24(32)23(31)22(30)20(9-28)39-27)25-14-10-37-26(15(14)11-36-25)13-7-18(34-2)21(29)19(8-13)35-3/h4-8,14-15,20,22-32H,9-11H2,1-3H3/t14-,15-,20+,22+,23-,24+,25+,26+,27+/m0/s1
SMILES:	OC[C@H]1O[C@@H](Oc2ccc(cc2OC)[C@H]2OC[C@H]3[C@@H]2CO[C@@H]3c2cc(OC)c(c(c2)OC)O)[C@@H]([C@H]([C@@H]1O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1077017
PubChem CID:	44206182
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
NPO18521	Capparis flavicans	Species	Capparaceae	Eukaryota	aerial parts	Khon Kaen Province, Thailand	2006-Aug	PMID[19943620]
NPO18521	Capparis flavicans	Species	Capparaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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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	7

Activity Type	# Activity
Cell Line	7

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT83	Cell Line	MCF7	Homo sapiens	Activity	<	0.1	uM	PMID[569994]
NPT396	Cell Line	T47D	Homo sapiens	Activity	<	0.1	uM	PMID[569994]
NPT396	Cell Line	T47D	Homo sapiens	Activity	>	100.0	uM	PMID[569994]
NPT396	Cell Line	T47D	Homo sapiens	Inhibition	>	90.0	%	PMID[569994]

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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 NPC286235 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	453
0.1-0.2	1391
0.2-0.3	3756
0.3-0.4	9585
0.4-0.5	9299
0.5-0.6	5520
0.6-0.7	7888
0.7-0.8	3698
0.8-0.85	730
0.85-0.9	281
0.9-0.95	71
0.95-1	25

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC55158
1.0	High Similarity	NPC51328
0.9929	High Similarity	NPC130449
0.9929	High Similarity	NPC248132
0.9858	High Similarity	NPC39657

Showing 1 to 5 of 200 entries

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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 NPC286235 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	347
0.1-0.2	771
0.2-0.3	1869
0.3-0.4	2879
0.4-0.5	1746
0.5-0.6	1027
0.6-0.7	436
0.7-0.8	66
0.8-0.85	9
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8652	High Similarity	NPD3027	Phase 3
0.8625	High Similarity	NPD7228	Approved
0.8601	High Similarity	NPD1612	Clinical (unspecified phase)
0.8601	High Similarity	NPD1613	Approved
0.8535	High Similarity	NPD6234	Discontinued

Showing 1 to 5 of 200 entries

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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