NPASS Compound

Structure

NPC202433 OpenBabel06302216142D 42 47 0 0 0 0 0 0 0 0999 V2000 0.8660 2.5000 0.0000 C 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 1.7321 1.0000 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 3.4641 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 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -0.0000 0.0000 O 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 3.4641 -2.0000 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 4.3301 -3.5000 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 3.4641 -5.0000 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 2.5981 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -6.0000 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 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 -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 -0.0000 -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 -0.8660 -0.5000 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 -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 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 -3.4641 -2.0000 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 -4.3301 -3.5000 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 -5.1962 -2.0000 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 -6.0622 -3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 O 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 -0.0000 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 O 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 4.3301 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 20 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 42 1 0 0 0 0 6 19 2 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 7 9 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 10 18 1 0 0 0 0 11 16 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 17 1 0 0 0 0 15 16 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 38 2 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 22 40 1 0 0 0 0 23 24 1 0 0 0 0 24 37 1 0 0 0 0 24 25 2 0 0 0 0 25 26 1 0 0 0 0 25 38 1 0 0 0 0 26 27 2 0 0 0 0 26 28 1 0 0 0 0 28 29 2 0 0 0 0 29 30 1 0 0 0 0 29 37 1 0 0 0 0 30 35 2 0 0 0 0 30 31 1 0 0 0 0 31 32 2 0 0 0 0 32 33 1 0 0 0 0 33 34 2 0 0 0 0 33 36 1 0 0 0 0 34 35 1 0 0 0 0 38 39 1 0 0 0 0 40 41 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	566.12
Volume:	556.408
LogP:	5.785
LogD:	2.413
LogS:	-4.588
# Rotatable Bonds:	5
TPSA:	159.8
# H-Bond Aceptor:	10
# H-Bond Donor:	4
# Rings:	6
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.203
Synthetic Accessibility Score:	3.01
Fsp3:	0.062
Lipinski Rule-of-5:	Rejected
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:	-4.985
MDCK Permeability:	1.37980496219825e-05
Pgp-inhibitor:	0.375
Pgp-substrate:	0.218
Human Intestinal Absorption (HIA):	0.315
20% Bioavailability (F20%):	0.242
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.001
Plasma Protein Binding (PPB):	92.48577880859375%
Volume Distribution (VD):	0.424
Pgp-substrate:	7.0321574211120605%

ADMET: Metabolism

CYP1A2-inhibitor:	0.443
CYP1A2-substrate:	0.67
CYP2C19-inhibitor:	0.759
CYP2C19-substrate:	0.048
CYP2C9-inhibitor:	0.635
CYP2C9-substrate:	0.933
CYP2D6-inhibitor:	0.028
CYP2D6-substrate:	0.83
CYP3A4-inhibitor:	0.21
CYP3A4-substrate:	0.119

ADMET: Excretion

Clearance (CL):	3.568
Half-life (T1/2):	0.226

ADMET: Toxicity

hERG Blockers:	0.052
Human Hepatotoxicity (H-HT):	0.14
Drug-inuced Liver Injury (DILI):	0.989
AMES Toxicity:	0.43
Rat Oral Acute Toxicity:	0.06
Maximum Recommended Daily Dose:	0.425
Skin Sensitization:	0.35
Carcinogencity:	0.056
Eye Corrosion:	0.003
Eye Irritation:	0.81
Respiratory Toxicity:	0.051

Download Data

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

Natural Product: NPC202433

Natural Product ID:	NPC202433
*Common Name:**	QPFBVCAQCZYOIT-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	QPFBVCAQCZYOIT-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C32H22O10/c1-39-24-13-20(36)27-19(35)11-23(16-5-9-18(34)10-6-16)42-32(27)30(24)29-25(40-2)14-26-28(31(29)38)21(37)12-22(41-26)15-3-7-17(33)8-4-15/h3-14,33-34,36,38H,1-2H3
SMILES:	COc1cc(c2c(=O)cc(c3ccc(cc3)O)oc2c1c1c(cc2c(c(=O)cc(c3ccc(cc3)O)o2)c1O)OC)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	9985405
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001586] Biflavonoids and polyflavonoids

*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

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO23434	Fissistigma latifolium	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29160716]
NPO23814	Elsholtzia splendens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22216	Chimonanthus fragrans	Species	Calycanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22216	Chimonanthus fragrans	Species	Calycanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23814	Elsholtzia splendens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13513	Agathis palmerstonii	Species	Araucariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11353	Viscaria vulgaris	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20124	Xylopia discreta	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22216	Chimonanthus fragrans	Species	Calycanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11353	Viscaria vulgaris	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7689	Cota triumfettii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23575	Aspergillus restrictus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24429	Cestrum pallidissimum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24351	Sclerotinia libertiana	Species	Sclerotiniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23153	Eria smithii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22216	Chimonanthus fragrans	Species	Calycanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24155	Nepeta annua	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24272	Akania lucens	Species	Akaniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20124	Xylopia discreta	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13513	Agathis palmerstonii	Species	Araucariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23434	Fissistigma latifolium	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24234	Agrocybe aegerita	Species	Bolbitiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23814	Elsholtzia splendens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25084	Dasiphora fruticosa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22365	Osbeckia chinensis	Species	Melastomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ 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

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ 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	1

Activity Type	# Activity
Individual Protein	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT78	Individual Protein	Beta amyloid A4 protein	Homo sapiens	IC50	=	32800.0	nM	PMID[538968]

☑ 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 NPC202433 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	464
0.1-0.2	1942
0.2-0.3	4240
0.3-0.4	10703
0.4-0.5	7575
0.5-0.6	4172
0.6-0.7	5670
0.7-0.8	4039
0.8-0.85	2534
0.85-0.9	1112
0.9-0.95	211
0.95-1	35

Similarity Score	Similarity Level	Natural Product ID

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 NPC202433 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	435
0.1-0.2	994
0.2-0.3	1571
0.3-0.4	2727
0.4-0.5	1924
0.5-0.6	1027
0.6-0.7	293
0.7-0.8	114
0.8-0.85	50
0.85-0.9	13
0.9-0.95	2
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage

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