NPASS Compound

Structure

NPC111341 OpenBabel07101718222D 30 33 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 4.3301 -0.5000 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 -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 -2.5981 1.5000 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 2.5981 -1.5000 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 2.5981 2.5000 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 -3.4641 1.0000 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 1.7321 -2.0000 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 -0.5000 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 1.7321 1.0000 0.0000 C 0 0 2 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 1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 3.0000 0.0000 C 0 0 2 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 -4.3301 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -0.0000 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 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 28 1 0 0 0 0 3 5 1 0 0 0 0 3 11 2 0 0 0 0 4 6 2 0 0 0 0 4 11 1 0 0 0 0 5 12 2 0 0 0 0 6 12 1 0 0 0 0 7 13 1 0 0 0 0 7 16 2 0 0 0 0 8 14 2 0 0 0 0 8 17 1 0 0 0 0 9 15 1 0 0 0 0 9 18 1 0 0 0 0 10 1 1 1 0 0 0 10 21 1 0 0 0 0 10 29 1 0 0 0 0 11 16 1 0 0 0 0 12 23 1 0 0 0 0 13 19 1 0 0 0 0 13 24 2 0 0 0 0 14 19 1 0 0 0 0 14 25 1 0 0 0 0 15 21 1 0 0 0 0 15 26 2 0 0 0 0 16 30 1 0 0 0 0 17 20 2 0 0 0 0 17 28 1 0 0 0 0 18 20 1 1 0 0 0 18 29 1 0 0 0 0 19 22 2 0 0 0 0 20 22 1 0 0 0 0 21 27 1 6 0 0 0 22 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	412.12
Volume:	401.436
LogP:	2.933
LogD:	2.046
LogS:	-4.209
# Rotatable Bonds:	3
TPSA:	126.43
# H-Bond Aceptor:	8
# H-Bond Donor:	3
# Rings:	4
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.599
Synthetic Accessibility Score:	3.919
Fsp3:	0.273
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.971
MDCK Permeability:	8.627679562778212e-06
Pgp-inhibitor:	0.003
Pgp-substrate:	0.96
Human Intestinal Absorption (HIA):	0.174
20% Bioavailability (F20%):	0.028
30% Bioavailability (F30%):	0.556

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.009
Plasma Protein Binding (PPB):	92.07801818847656%
Volume Distribution (VD):	0.786
Pgp-substrate:	6.991105556488037%

ADMET: Metabolism

CYP1A2-inhibitor:	0.379
CYP1A2-substrate:	0.81
CYP2C19-inhibitor:	0.163
CYP2C19-substrate:	0.101
CYP2C9-inhibitor:	0.764
CYP2C9-substrate:	0.921
CYP2D6-inhibitor:	0.065
CYP2D6-substrate:	0.279
CYP3A4-inhibitor:	0.279
CYP3A4-substrate:	0.207

ADMET: Excretion

Clearance (CL):	7.734
Half-life (T1/2):	0.686

ADMET: Toxicity

hERG Blockers:	0.025
Human Hepatotoxicity (H-HT):	0.601
Drug-inuced Liver Injury (DILI):	0.977
AMES Toxicity:	0.619
Rat Oral Acute Toxicity:	0.763
Maximum Recommended Daily Dose:	0.761
Skin Sensitization:	0.105
Carcinogencity:	0.749
Eye Corrosion:	0.003
Eye Irritation:	0.212
Respiratory Toxicity:	0.152

Download Data

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

Natural Product: NPC111341

Natural Product ID:	NPC111341
*Common Name:**	Aciculatinone
IUPAC Name:	5-hydroxy-8-[(2R,5R,6R)-5-hydroxy-6-methyl-4-oxooxan-2-yl]-2-(4-hydroxyphenyl)-7-methoxychromen-4-one
Synonyms:	Aciculatinone
Standard InCHIKey:	CFHMTDWOLGJZEJ-LMCQJGHKSA-N
Standard InCHI:	InChI=1S/C22H20O8/c1-10-21(27)15(26)9-18(29-10)20-17(28-2)8-14(25)19-13(24)7-16(30-22(19)20)11-3-5-12(23)6-4-11/h3-8,10,18,21,23,25,27H,9H2,1-2H3/t10-,18-,21-/m1/s1
SMILES:	C[C@@H]1[C@H](C(=O)C[C@H](c2c(cc(c3c(=O)cc(c4ccc(cc4)O)oc23)O)OC)O1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL2011652
PubChem CID:	57332647
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0002585] O-methylated flavonoids [CHEMONTID:0002592] 7-O-methylated flavonoids

*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

Show entries

Search:

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO32718	chrysopogon aciculatis	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[22272829]

Showing 1 to 1 of 1 entries

Previous1Next

☑ 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

Show entries

Search:

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

Showing 0 to 0 of 0 entries

PreviousNext

☑ 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	4

Activity Type	# Activity
Cell Line	4

Show entries

Search:

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT83	Cell Line	MCF7	Homo sapiens	IC50	=	18360.0	nM	PMID[573211]
NPT397	Cell Line	NCI-H460	Homo sapiens	IC50	=	18060.0	nM	PMID[573211]
NPT139	Cell Line	HT-29	Homo sapiens	IC50	=	11590.0	nM	PMID[573211]
NPT404	Cell Line	CCRF-CEM	Homo sapiens	IC50	=	13330.0	nM	PMID[573211]

Showing 1 to 4 of 4 entries

Previous1Next

☑ 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 NPC111341 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	1634
0.2-0.3	3730
0.3-0.4	9454
0.4-0.5	9239
0.5-0.6	4068
0.6-0.7	5616
0.7-0.8	4183
0.8-0.85	2443
0.85-0.9	1758
0.9-0.95	149
0.95-1	11

Show entries

Search:

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC304745
0.9932	High Similarity	NPC268193
0.9865	High Similarity	NPC48579
0.9865	High Similarity	NPC304207
0.9865	High Similarity	NPC207809

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

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 NPC111341 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	381
0.1-0.2	872
0.2-0.3	1683
0.3-0.4	2649
0.4-0.5	1970
0.5-0.6	1059
0.6-0.7	345
0.7-0.8	125
0.8-0.85	42
0.85-0.9	22
0.9-0.95	2
0.95-1	0

Show entries

Search:

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9595	High Similarity	NPD4380	Phase 2
0.9388	High Similarity	NPD4378	Clinical (unspecified phase)
0.9346	High Similarity	NPD7075	Discontinued
0.9304	High Similarity	NPD7804	Clinical (unspecified phase)
0.9221	High Similarity	NPD4381	Clinical (unspecified phase)

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

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