NPASS Compound

Structure

NPC471473 OpenBabel07101718242D 39 42 0 0 1 0 0 0 0 0999 V2000 -3.4641 -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 -1.7321 -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 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 3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -4.5000 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 2.5981 -1.5000 0.0000 C 0 0 0 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 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -5.5000 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 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 -2.5981 -5.5000 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 -1.0000 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 -1.7321 -4.0000 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 -3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 3 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 4.3301 -1.5000 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 -4.5000 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 -4.3301 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -5.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -7.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -1.0000 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 -3.4641 -4.0000 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 1 38 1 0 0 0 0 2 39 1 0 0 0 0 3 10 1 0 0 0 0 3 20 2 0 0 0 0 4 11 2 0 0 0 0 4 20 1 0 0 0 0 5 12 1 0 0 0 0 5 21 2 0 0 0 0 6 13 2 0 0 0 0 6 21 1 0 0 0 0 7 14 2 0 0 0 0 7 22 1 0 0 0 0 8 15 1 0 0 0 0 8 22 1 0 0 0 0 9 16 1 0 0 0 0 9 23 1 0 0 0 0 10 24 2 0 0 0 0 11 24 1 0 0 0 0 12 25 2 0 0 0 0 13 25 1 0 0 0 0 14 26 1 0 0 0 0 15 27 1 0 0 0 0 16 29 1 0 0 0 0 17 23 1 0 0 0 0 17 28 2 0 0 0 0 18 26 2 0 0 0 0 18 31 1 0 0 0 0 19 30 2 0 0 0 0 19 32 1 0 0 0 0 20 27 1 0 0 0 0 21 29 1 0 0 0 0 22 31 2 0 0 0 0 23 32 2 0 0 0 0 24 33 1 0 0 0 0 25 34 1 0 0 0 0 26 35 1 0 0 0 0 27 28 1 0 0 0 0 28 30 1 0 0 0 0 29 36 2 0 0 0 0 30 37 1 0 0 0 0 31 38 1 0 0 0 0 32 39 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	528.21
Volume:	555.06
LogP:	4.975
LogD:	4.037
LogS:	-3.655
# Rotatable Bonds:	11
TPSA:	116.45
# H-Bond Aceptor:	7
# H-Bond Donor:	4
# Rings:	4
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.174
Synthetic Accessibility Score:	3.116
Fsp3:	0.219
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.215
MDCK Permeability:	9.644540114095435e-06
Pgp-inhibitor:	0.496
Pgp-substrate:	0.141
Human Intestinal Absorption (HIA):	0.033
20% Bioavailability (F20%):	0.986
30% Bioavailability (F30%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.017
Plasma Protein Binding (PPB):	99.3565444946289%
Volume Distribution (VD):	0.499
Pgp-substrate:	0.8355116248130798%

ADMET: Metabolism

CYP1A2-inhibitor:	0.458
CYP1A2-substrate:	0.96
CYP2C19-inhibitor:	0.956
CYP2C19-substrate:	0.064
CYP2C9-inhibitor:	0.919
CYP2C9-substrate:	0.985
CYP2D6-inhibitor:	0.833
CYP2D6-substrate:	0.935
CYP3A4-inhibitor:	0.87
CYP3A4-substrate:	0.751

ADMET: Excretion

Clearance (CL):	9.596
Half-life (T1/2):	0.791

ADMET: Toxicity

hERG Blockers:	0.181
Human Hepatotoxicity (H-HT):	0.12
Drug-inuced Liver Injury (DILI):	0.088
AMES Toxicity:	0.231
Rat Oral Acute Toxicity:	0.562
Maximum Recommended Daily Dose:	0.951
Skin Sensitization:	0.915
Carcinogencity:	0.099
Eye Corrosion:	0.003
Eye Irritation:	0.641
Respiratory Toxicity:	0.066

Download Data

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

Natural Product: NPC471473

Natural Product ID:	NPC471473
*Common Name:**	1-[5-(2-Methoxy-4,4-Dihydroxydihydrochalconyl)]-1-(4-Hydroxyphenyl)-3-(2-Methoxy-4-Hydroxyphenyl)Propane
IUPAC Name:	3-[4-hydroxy-5-[3-(4-hydroxy-2-methoxyphenyl)-1-(4-hydroxyphenyl)propyl]-2-methoxyphenyl]-1-(4-hydroxyphenyl)propan-1-one
Synonyms:
Standard InCHIKey:	KJDKNNNKRLAENJ-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C32H32O7/c1-38-31-18-26(35)14-7-22(31)8-15-27(20-3-10-24(33)11-4-20)28-17-23(32(39-2)19-30(28)37)9-16-29(36)21-5-12-25(34)13-6-21/h3-7,10-14,17-19,27,33-35,37H,8-9,15-16H2,1-2H3
SMILES:	COc1cc(O)c(cc1CCC(=O)c1ccc(cc1)O)C(c1ccc(cc1)O)CCc1ccc(cc1OC)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL251977
PubChem CID:	44445075
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
NPO12714	Dracaena cochinchinensis	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21661731]
NPO12714	Dracaena cochinchinensis	Species	Asparagaceae	Eukaryota	stems	Ningming County, Guangxi autonomous region, China	2006-Jan	PMID[17883259]
NPO12714	Dracaena cochinchinensis	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12016928]
NPO12714	Dracaena cochinchinensis	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12714	Dracaena cochinchinensis	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12714	Dracaena cochinchinensis	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12714	Dracaena cochinchinensis	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]

Showing 1 to 7 of 7 entries

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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
MIC	1

Activity Type	# Activity
Individual Protein	2
Organism	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1592	Individual Protein	Dipeptidyl peptidase IV	Homo sapiens	IC50	>	36900.0	nM	PMID[522271]
NPT451	Organism	Helicobacter pylori	Helicobacter pylori	MIC	=	60600.0	nM	PMID[522271]
NPT670	Individual Protein	Thrombin	Homo sapiens	IC50	=	26300.0	nM	PMID[522271]

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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 NPC471473 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	378
0.1-0.2	1547
0.2-0.3	3526
0.3-0.4	9277
0.4-0.5	9302
0.5-0.6	3518
0.6-0.7	6138
0.7-0.8	6581
0.8-0.85	1575
0.85-0.9	756
0.9-0.95	89
0.95-1	10

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC471523
1.0	High Similarity	NPC471524
0.9787	High Similarity	NPC152233
0.9716	High Similarity	NPC261271
0.9716	High Similarity	NPC475348

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 NPC471473 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	348
0.1-0.2	962
0.2-0.3	1334
0.3-0.4	2531
0.4-0.5	2068
0.5-0.6	1239
0.6-0.7	481
0.7-0.8	154
0.8-0.85	23
0.85-0.9	10
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9	High Similarity	NPD8443	Clinical (unspecified phase)
0.8816	High Similarity	NPD7768	Phase 2
0.8776	High Similarity	NPD7410	Clinical (unspecified phase)
0.8671	High Similarity	NPD1510	Phase 2
0.8662	High Similarity	NPD7852	Clinical (unspecified phase)

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