NPASS Compound

Structure

NPC201587 OpenBabel07101718282D 26 28 0 0 1 0 0 0 0 0999 V2000 1.7321 1.0000 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 0.0000 0.0000 C 0 0 0 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 -6.9282 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -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 -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 0 0 0 0 0 0 0 0 0 0 -4.3301 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -0.5000 0.0000 C 0 0 0 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 -7.7942 -1.5000 0.0000 C 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 -4.3301 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 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 0.0000 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 -8.6603 -2.0000 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 -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 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 -3.4641 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 25 1 0 0 0 0 2 5 1 0 0 0 0 2 12 2 0 0 0 0 3 6 2 0 0 0 0 3 12 1 0 0 0 0 4 7 1 0 0 0 0 4 12 1 0 0 0 0 5 14 2 0 0 0 0 6 14 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 19 2 0 0 0 0 10 15 1 0 0 0 0 10 16 1 0 0 0 0 11 15 1 0 0 0 0 11 18 1 0 0 0 0 14 21 1 0 0 0 0 15 22 1 1 0 0 0 16 7 1 1 0 0 0 16 26 1 0 0 0 0 17 20 2 0 0 0 0 17 23 1 0 0 0 0 18 13 1 1 0 0 0 18 26 1 0 0 0 0 19 20 1 0 0 0 0 19 25 1 0 0 0 0 20 24 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	360.16
Volume:	365.729
LogP:	2.509
LogD:	2.49
LogS:	-3.528
# 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:	0.612
Synthetic Accessibility Score:	3.431
Fsp3:	0.4
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	2
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.893
MDCK Permeability:	8.320379492943175e-06
Pgp-inhibitor:	0.012
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.013
20% Bioavailability (F20%):	0.295
30% Bioavailability (F30%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.026
Plasma Protein Binding (PPB):	91.20033264160156%
Volume Distribution (VD):	1.101
Pgp-substrate:	8.249626159667969%

ADMET: Metabolism

CYP1A2-inhibitor:	0.456
CYP1A2-substrate:	0.634
CYP2C19-inhibitor:	0.342
CYP2C19-substrate:	0.237
CYP2C9-inhibitor:	0.766
CYP2C9-substrate:	0.901
CYP2D6-inhibitor:	0.478
CYP2D6-substrate:	0.814
CYP3A4-inhibitor:	0.385
CYP3A4-substrate:	0.496

ADMET: Excretion

Clearance (CL):	15.868
Half-life (T1/2):	0.89

ADMET: Toxicity

hERG Blockers:	0.078
Human Hepatotoxicity (H-HT):	0.656
Drug-inuced Liver Injury (DILI):	0.04
AMES Toxicity:	0.184
Rat Oral Acute Toxicity:	0.153
Maximum Recommended Daily Dose:	0.993
Skin Sensitization:	0.969
Carcinogencity:	0.614
Eye Corrosion:	0.084
Eye Irritation:	0.883
Respiratory Toxicity:	0.898

Download Data

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

Natural Product: NPC201587

Natural Product ID:	NPC201587
*Common Name:**	5-[4-Hydroxy-6-(4-Hydroxyphenethyl)Tetrahydro-2H-Pyran-2-Yl]-3-Methoxybenzene-1,2-Diol
IUPAC Name:	5-[(2S,4R,6S)-4-hydroxy-6-[2-(4-hydroxyphenyl)ethyl]oxan-2-yl]-3-methoxybenzene-1,2-diol
Synonyms:
Standard InCHIKey:	PWDBBSBHBDCKBE-RYRKJORJSA-N
Standard InCHI:	InChI=1S/C20H24O6/c1-25-19-9-13(8-17(23)20(19)24)18-11-15(22)10-16(26-18)7-4-12-2-5-14(21)6-3-12/h2-3,5-6,8-9,15-16,18,21-24H,4,7,10-11H2,1H3/t15-,16+,18+/m1/s1
SMILES:	COc1cc(cc(c1O)O)[C@H]1O[C@@H](CCc2ccc(cc2)O)C[C@H](C1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL255317
PubChem CID:	24769969
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002650] Diarylheptanoids [CHEMONTID:0002651] Linear diarylheptanoids

*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
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[8064299]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8064299]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20590154]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19271742]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	rhizomes	n.a.	n.a.	PMID[18177011]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]

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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	2

Activity Type	# Activity
NON-MOLECULAR	1
Tissue	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	48140.0	nM	PMID[469491]
NPT625	Tissue	Liver	Mus musculus	IC50	=	27900.0	nM	PMID[469491]

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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 NPC201587 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	392
0.1-0.2	1412
0.2-0.3	3870
0.3-0.4	10858
0.4-0.5	7930
0.5-0.6	4145
0.6-0.7	6897
0.7-0.8	5351
0.8-0.85	1006
0.85-0.9	618
0.9-0.95	203
0.95-1	15

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC253105
0.976	High Similarity	NPC476968
0.976	High Similarity	NPC170844
0.969	High Similarity	NPC306441
0.969	High Similarity	NPC16435

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 NPC201587 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	327
0.1-0.2	817
0.2-0.3	1732
0.3-0.4	2731
0.4-0.5	1747
0.5-0.6	995
0.6-0.7	629
0.7-0.8	164
0.8-0.85	5
0.85-0.9	0
0.9-0.95	2
0.95-1	1

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.976	High Similarity	NPD3027	Phase 3
0.938	High Similarity	NPD1613	Approved
0.938	High Similarity	NPD1612	Clinical (unspecified phase)
0.907	High Similarity	NPD1529	Clinical (unspecified phase)
0.8992	High Similarity	NPD1530	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