NPASS Compound

Structure

NPC119056 OpenBabel06302215432D 38 42 0 0 1 0 0 0 0 0999 V2000 0.8459 1.4651 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8459 0.4884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6918 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6918 -0.9767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8459 -1.4651 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.9767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6918 -1.9535 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5377 -1.4651 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3835 -1.9535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2294 -1.4651 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2294 -0.4884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3835 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5377 -0.4884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6918 -2.9302 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8459 -3.4186 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8459 -4.3953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -4.8837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6918 -4.8837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5377 -4.3953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3835 -4.8837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3835 -5.8605 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2294 -4.3953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2294 -3.4186 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.0753 -2.9302 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9212 -3.4186 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7671 -2.9302 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7671 -1.9535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9212 -1.4651 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0753 -1.9535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3835 -2.9302 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5377 -3.4186 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6918 -5.8605 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -2.9302 0.0000 O 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 -0.8459 0.4884 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8459 -2.4419 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5377 0.4884 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3835 -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 34 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 3 37 1 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 5 36 1 0 0 0 0 6 34 1 0 0 0 0 7 6 1 1 0 0 0 7 8 1 0 0 0 0 7 14 1 0 0 0 0 8 13 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 2 0 0 0 0 12 13 1 0 0 0 0 14 31 2 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 15 33 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 2 0 0 0 0 18 32 1 0 0 0 0 19 31 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 1 0 0 0 23 30 1 0 0 0 0 24 29 2 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 28 29 1 0 0 0 0 30 31 1 0 0 0 0 34 35 1 0 0 0 0 37 38 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	512.18
Volume:	529.207
LogP:	6.069
LogD:	3.332
LogS:	-3.686
# Rotatable Bonds:	5
TPSA:	116.45
# H-Bond Aceptor:	7
# H-Bond Donor:	4
# Rings:	5
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.242
Synthetic Accessibility Score:	3.673
Fsp3:	0.194
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.327
MDCK Permeability:	1.9640598111436702e-05
Pgp-inhibitor:	0.063
Pgp-substrate:	0.883
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.047
30% Bioavailability (F30%):	0.1

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.004
Plasma Protein Binding (PPB):	100.3463363647461%
Volume Distribution (VD):	0.427
Pgp-substrate:	1.7412692308425903%

ADMET: Metabolism

CYP1A2-inhibitor:	0.031
CYP1A2-substrate:	0.887
CYP2C19-inhibitor:	0.912
CYP2C19-substrate:	0.855
CYP2C9-inhibitor:	0.918
CYP2C9-substrate:	0.982
CYP2D6-inhibitor:	0.467
CYP2D6-substrate:	0.29
CYP3A4-inhibitor:	0.182
CYP3A4-substrate:	0.914

ADMET: Excretion

Clearance (CL):	8.13
Half-life (T1/2):	0.074

ADMET: Toxicity

hERG Blockers:	0.038
Human Hepatotoxicity (H-HT):	0.277
Drug-inuced Liver Injury (DILI):	0.959
AMES Toxicity:	0.02
Rat Oral Acute Toxicity:	0.932
Maximum Recommended Daily Dose:	0.986
Skin Sensitization:	0.948
Carcinogencity:	0.044
Eye Corrosion:	0.003
Eye Irritation:	0.913
Respiratory Toxicity:	0.844

Download Data

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

Natural Product: NPC119056

Natural Product ID:	NPC119056
*Common Name:**	KYRONYOKKZDLAV-ZEQRLZLVSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	KYRONYOKKZDLAV-ZEQRLZLVSA-N
Standard InCHI:	InChI=1S/C31H28O7/c1-16-22(37-3)14-20(32)25(28(16)34)24(19-12-8-5-9-13-19)27-30(36)17(2)29(35)26-21(33)15-23(38-31(26)27)18-10-6-4-7-11-18/h4-14,23-24,32,34-36H,15H2,1-3H3/t23-,24-/m0/s1
SMILES:	Cc1c(cc(c([C@H](c2ccccc2)c2c(c(C)c(c3C(=O)C[C@@H](c4ccccc4)Oc23)O)O)c1O)O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002650] Diarylheptanoids [CHEMONTID:0002651] Linear diarylheptanoids

*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
NPO16098	Boronia pinnata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11076549]
NPO22142	Hippocratea excelsa	Species	n.a.	n.a.	n.a.	root	n.a.	PMID[17385912]
NPO22142	Hippocratea excelsa	Species	n.a.	n.a.	root bark	n.a.	n.a.	PMID[17385912]
NPO6364	Pongamiopsis pervilleana	Species	Fabaceae	Eukaryota	n.a.	Madagascar Dry Forest	n.a.	PMID[20804165]
NPO22142	Hippocratea excelsa	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[2292687]
NPO7890	Cleistanthus indochinensis	Species	Phyllanthaceae	Eukaryota	fruits	n.a.	n.a.	PMID[22938151]
NPO15319	Glochidion sphaerogynum	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12835	Cyrtomium falcatum	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12101	Ajuga genevensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8679	Streptomyces sparsogenes	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO16098	Boronia pinnata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7890	Cleistanthus indochinensis	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1118	Elymus repens	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15005	Sargassum muticum	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6364	Pongamiopsis pervilleana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22142	Hippocratea excelsa	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO15319	Glochidion sphaerogynum	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21904	Tarenaya spinosa	Species	Cleomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17282	Pinguicula vulgaris	Species	Lentibulariaceae	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 NPC119056 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	392
0.1-0.2	1617
0.2-0.3	3694
0.3-0.4	9363
0.4-0.5	9193
0.5-0.6	3721
0.6-0.7	5807
0.7-0.8	5271
0.8-0.85	2165
0.85-0.9	1024
0.9-0.95	391
0.95-1	59

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 NPC119056 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	357
0.1-0.2	980
0.2-0.3	1465
0.3-0.4	2626
0.4-0.5	1921
0.5-0.6	1166
0.6-0.7	428
0.7-0.8	152
0.8-0.85	33
0.85-0.9	15
0.9-0.95	7
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