NPASS Compound

Structure

NPC13489 OpenBabel06302216212D 31 35 0 0 1 0 0 0 0 0999 V2000 -4.6563 -1.8331 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9653 -0.8820 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2962 -0.1389 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6052 0.8122 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9361 1.5553 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9579 1.3474 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6489 0.3963 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6708 0.1884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0016 0.9316 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3106 1.8826 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2888 2.0905 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5978 3.0416 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5760 3.2495 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0235 0.7237 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.3833 -0.1899 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.1753 -1.1680 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0414 -1.6680 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7845 -0.9989 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.3198 0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3198 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4538 -1.3090 0.0000 C 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 0.5878 0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4538 0.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3633 0.5000 0.0000 O 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 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3778 -0.0854 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.5857 0.8928 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7197 1.3928 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9435 -0.6741 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 31 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 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 9 10 2 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 14 9 1 6 0 0 0 14 15 1 0 0 0 0 14 30 1 0 0 0 0 15 16 1 6 0 0 0 15 28 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 1 0 0 0 18 28 1 0 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 28 29 1 6 0 0 0 29 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	424.19
Volume:	432.46
LogP:	5.526
LogD:	4.025
LogS:	-6.278
# Rotatable Bonds:	6
TPSA:	55.38
# H-Bond Aceptor:	6
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.619
Synthetic Accessibility Score:	3.874
Fsp3:	0.44
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.859
MDCK Permeability:	4.522542076301761e-05
Pgp-inhibitor:	0.997
Pgp-substrate:	0.009
Human Intestinal Absorption (HIA):	0.001
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.029

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.036
Plasma Protein Binding (PPB):	92.36666107177734%
Volume Distribution (VD):	0.862
Pgp-substrate:	2.5467472076416016%

ADMET: Metabolism

CYP1A2-inhibitor:	0.15
CYP1A2-substrate:	0.74
CYP2C19-inhibitor:	0.9
CYP2C19-substrate:	0.535
CYP2C9-inhibitor:	0.653
CYP2C9-substrate:	0.611
CYP2D6-inhibitor:	0.923
CYP2D6-substrate:	0.901
CYP3A4-inhibitor:	0.88
CYP3A4-substrate:	0.643

ADMET: Excretion

Clearance (CL):	15.013
Half-life (T1/2):	0.086

ADMET: Toxicity

hERG Blockers:	0.389
Human Hepatotoxicity (H-HT):	0.789
Drug-inuced Liver Injury (DILI):	0.916
AMES Toxicity:	0.719
Rat Oral Acute Toxicity:	0.039
Maximum Recommended Daily Dose:	0.711
Skin Sensitization:	0.576
Carcinogencity:	0.433
Eye Corrosion:	0.003
Eye Irritation:	0.07
Respiratory Toxicity:	0.1

Download Data

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

Natural Product: NPC13489

Natural Product ID:	NPC13489
*Common Name:**	WXYFFRZGPDZASV-QXVOXHNYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	WXYFFRZGPDZASV-QXVOXHNYSA-N
Standard InCHI:	InChI=1S/C25H28O6/c1-15(2)8-9-27-20-6-4-16(10-22(20)26-3)24-18-12-29-25(19(18)13-28-24)17-5-7-21-23(11-17)31-14-30-21/h4-8,10-11,18-19,24-25H,9,12-14H2,1-3H3/t18-,19-,24-,25+/m0/s1
SMILES:	CC(=CCOc1ccc(cc1OC)[C@H]1[C@H]2CO[C@H](c3ccc4c(c3)OCO4)[C@H]2CO1)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0003686] Furanoid lignans

*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
NPO9553	Phyllodium pulchellum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15921433]
NPO5131	Scorzonera hispanica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9783	Mikania scandens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9783	Mikania scandens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5131	Scorzonera hispanica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9783	Mikania scandens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12591	Archaster typicus	Species	Archasteridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6386	Gutenbergia cordifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8601	Petrosia volcano	Species	Petrosiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13042	Diospyros abyssinica	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12233	Diospyros peregrina	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4746	Centaurea arenaria	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11333	Trapa japonica	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9553	Phyllodium pulchellum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9361	Aplophyllum villosum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO1326	Cratystylis conocephala	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22899	Phaeotremella fagi	Species	Phaeotremellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9783	Mikania scandens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5131	Scorzonera hispanica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12367	Diospyros elliptifolia	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13555	Beaucarnea recurvata	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7870	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12819	Clitocybe subilludens	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9989	Cotylelobium scabriusculum	Species	Dipterocarpaceae	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

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ 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 NPC13489 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	493
0.1-0.2	1474
0.2-0.3	4054
0.3-0.4	11171
0.4-0.5	7863
0.5-0.6	6551
0.6-0.7	8426
0.7-0.8	2120
0.8-0.85	374
0.85-0.9	126
0.9-0.95	33
0.95-1	12

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 NPC13489 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	373
0.1-0.2	850
0.2-0.3	1819
0.3-0.4	2779
0.4-0.5	1770
0.5-0.6	1009
0.6-0.7	483
0.7-0.8	65
0.8-0.85	2
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