NPASS Compound

Structure

NPC163872 OpenBabel06302215222D 26 31 0 0 1 0 0 0 0 0999 V2000 -1.5165 -4.8459 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1412 -3.9393 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.4723 -3.9392 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0006 -3.4661 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0005 -2.7972 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8080 -2.3309 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8079 -1.3986 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6152 -0.9323 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6150 0.0488 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4227 -1.3983 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4228 -2.3306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6155 -2.7969 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6157 -3.7781 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0002 -0.9323 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8070 -1.3989 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6147 -0.9326 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4222 -1.3992 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4221 -2.3315 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6144 -2.7975 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6142 -3.4664 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9208 -3.5322 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5171 -2.9646 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8068 -2.3312 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6149 -0.0003 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2461 0.6307 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 2 1 0 0 0 0 2 3 1 0 0 0 0 2 20 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 5 23 1 0 0 0 0 6 12 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 14 1 0 0 0 0 8 9 2 0 0 0 0 8 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 14 15 1 0 0 0 0 14 26 1 0 0 0 0 15 16 1 0 0 0 0 15 23 1 0 0 0 0 16 17 1 0 0 0 0 16 24 1 0 0 0 0 17 18 1 0 0 0 0 19 18 1 6 0 0 0 19 20 1 0 0 0 0 19 23 1 0 0 0 0 20 21 1 1 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	610.31
Volume:	629.154
LogP:	4.851
LogD:	3.724
LogS:	-4.27
# Rotatable Bonds:	12
TPSA:	150.59
# H-Bond Aceptor:	9
# H-Bond Donor:	4
# Rings:	5
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.177
Synthetic Accessibility Score:	5.251
Fsp3:	0.629
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:	-4.955
MDCK Permeability:	2.4573184418841265e-05
Pgp-inhibitor:	0.993
Pgp-substrate:	0.89
Human Intestinal Absorption (HIA):	0.508
20% Bioavailability (F20%):	0.92
30% Bioavailability (F30%):	0.573

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.148
Plasma Protein Binding (PPB):	95.81182098388672%
Volume Distribution (VD):	1.994
Pgp-substrate:	3.5169999599456787%

ADMET: Metabolism

CYP1A2-inhibitor:	0.024
CYP1A2-substrate:	0.092
CYP2C19-inhibitor:	0.212
CYP2C19-substrate:	0.275
CYP2C9-inhibitor:	0.9
CYP2C9-substrate:	0.067
CYP2D6-inhibitor:	0.01
CYP2D6-substrate:	0.018
CYP3A4-inhibitor:	0.926
CYP3A4-substrate:	0.574

ADMET: Excretion

Clearance (CL):	3.13
Half-life (T1/2):	0.583

ADMET: Toxicity

hERG Blockers:	0.066
Human Hepatotoxicity (H-HT):	0.943
Drug-inuced Liver Injury (DILI):	0.984
AMES Toxicity:	0.01
Rat Oral Acute Toxicity:	0.808
Maximum Recommended Daily Dose:	0.422
Skin Sensitization:	0.13
Carcinogencity:	0.023
Eye Corrosion:	0.003
Eye Irritation:	0.017
Respiratory Toxicity:	0.488

Download Data

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

Natural Product: NPC163872

Natural Product ID:	NPC163872
*Common Name:**	QCPDBEXGCHOIDE-FJKCABEUSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	QCPDBEXGCHOIDE-FJKCABEUSA-N
Standard InCHI:	InChI=1S/C21H22O5/c1-9-8-25-19-16-14(23)5-4-13(22)15(16)18-17-11(20(24)26-18)2-3-12-10(9)6-7-21(12,17)19/h4-5,9-12,17-19H,2-3,6-8H2,1H3/t9-,10-,11-,12+,17-,18-,19-,21-/m1/s1
SMILES:	C[C@@H]1CO[C@@H]2C3=C(C(=O)C=CC3=O)[C@@H]3[C@H]4[C@@H](CC[C@H]5[C@@H]1CC[C@]245)C(=O)O3
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10247550
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000018] Anthracenes [CHEMONTID:0000151] Anthraquinones

*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
NPO11185	Hohenbuehelia grisea	Species	Pleurotaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29356520]
NPO11185	Hohenbuehelia grisea	Species	Pleurotaceae	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	2
MIC	7

Activity Type	# Activity
Cell Line	2
Organism	7

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1178	Cell Line	KB 3-1	Homo sapiens	IC50	=	2.8	ug.mL-1	PMID[29356520]
NPT1460	Cell Line	L929	Mus musculus	IC50	=	2.2	ug.mL-1	PMID[29356520]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	66.7	ug.mL-1	PMID[29356520]
NPT3481	Organism	Mucor hiemalis	Mucor hiemalis	MIC	=	16.7	ug.mL-1	PMID[29356520]
NPT772	Organism	Pichia anomala	Wickerhamomyces anomalus	MIC	=	66.7	ug.mL-1	PMID[29356520]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	MIC	=	100.0	ug.mL-1	PMID[29356520]
NPT5915	Organism	Candida tenuis	Candida tenuis	MIC	=	100.0	ug.mL-1	PMID[29356520]
NPT24136	ORGANISM	Mucor plumbeus	Mucor plumbeus	MIC	=	100.0	ug.mL-1	PMID[29356520]
NPT3628	Organism	Rhodotorula glutinis	Rhodotorula glutinis	MIC	=	33.3	ug.mL-1	PMID[29356520]

☑ 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 NPC163872 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	262
0.1-0.2	1525
0.2-0.3	5551
0.3-0.4	10018
0.4-0.5	11819
0.5-0.6	7569
0.6-0.7	5025
0.7-0.8	911
0.8-0.85	15
0.85-0.9	0
0.9-0.95	1
0.95-1	1

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 NPC163872 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	226
0.1-0.2	1792
0.2-0.3	4126
0.3-0.4	1998
0.4-0.5	589
0.5-0.6	213
0.6-0.7	184
0.7-0.8	22
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
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