NPASS Compound

Structure

NPC472261 OpenBabel07101718242D 40 45 0 0 1 0 0 0 0 0999 V2000 -3.4641 2.0000 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 -8.5981 -2.2321 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 -2.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -3.0000 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 0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2321 -0.1340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2321 -0.1340 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 -5.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2321 -1.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2321 -3.5981 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 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2321 -1.8660 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 -2.7321 -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 -6.2321 -3.5981 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 -5.7321 -2.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2321 -1.8660 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 -3.2321 -1.8660 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 -4.7321 -2.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7321 -2.7321 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -5.7321 -4.4641 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7321 -2.7321 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 -4.2321 -3.5981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.5981 -3.2321 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 -2.2321 -1.8660 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 4 38 1 0 0 0 0 5 39 1 0 0 0 0 6 7 2 0 0 0 0 6 8 1 0 0 0 0 7 19 1 0 0 0 0 8 23 2 0 0 0 0 9 10 2 0 0 0 0 9 17 1 0 0 0 0 10 20 1 0 0 0 0 11 15 1 0 0 0 0 11 21 1 0 0 0 0 12 17 2 0 0 0 0 12 18 1 0 0 0 0 13 18 1 0 0 0 0 13 31 1 0 0 0 0 14 22 1 0 0 0 0 14 31 1 0 0 0 0 15 1 1 6 0 0 0 15 40 1 0 0 0 0 16 2 1 6 0 0 0 16 24 1 0 0 0 0 16 40 1 0 0 0 0 17 26 1 0 0 0 0 18 25 2 0 0 0 0 19 27 2 0 0 0 0 19 32 1 0 0 0 0 20 28 2 0 0 0 0 20 32 1 0 0 0 0 21 24 2 0 0 0 0 21 32 1 0 0 0 0 22 25 1 0 0 0 0 22 33 2 0 0 0 0 23 27 1 0 0 0 0 23 38 1 0 0 0 0 24 29 1 0 0 0 0 25 30 1 0 0 0 0 26 28 1 0 0 0 0 26 30 2 0 0 0 0 27 29 1 0 0 0 0 28 34 1 0 0 0 0 29 35 2 0 0 0 0 30 36 1 0 0 0 0 31 3 1 6 0 0 0 31 37 1 0 0 0 0 32 39 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	544.21
Volume:	552.01
LogP:	4.287
LogD:	3.039
LogS:	-4.588
# Rotatable Bonds:	3
TPSA:	122.52
# H-Bond Aceptor:	8
# H-Bond Donor:	3
# Rings:	6
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.433
Synthetic Accessibility Score:	4.741
Fsp3:	0.375
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:	-5.017
MDCK Permeability:	1.14279328045086e-05
Pgp-inhibitor:	0.533
Pgp-substrate:	0.186
Human Intestinal Absorption (HIA):	0.027
20% Bioavailability (F20%):	0.013
30% Bioavailability (F30%):	0.68

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.028
Plasma Protein Binding (PPB):	97.8105239868164%
Volume Distribution (VD):	0.858
Pgp-substrate:	2.5684947967529297%

ADMET: Metabolism

CYP1A2-inhibitor:	0.161
CYP1A2-substrate:	0.926
CYP2C19-inhibitor:	0.436
CYP2C19-substrate:	0.843
CYP2C9-inhibitor:	0.824
CYP2C9-substrate:	0.513
CYP2D6-inhibitor:	0.131
CYP2D6-substrate:	0.153
CYP3A4-inhibitor:	0.654
CYP3A4-substrate:	0.921

ADMET: Excretion

Clearance (CL):	6.034
Half-life (T1/2):	0.056

ADMET: Toxicity

hERG Blockers:	0.043
Human Hepatotoxicity (H-HT):	0.358
Drug-inuced Liver Injury (DILI):	0.947
AMES Toxicity:	0.763
Rat Oral Acute Toxicity:	0.746
Maximum Recommended Daily Dose:	0.978
Skin Sensitization:	0.307
Carcinogencity:	0.906
Eye Corrosion:	0.003
Eye Irritation:	0.019
Respiratory Toxicity:	0.975

Download Data

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

Natural Product: NPC472261

Natural Product ID:	NPC472261
*Common Name:**	HCQUPSKUOXQBMU-GLDMDUAVSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HCQUPSKUOXQBMU-GLDMDUAVSA-N
Standard InCHI:	InChI=1S/C32H32O8/c1-15-11-21-24(16(2)40-15)29(35)27-19(7-6-8-23(27)38-4)32(21,39-5)20-10-9-17-12-18-13-31(3,37)14-22(33)25(18)30(36)26(17)28(20)34/h6-10,12,15-16,34,36-37H,11,13-14H2,1-5H3/t15-,16+,31-,32?/m0/s1
SMILES:	CC1CC2=C(C(O1)C)C(=O)C3=C(C2(C4=C(C5=C(C6=C(CC(CC6=O)(C)O)C=C5C=C4)O)O)OC)C=CC=C3OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL3355660
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001640] Naphthopyrans [CHEMONTID:0001641] Naphthopyranones

*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
NPO3206	Karwinskia parvifolia	Species	Rhamnaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[25402632]
NPO3206	Karwinskia parvifolia	Species	Rhamnaceae	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
IC50	6

Activity Type	# Activity
Cell Line	3
NON-MOLECULAR	3

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT81	Cell Line	A549	Homo sapiens	IC50	>	10000.0	nM	PMID[495526]
NPT165	Cell Line	HeLa	Homo sapiens	IC50	>	10000.0	nM	PMID[495526]
NPT65	Cell Line	HepG2	Homo sapiens	IC50	=	4600.0	nM	PMID[495526]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	5500.0	nM	PMID[495526]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	4600.0	nM	PMID[495526]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	>	10000.0	nM	PMID[495526]

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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 NPC472261 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	412
0.1-0.2	1536
0.2-0.3	3060
0.3-0.4	8184
0.4-0.5	10664
0.5-0.6	3905
0.6-0.7	6050
0.7-0.8	6448
0.8-0.85	2119
0.85-0.9	290
0.9-0.95	28
0.95-1	1

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Similarity Score	Similarity Level	Natural Product ID
0.9193	High Similarity	NPC470341
0.9193	High Similarity	NPC234497
0.9193	High Similarity	NPC324522
0.9193	High Similarity	NPC472058
0.9193	High Similarity	NPC105414

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 NPC472261 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	354
0.1-0.2	958
0.2-0.3	1501
0.3-0.4	2627
0.4-0.5	2006
0.5-0.6	1097
0.6-0.7	406
0.7-0.8	169
0.8-0.85	27
0.85-0.9	4
0.9-0.95	1
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9	High Similarity	NPD6959	Discontinued
0.8571	High Similarity	NPD8443	Clinical (unspecified phase)
0.8554	High Similarity	NPD7473	Discontinued
0.8485	Intermediate Similarity	NPD6232	Discontinued
0.8408	Intermediate Similarity	NPD7390	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