NPASS Compound

Structure

NPC172033 OpenBabel07101719142D 44 47 0 0 1 0 0 0 0 0999 V2000 -4.3301 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 3.0000 0.0000 C 0 0 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 3.4641 2.0000 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 -6.9282 2.0000 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 -5.1962 2.0000 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 -7.7942 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 -3.4641 2.0000 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 -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 0.8660 -1.5000 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 1.7321 2.0000 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 -7.7942 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 3.5000 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 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 -2.5981 3.5000 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 -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 -0.8660 0.5000 0.0000 C 0 0 2 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 -8.6603 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 4.5000 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 -0.8660 3.5000 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 1.7321 -1.0000 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 -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 18 1 0 0 0 0 2 3 2 0 0 0 0 2 4 1 0 0 0 0 3 5 1 0 0 0 0 4 6 2 0 0 0 0 5 19 2 0 0 0 0 6 19 1 0 0 0 0 7 11 1 0 0 0 0 7 20 2 0 0 0 0 8 12 2 0 0 0 0 8 20 1 0 0 0 0 9 14 2 0 0 0 0 9 20 1 0 0 0 0 10 16 2 0 0 0 0 10 19 1 0 0 0 0 11 21 2 0 0 0 0 12 21 1 0 0 0 0 13 15 2 0 0 0 0 13 22 1 0 0 0 0 14 23 1 0 0 0 0 15 24 1 0 0 0 0 16 26 1 0 0 0 0 17 41 1 0 0 0 0 18 33 2 0 0 0 0 18 42 1 0 0 0 0 21 34 1 0 0 0 0 22 23 1 0 0 0 0 22 27 2 0 0 0 0 23 35 2 0 0 0 0 24 28 2 0 0 0 0 24 43 1 0 0 0 0 25 17 1 6 0 0 0 25 29 1 0 0 0 0 25 44 1 0 0 0 0 26 36 2 0 0 0 0 26 41 1 0 0 0 0 27 28 1 0 0 0 0 27 37 1 0 0 0 0 28 38 1 0 0 0 0 29 30 1 0 0 0 0 29 39 1 1 0 0 0 30 31 1 0 0 0 0 30 40 1 6 0 0 0 31 32 1 0 0 0 0 31 42 1 1 0 0 0 32 43 1 6 0 0 0 32 44 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	606.17
Volume:	596.374
LogP:	3.173
LogD:	2.359
LogS:	-4.131
# Rotatable Bonds:	12
TPSA:	189.28
# H-Bond Aceptor:	12
# H-Bond Donor:	5
# Rings:	4
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.098
Synthetic Accessibility Score:	4.121
Fsp3:	0.219
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	2
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.776
MDCK Permeability:	2.073894938803278e-05
Pgp-inhibitor:	0.05
Pgp-substrate:	0.072
Human Intestinal Absorption (HIA):	0.576
20% Bioavailability (F20%):	0.815
30% Bioavailability (F30%):	0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.126
Plasma Protein Binding (PPB):	102.30573272705078%
Volume Distribution (VD):	0.428
Pgp-substrate:	0.857779860496521%

ADMET: Metabolism

CYP1A2-inhibitor:	0.408
CYP1A2-substrate:	0.014
CYP2C19-inhibitor:	0.341
CYP2C19-substrate:	0.052
CYP2C9-inhibitor:	0.73
CYP2C9-substrate:	0.858
CYP2D6-inhibitor:	0.86
CYP2D6-substrate:	0.162
CYP3A4-inhibitor:	0.695
CYP3A4-substrate:	0.142

ADMET: Excretion

Clearance (CL):	2.968
Half-life (T1/2):	0.931

ADMET: Toxicity

hERG Blockers:	0.059
Human Hepatotoxicity (H-HT):	0.127
Drug-inuced Liver Injury (DILI):	0.9
AMES Toxicity:	0.798
Rat Oral Acute Toxicity:	0.066
Maximum Recommended Daily Dose:	0.016
Skin Sensitization:	0.946
Carcinogencity:	0.497
Eye Corrosion:	0.003
Eye Irritation:	0.847
Respiratory Toxicity:	0.03

Download Data

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

Natural Product: NPC172033

Natural Product ID:	NPC172033
*Common Name:**	4'-O-Beta-D-(2''-Acetyl-6''-Cinnamoyl)Glucopyranosyl-4,2',3'-Trihydroxychalcone
IUPAC Name:	[(2R,3S,4S,5R,6S)-5-acetyloxy-6-[2,3-dihydroxy-4-[(E)-3-(4-hydroxyphenyl)prop-2-enoyl]phenoxy]-3,4-dihydroxyoxan-2-yl]methyl (E)-3-phenylprop-2-enoate
Synonyms:
Standard InCHIKey:	SBEYXFRVWXXGPA-KHVJMIKNSA-N
Standard InCHI:	InChI=1S/C32H30O12/c1-18(33)42-31-30(40)29(39)25(17-41-26(36)16-10-19-5-3-2-4-6-19)44-32(31)43-24-15-13-22(27(37)28(24)38)23(35)14-9-20-7-11-21(34)12-8-20/h2-16,25,29-32,34,37-40H,17H2,1H3/b14-9+,16-10+/t25-,29-,30+,31-,32-/m1/s1
SMILES:	CC(=O)O[C@H]1[C@@H](O[C@@H]([C@H]([C@@H]1O)O)COC(=O)/C=C/c1ccccc1)Oc1ccc(c(c1O)O)C(=O)/C=C/c1ccc(cc1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL463197
PubChem CID:	10579559
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-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
NPO27239	Maclura tinctoria	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12932124]
NPO27239	Maclura tinctoria	Species	Moraceae	Eukaryota	n.a.	stem	n.a.	PMID[12932124]
NPO27239	Maclura tinctoria	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11087602]
NPO27239	Maclura tinctoria	Species	Moraceae	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	1

Activity Type	# Activity
NON-MOLECULAR	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.	Activity	=	1.6	mM	PMID[480505]

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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 NPC172033 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	380
0.1-0.2	1663
0.2-0.3	3929
0.3-0.4	8551
0.4-0.5	9291
0.5-0.6	4334
0.6-0.7	4942
0.7-0.8	5710
0.8-0.85	2335
0.85-0.9	1071
0.9-0.95	463
0.95-1	28

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC88560
1.0	High Similarity	NPC175230
0.9876	High Similarity	NPC204937
0.9876	High Similarity	NPC149011
0.9755	High Similarity	NPC472993

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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 NPC172033 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	342
0.1-0.2	914
0.2-0.3	1922
0.3-0.4	2604
0.4-0.5	1850
0.5-0.6	944
0.6-0.7	375
0.7-0.8	144
0.8-0.85	34
0.85-0.9	14
0.9-0.95	7
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9341	High Similarity	NPD4338	Clinical (unspecified phase)
0.9333	High Similarity	NPD7054	Approved
0.9277	High Similarity	NPD7472	Approved
0.9277	High Similarity	NPD7074	Phase 3
0.9273	High Similarity	NPD3818	Discontinued

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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