NPASS Compound

Structure

NPC488985 OpenBabel06302216202D 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 1 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 2 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 2 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 1 0 0 0 3 5 1 0 0 0 0 5 6 1 6 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 6 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:	4.644
LogD:	4.169
LogS:	-5.559
# 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:	-4.756
MDCK Permeability:	2.640871207404416e-05
Pgp-inhibitor:	0.381
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.002
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.022

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.074
Plasma Protein Binding (PPB):	96.22457885742188%
Volume Distribution (VD):	1.0
Pgp-substrate:	3.2991104125976562%

ADMET: Metabolism

CYP1A2-inhibitor:	0.295
CYP1A2-substrate:	0.946
CYP2C19-inhibitor:	0.927
CYP2C19-substrate:	0.856
CYP2C9-inhibitor:	0.875
CYP2C9-substrate:	0.851
CYP2D6-inhibitor:	0.902
CYP2D6-substrate:	0.872
CYP3A4-inhibitor:	0.936
CYP3A4-substrate:	0.83

ADMET: Excretion

Clearance (CL):	14.924
Half-life (T1/2):	0.223

ADMET: Toxicity

hERG Blockers:	0.144
Human Hepatotoxicity (H-HT):	0.166
Drug-inuced Liver Injury (DILI):	0.744
AMES Toxicity:	0.035
Rat Oral Acute Toxicity:	0.042
Maximum Recommended Daily Dose:	0.08
Skin Sensitization:	0.712
Carcinogencity:	0.376
Eye Corrosion:	0.004
Eye Irritation:	0.08
Respiratory Toxicity:	0.377

Download Data

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

Natural Product: NPC488985

Natural Product ID:	NPC488985
*Common Name:**	RYXZHMFDFUHLJB-DRLYEABHSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	RYXZHMFDFUHLJB-DRLYEABHSA-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:	118711164
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	>	40000.0	nM	PMID[25116183]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	>	40000.0	nM	PMID[25116183]
NPT81	Cell Line	A549	Homo sapiens	IC50	>	40000.0	nM	PMID[25116183]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	>	40000.0	nM	PMID[25116183]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	67.0	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 NPC488985 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 NPC488985 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