NPASS Compound

Structure

NPC488984 OpenBabel06302216192D 27 30 0 0 1 0 0 0 0 0999 V2000 2.9105 3.4727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6537 2.8035 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.6318 3.0115 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.0385 3.9250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1318 2.1454 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.1263 2.0409 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7141 2.8499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7086 2.7454 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1154 1.8318 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5276 1.0228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5331 1.1274 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9343 0.1093 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.3465 -0.6997 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1099 1.7273 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.6977 2.5363 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2964 3.5544 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4627 1.4023 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5491 1.8090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.6831 1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 -0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.6180 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5878 0.8090 0.0000 C 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 1 1 6 0 0 0 2 3 1 0 0 0 0 2 18 1 0 0 0 0 3 4 1 6 0 0 0 3 5 1 0 0 0 0 5 6 1 1 0 0 0 5 17 1 0 0 0 0 6 11 2 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 8 16 1 0 0 0 0 9 10 2 0 0 0 0 9 14 1 0 0 0 0 10 11 1 0 0 0 0 10 12 1 0 0 0 0 12 13 1 0 0 0 0 14 15 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 1 0 0 0 19 24 2 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 21 22 1 0 0 0 0 22 27 1 0 0 0 0 22 23 2 0 0 0 0 23 24 1 0 0 0 0 23 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	372.16
Volume:	374.469
LogP:	4.431
LogD:	4.007
LogS:	-5.349
# Rotatable Bonds:	4
TPSA:	66.38
# H-Bond Aceptor:	6
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.867
Synthetic Accessibility Score:	3.619
Fsp3:	0.429
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.736
MDCK Permeability:	4.522368544712663e-05
Pgp-inhibitor:	0.105
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.002
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.024

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.065
Plasma Protein Binding (PPB):	96.0396728515625%
Volume Distribution (VD):	1.124
Pgp-substrate:	3.049612045288086%

ADMET: Metabolism

CYP1A2-inhibitor:	0.381
CYP1A2-substrate:	0.945
CYP2C19-inhibitor:	0.947
CYP2C19-substrate:	0.833
CYP2C9-inhibitor:	0.888
CYP2C9-substrate:	0.871
CYP2D6-inhibitor:	0.89
CYP2D6-substrate:	0.875
CYP3A4-inhibitor:	0.941
CYP3A4-substrate:	0.745

ADMET: Excretion

Clearance (CL):	15.904
Half-life (T1/2):	0.22

ADMET: Toxicity

hERG Blockers:	0.146
Human Hepatotoxicity (H-HT):	0.17
Drug-inuced Liver Injury (DILI):	0.851
AMES Toxicity:	0.081
Rat Oral Acute Toxicity:	0.048
Maximum Recommended Daily Dose:	0.111
Skin Sensitization:	0.897
Carcinogencity:	0.673
Eye Corrosion:	0.004
Eye Irritation:	0.096
Respiratory Toxicity:	0.605

Download Data

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

Natural Product: NPC488984

Natural Product ID:	NPC488984
*Common Name:**	RYXZHMFDFUHLJB-VTLGYEHRSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	RYXZHMFDFUHLJB-VTLGYEHRSA-N
Standard InCHI:	InChI=1S/C21H24O6/c1-11-12(2)20(14-7-15(22)21(24-4)18(9-14)23-3)27-19(11)13-5-6-16-17(8-13)26-10-25-16/h5-9,11-12,19-20,22H,10H2,1-4H3/t11-,12+,19-,20+/m1/s1
SMILES:	C[C@@H]1[C@H](C)[C@@H](c2cc(c(c(c2)OC)OC)O)O[C@H]1c1ccc2c(c1)OCO2
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101913976
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0003686] Furanoid lignans [CHEMONTID:0001604] Tetrahydrofuran lignans [CHEMONTID:0003423] 7,7'-epoxylignans

*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
NPO7118	Manglietiastrum sinicum	Species	Magnoliaceae	Eukaryota	Mature Carpels	n.a.	n.a.	PMID[25116183]
NPO7118	Manglietiastrum sinicum	Species	Magnoliaceae	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	5
MIC	5

Activity Type	# Activity
Cell Line	3
NON-MOLECULAR	2
Organism	5

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT660	Cell Line	SW480	Homo sapiens	IC50	=	19060.0	nM	PMID[25116183]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	=	14020.0	nM	PMID[25116183]
NPT81	Cell Line	A549	Homo sapiens	IC50	=	27410.0	nM	PMID[25116183]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	>	40000.0	nM	PMID[25116183]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	39750.0	nM	PMID[25116183]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	67.0	nM	PMID[25116183]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	130.0	nM	PMID[25116183]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	34.0	nM	PMID[25116183]

☑ 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 NPC488984 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	393
0.1-0.2	1407
0.2-0.3	3805
0.3-0.4	10375
0.4-0.5	8596
0.5-0.6	4902
0.6-0.7	8458
0.7-0.8	3318
0.8-0.85	876
0.85-0.9	428
0.9-0.95	130
0.95-1	9

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 NPC488984 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	312
0.1-0.2	829
0.2-0.3	1796
0.3-0.4	2849
0.4-0.5	1748
0.5-0.6	1023
0.6-0.7	505
0.7-0.8	79
0.8-0.85	4
0.85-0.9	5
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