NPASS Compound

Structure

NPC28883 OpenBabel06302216212D 33 36 0 0 1 0 0 0 0 0999 V2000 5.0823 -1.0803 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1570 -0.7796 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7108 -2.0817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8125 -3.0493 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6552 -3.5358 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.6552 -4.5088 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4978 -4.9953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4978 -5.9683 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6552 -6.4548 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8125 -5.9683 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8125 -4.9953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4978 -3.0493 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.3404 -3.5358 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1830 -3.0493 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0256 -3.5358 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0256 -4.5088 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1830 -4.9953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3404 -4.5088 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4978 -2.0764 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6552 -1.5899 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.3404 -1.5899 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.1830 -2.0764 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9237 -3.4451 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7214 -4.3968 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2726 -2.7220 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7591 -1.8794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3634 -0.9906 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3957 -0.8889 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1762 -1.6760 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1438 -1.5743 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5395 -0.6854 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9676 0.1017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 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 3 26 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 4 23 1 0 0 0 0 5 6 1 0 0 0 0 5 12 1 6 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 12 13 1 0 0 0 0 12 19 1 6 0 0 0 13 18 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 17 18 1 0 0 0 0 19 20 2 0 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 23 24 2 0 0 0 0 23 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 2 0 0 0 0 27 28 1 0 0 0 0 28 33 2 0 0 0 0 28 29 1 0 0 0 0 29 30 2 0 0 0 0 30 31 1 0 0 0 0 31 32 2 0 0 0 0 32 33 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	440.16
Volume:	468.295
LogP:	4.686
LogD:	4.314
LogS:	-5.41
# Rotatable Bonds:	8
TPSA:	61.83
# H-Bond Aceptor:	5
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.471
Synthetic Accessibility Score:	3.359
Fsp3:	0.143
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:	-4.878
MDCK Permeability:	3.423366433707997e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.93
30% Bioavailability (F30%):	0.986

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.071
Plasma Protein Binding (PPB):	99.42588806152344%
Volume Distribution (VD):	0.471
Pgp-substrate:	1.3509434461593628%

ADMET: Metabolism

CYP1A2-inhibitor:	0.885
CYP1A2-substrate:	0.817
CYP2C19-inhibitor:	0.962
CYP2C19-substrate:	0.135
CYP2C9-inhibitor:	0.971
CYP2C9-substrate:	0.028
CYP2D6-inhibitor:	0.697
CYP2D6-substrate:	0.043
CYP3A4-inhibitor:	0.928
CYP3A4-substrate:	0.652

ADMET: Excretion

Clearance (CL):	5.595
Half-life (T1/2):	0.023

ADMET: Toxicity

hERG Blockers:	0.016
Human Hepatotoxicity (H-HT):	0.931
Drug-inuced Liver Injury (DILI):	0.975
AMES Toxicity:	0.504
Rat Oral Acute Toxicity:	0.109
Maximum Recommended Daily Dose:	0.355
Skin Sensitization:	0.928
Carcinogencity:	0.189
Eye Corrosion:	0.003
Eye Irritation:	0.052
Respiratory Toxicity:	0.926

Download Data

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

Natural Product: NPC28883

Natural Product ID:	NPC28883
*Common Name:**	ZDYAFMHRSFOATI-GAAGCOIUSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ZDYAFMHRSFOATI-GAAGCOIUSA-N
Standard InCHI:	InChI=1S/C28H24O5/c1-31-26-22(18-19-12-6-3-7-13-19)33-28(30)25(26)23(20-14-8-4-9-15-20)24(27(29)32-2)21-16-10-5-11-17-21/h3-18,23-24H,1-2H3/b22-18-/t23-,24+/m0/s1
SMILES:	COC1=C([C@@H](c2ccccc2)[C@@H](c2ccccc2)C(=O)OC)C(=O)O/C/1=Cc1ccccc1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11729888
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000253] Stilbenes

*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
NPO23208	Pulveroboletus ravenelii	Species	Boletaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12542354]
NPO24047	Hydnellum suaveolens	Species	Thelephoraceae	Eukaryota	n.a.	fruit body	n.a.	PMID[16755070]
NPO23543	Hypoxylon fuscum	Species	Xylariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18928	Heimia myrtifolia	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24289	Arctodiaptomus salinus	Species	Diaptomidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18928	Heimia myrtifolia	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21616	Cyclosorus striatus	Species	Thelypteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23208	Pulveroboletus ravenelii	Species	Boletaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24003	Argemone alba	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23543	Hypoxylon fuscum	Species	Xylariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9592.1	Codonopsis foetens subsp. nervosa	Subspecies	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24047	Hydnellum suaveolens	Species	Thelephoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23280	Cyclamen graecum	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28079	Holothuria floridana	Species	Holothuriidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23411	Pseudochlorodesmis furcellata	Species	Bryopsidaceae	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 NPC28883 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	266
0.1-0.2	1159
0.2-0.3	2356
0.3-0.4	6256
0.4-0.5	12650
0.5-0.6	11668
0.6-0.7	7951
0.7-0.8	385
0.8-0.85	3
0.85-0.9	1
0.9-0.95	0
0.95-1	2

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 NPC28883 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	240
0.1-0.2	812
0.2-0.3	1074
0.3-0.4	2644
0.4-0.5	2635
0.5-0.6	1270
0.6-0.7	438
0.7-0.8	36
0.8-0.85	1
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