NPASS Compound

Structure

CID307050 OpenBabel06191716112D 26 28 0 0 1 0 0 0 0 0999 V2000 -6.0622 2.5000 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 -3.4641 -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 -0.8660 2.5000 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 -0.0000 1.0000 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 -1.7321 4.0000 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 -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 0 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 2.5000 0.0000 C 0 0 1 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 -0.8660 -0.5000 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 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 4.0000 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 -0.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 1.5000 0.0000 O 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 25 1 0 0 0 0 2 26 1 0 0 0 0 3 4 2 0 0 0 0 3 11 1 0 0 0 0 4 16 1 0 0 0 0 5 12 1 0 0 0 0 5 13 1 0 0 0 0 6 11 2 0 0 0 0 6 18 1 0 0 0 0 7 12 2 0 0 0 0 7 19 1 0 0 0 0 8 14 2 0 0 0 0 8 17 1 0 0 0 0 9 21 1 0 0 0 0 10 22 1 0 0 0 0 12 14 1 0 0 0 0 13 9 1 6 0 0 0 13 15 1 0 0 0 0 14 20 1 0 0 0 0 15 10 1 1 0 0 0 15 20 1 0 0 0 0 16 18 2 0 0 0 0 16 23 1 0 0 0 0 17 19 2 0 0 0 0 17 24 1 0 0 0 0 18 25 1 0 0 0 0 19 26 1 0 0 0 0 20 11 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	360.16
Volume:	365.729
LogP:	1.989
LogD:	2.066
LogS:	-3.114
# Rotatable Bonds:	5
TPSA:	99.38
# H-Bond Aceptor:	6
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.651
Synthetic Accessibility Score:	3.53
Fsp3:	0.4
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.908
MDCK Permeability:	3.5252946872788016e-06
Pgp-inhibitor:	0.005
Pgp-substrate:	0.822
Human Intestinal Absorption (HIA):	0.054
20% Bioavailability (F20%):	0.203
30% Bioavailability (F30%):	0.012

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.051
Plasma Protein Binding (PPB):	97.1822738647461%
Volume Distribution (VD):	0.564
Pgp-substrate:	5.732680797576904%

ADMET: Metabolism

CYP1A2-inhibitor:	0.087
CYP1A2-substrate:	0.852
CYP2C19-inhibitor:	0.027
CYP2C19-substrate:	0.779
CYP2C9-inhibitor:	0.142
CYP2C9-substrate:	0.706
CYP2D6-inhibitor:	0.085
CYP2D6-substrate:	0.834
CYP3A4-inhibitor:	0.461
CYP3A4-substrate:	0.823

ADMET: Excretion

Clearance (CL):	13.747
Half-life (T1/2):	0.798

ADMET: Toxicity

hERG Blockers:	0.052
Human Hepatotoxicity (H-HT):	0.261
Drug-inuced Liver Injury (DILI):	0.304
AMES Toxicity:	0.045
Rat Oral Acute Toxicity:	0.129
Maximum Recommended Daily Dose:	0.904
Skin Sensitization:	0.309
Carcinogencity:	0.06
Eye Corrosion:	0.003
Eye Irritation:	0.274
Respiratory Toxicity:	0.31

Download Data

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

Natural Product: NPC307050

Natural Product ID:	NPC307050
*Common Name:**	Isolariciresinol
IUPAC Name:	(6R,7R,8S)-8-(4-hydroxy-3-methoxyphenyl)-6,7-bis(hydroxymethyl)-3-methoxy-5,6,7,8-tetrahydronaphthalen-2-ol
Synonyms:	Isolariciresinol
Standard InCHIKey:	OGFXBIXJCWAUCH-KPHUOKFYSA-N
Standard InCHI:	InChI=1S/C20H24O6/c1-25-18-6-11(3-4-16(18)23)20-14-8-17(24)19(26-2)7-12(14)5-13(9-21)15(20)10-22/h3-4,6-8,13,15,20-24H,5,9-10H2,1-2H3/t13-,15-,20-/m0/s1
SMILES:	OC[C@@H]1Cc2cc(OC)c(cc2[C@@H]([C@H]1CO)c1ccc(c(c1)OC)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL399512
PubChem CID:	160521
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0003425] Aryltetralin lignans [CHEMONTID:0003426] 9,9p-dihydroxyaryltetralin lignans

*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
NPO9420	Aspergillus arenarius	Species	Aspergillaceae	Eukaryota	sclerotia	n.a.	n.a.	PMID[9599285]
NPO6836	Alpinia blepharocalyx	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9461664]
NPO211	Aplysina cauliformis	Species	Aplysinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[8350091]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7561896]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6481366]
NPO28043	Streblus asper	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[4093781]
NPO2697	Monodora tenuifolia	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3509958]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	Seeds	Xinjiang,China		PMID[33063333]
NPO14826	Streptomyces mobaraensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[32998509]
NPO9798	Paeonia lactiflora	Species	Paeoniaceae	Eukaryota	Roots	n.a.	n.a.	PMID[32951423]

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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
NPO24778	NPC307050	Dried Or Powder	n.a.	1.774999976	n.a.	n.a.	mg/100g	Database [PHENOL EXPLORER]

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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	12
Others	20

Activity Type	# Activity
Cell Line	5
Individual Protein	4
NON-MOLECULAR	3
Organism	3
Others	17

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified		Activity	=	500.0	uM	PMID[539143]
NPT2	Others	Unspecified		FC	=	1.8	n.a.	PMID[539143]
NPT2	Others	Unspecified		Activity	=	8.0	%	PMID[539143]
NPT2	Others	Unspecified		Activity	=	24.0	%	PMID[539143]
NPT2	Others	Unspecified		Activity	=	68.0	%	PMID[539143]
NPT2	Others	Unspecified		FC	=	1.2	n.a.	PMID[539143]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	FC	=	1.9	n.a.	PMID[539143]
NPT2	Others	Unspecified		FC	=	1.6	n.a.	PMID[539143]
NPT2	Others	Unspecified		Ratio CC50/IC50	=	10.18	n.a.	PMID[539142]
NPT963	Organism	Hepatitis B virus	Hepatitis B virus	IC50	=	12720.0	nM	PMID[539142]

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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 NPC307050 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	360
0.1-0.2	1455
0.2-0.3	3603
0.3-0.4	11397
0.4-0.5	7532
0.5-0.6	4988
0.6-0.7	8834
0.7-0.8	3460
0.8-0.85	780
0.85-0.9	232
0.9-0.95	48
0.95-1	8

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC277458
0.9752	High Similarity	NPC266705
0.9752	High Similarity	NPC29008
0.9752	High Similarity	NPC228771
0.959	High Similarity	NPC9067

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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 NPC307050 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	312
0.1-0.2	915
0.2-0.3	1513
0.3-0.4	2715
0.4-0.5	1811
0.5-0.6	1006
0.6-0.7	687
0.7-0.8	179
0.8-0.85	7
0.85-0.9	5
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.907	High Similarity	NPD3619	Clinical (unspecified phase)
0.907	High Similarity	NPD3620	Phase 2
0.8692	High Similarity	NPD3027	Phase 3
0.8678	High Similarity	NPD5283	Phase 1
0.8512	High Similarity	NPD228	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