NPASS Compound

Structure

NPC11411 OpenBabel07101718332D 50 55 0 0 1 0 0 0 0 0999 V2000 3.4641 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.2905 2.4297 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 2.5981 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 0 0 0 0 0 0 0 0 0 0 -7.6924 4.9297 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 3.4641 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5584 5.4297 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 0.8660 0.5000 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 -8.5584 3.4297 0.0000 C 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 -5.4128 4.7024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7437 2.2272 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 -7.6924 3.9297 0.0000 C 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 -5.9128 3.8364 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.2437 3.0933 0.0000 C 0 0 2 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 -9.4244 4.9297 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 2.5981 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.4244 3.9297 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 0.0000 -1.0000 0.0000 C 0 0 2 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 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 -1.7321 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.8263 3.4297 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3301 3.5000 0.0000 C 0 0 1 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 4.3301 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.2905 5.4297 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 -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 2.5981 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.2905 3.4297 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 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.7218 2.4351 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4347 4.4945 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 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 43 1 0 0 0 0 2 44 1 0 0 0 0 3 45 1 0 0 0 0 4 8 2 0 0 0 0 4 18 1 0 0 0 0 5 11 2 0 0 0 0 5 18 1 0 0 0 0 6 9 2 0 0 0 0 6 19 1 0 0 0 0 7 10 2 0 0 0 0 7 20 1 0 0 0 0 8 23 1 0 0 0 0 9 24 1 0 0 0 0 10 25 1 0 0 0 0 11 30 1 0 0 0 0 12 18 2 0 0 0 0 12 26 1 0 0 0 0 13 19 2 0 0 0 0 13 27 1 0 0 0 0 14 20 2 0 0 0 0 14 28 1 0 0 0 0 15 48 1 0 0 0 0 16 47 1 0 0 0 0 17 46 1 0 0 0 0 21 15 1 6 0 0 0 21 22 1 0 0 0 0 21 34 1 0 0 0 0 22 16 1 6 0 0 0 22 35 1 0 0 0 0 23 26 2 0 0 0 0 23 37 1 0 0 0 0 24 27 2 0 0 0 0 24 38 1 0 0 0 0 25 28 2 0 0 0 0 25 49 1 0 0 0 0 26 43 1 0 0 0 0 27 44 1 0 0 0 0 28 45 1 0 0 0 0 29 17 1 6 0 0 0 29 31 1 0 0 0 0 29 50 1 0 0 0 0 30 39 2 0 0 0 0 30 46 1 0 0 0 0 31 32 1 0 0 0 0 31 40 1 1 0 0 0 32 33 1 0 0 0 0 32 41 1 6 0 0 0 33 36 1 0 0 0 0 33 42 1 1 0 0 0 34 19 1 1 0 0 0 34 47 1 0 0 0 0 35 20 1 1 0 0 0 35 48 1 0 0 0 0 36 49 1 6 0 0 0 36 50 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	696.24
Volume:	673.935
LogP:	2.959
LogD:	2.681
LogS:	-4.345
# Rotatable Bonds:	12
TPSA:	192.06
# H-Bond Aceptor:	14
# H-Bond Donor:	5
# Rings:	6
# Heavy Atoms:	14

MedChem Properties

QED Drug-Likeness Score:	0.145
Synthetic Accessibility Score:	4.786
Fsp3:	0.417
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:	-5.919
MDCK Permeability:	5.107838660478592e-05
Pgp-inhibitor:	0.308
Pgp-substrate:	0.945
Human Intestinal Absorption (HIA):	0.443
20% Bioavailability (F20%):	0.011
30% Bioavailability (F30%):	0.966

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.028
Plasma Protein Binding (PPB):	95.44512176513672%
Volume Distribution (VD):	0.391
Pgp-substrate:	5.745607852935791%

ADMET: Metabolism

CYP1A2-inhibitor:	0.03
CYP1A2-substrate:	0.685
CYP2C19-inhibitor:	0.143
CYP2C19-substrate:	0.321
CYP2C9-inhibitor:	0.534
CYP2C9-substrate:	0.825
CYP2D6-inhibitor:	0.272
CYP2D6-substrate:	0.504
CYP3A4-inhibitor:	0.377
CYP3A4-substrate:	0.251

ADMET: Excretion

Clearance (CL):	5.142
Half-life (T1/2):	0.668

ADMET: Toxicity

hERG Blockers:	0.541
Human Hepatotoxicity (H-HT):	0.183
Drug-inuced Liver Injury (DILI):	0.2
AMES Toxicity:	0.496
Rat Oral Acute Toxicity:	0.055
Maximum Recommended Daily Dose:	0.451
Skin Sensitization:	0.954
Carcinogencity:	0.263
Eye Corrosion:	0.003
Eye Irritation:	0.04
Respiratory Toxicity:	0.175

Download Data

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

Natural Product: NPC11411

Natural Product ID:	NPC11411
*Common Name:**	Pinoresinol-4'-O-[6'-O-(E)-Feruloyl]-Beta-D-Glucopyranoside
IUPAC Name:	[(2R,3S,4S,5R,6S)-6-[4-[(3R,3aS,6R,6aS)-3-(4-hydroxy-3-methoxyphenyl)-1,3,3a,4,6,6a-hexahydrofuro[3,4-c]furan-6-yl]-2-methoxyphenoxy]-3,4,5-trihydroxyoxan-2-yl]methyl (E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enoate
Synonyms:
Standard InCHIKey:	YJJBMEAGCOFGGM-QIWKOVHQSA-N
Standard InCHI:	InChI=1S/C36H40O14/c1-43-26-12-18(4-8-23(26)37)5-11-30(39)46-17-29-31(40)32(41)33(42)36(50-29)49-25-10-7-20(14-28(25)45-3)35-22-16-47-34(21(22)15-48-35)19-6-9-24(38)27(13-19)44-2/h4-14,21-22,29,31-38,40-42H,15-17H2,1-3H3/b11-5+/t21-,22-,29-,31-,32+,33-,34+,35+,36-/m1/s1
SMILES:	COc1cc(ccc1O)/C=C/C(=O)OC[C@@H]1[C@H]([C@@H]([C@H]([C@H](Oc2ccc(cc2OC)[C@H]2[C@@H]3CO[C@@H](c4ccc(c(c4)OC)O)[C@@H]3CO2)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL2251617
PubChem CID:	17755816
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
NPO33277.1	rhus javanica	Under-species	n.a.	n.a.	root	n.a.	n.a.	PMID[17616139]

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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	1

Activity Type	# Activity
Organism	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT786	Organism	Tobacco mosaic virus	Tobacco mosaic virus	Inhibition	=	34.3	%	PMID[549981]

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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 NPC11411 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	355
0.1-0.2	1337
0.2-0.3	3274
0.3-0.4	7855
0.4-0.5	10460
0.5-0.6	6513
0.6-0.7	8598
0.7-0.8	3728
0.8-0.85	410
0.85-0.9	148
0.9-0.95	16
0.95-1	3

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Similarity Score	Similarity Level	Natural Product ID
0.9737	High Similarity	NPC7191
0.9737	High Similarity	NPC149873
0.973	High Similarity	NPC478268
0.9605	High Similarity	NPC478269
0.9487	High Similarity	NPC59516

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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 NPC11411 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	283
0.1-0.2	805
0.2-0.3	1730
0.3-0.4	2750
0.4-0.5	2039
0.5-0.6	1065
0.6-0.7	420
0.7-0.8	55
0.8-0.85	2
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
0.8725	High Similarity	NPD7266	Discontinued
0.8485	Intermediate Similarity	NPD7228	Approved
0.8291	Intermediate Similarity	NPD1653	Approved
0.8282	Intermediate Similarity	NPD6234	Discontinued
0.8198	Intermediate Similarity	NPD8055	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