NPASS Compound

Structure

NPC302124 OpenBabel06302215142D 28 30 0 0 1 0 0 0 0 0999 V2000 1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1962 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3660 0.6340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 O 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 4 3 1 6 0 0 0 4 5 1 0 0 0 0 4 27 1 0 0 0 0 5 15 1 0 0 0 0 5 6 2 0 0 0 0 6 7 1 0 0 0 0 6 18 1 0 0 0 0 7 8 2 0 0 0 0 7 9 1 0 0 0 0 9 10 2 0 0 0 0 9 17 1 0 0 0 0 10 11 1 0 0 0 0 10 15 1 0 0 0 0 11 12 1 6 0 0 0 11 13 1 0 0 0 0 13 14 1 0 0 0 0 15 16 2 0 0 0 0 18 26 1 0 0 0 0 18 19 1 1 0 0 0 18 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 23 25 1 0 0 0 0 26 23 1 1 0 0 0 26 27 1 0 0 0 0 27 28 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	392.22
Volume:	405.594
LogP:	3.182
LogD:	1.07
LogS:	-2.829
# Rotatable Bonds:	4
TPSA:	107.22
# H-Bond Aceptor:	6
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.46
Synthetic Accessibility Score:	4.726
Fsp3:	0.682
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.811
MDCK Permeability:	1.2689446521108039e-05
Pgp-inhibitor:	0.045
Pgp-substrate:	0.171
Human Intestinal Absorption (HIA):	0.048
20% Bioavailability (F20%):	0.833
30% Bioavailability (F30%):	0.014

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.1
Plasma Protein Binding (PPB):	92.31536102294922%
Volume Distribution (VD):	3.323
Pgp-substrate:	6.054044723510742%

ADMET: Metabolism

CYP1A2-inhibitor:	0.023
CYP1A2-substrate:	0.834
CYP2C19-inhibitor:	0.012
CYP2C19-substrate:	0.792
CYP2C9-inhibitor:	0.11
CYP2C9-substrate:	0.836
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.172
CYP3A4-inhibitor:	0.111
CYP3A4-substrate:	0.289

ADMET: Excretion

Clearance (CL):	7.986
Half-life (T1/2):	0.112

ADMET: Toxicity

hERG Blockers:	0.007
Human Hepatotoxicity (H-HT):	0.219
Drug-inuced Liver Injury (DILI):	0.874
AMES Toxicity:	0.085
Rat Oral Acute Toxicity:	0.304
Maximum Recommended Daily Dose:	0.533
Skin Sensitization:	0.936
Carcinogencity:	0.022
Eye Corrosion:	0.003
Eye Irritation:	0.8
Respiratory Toxicity:	0.946

Download Data

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

Natural Product: NPC302124

Natural Product ID:	NPC302124
*Common Name:**	RKFLDMZOLRTDIZ-CVYZWJSISA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	RKFLDMZOLRTDIZ-CVYZWJSISA-N
Standard InCHI:	InChI=1S/C22H32O6/c1-6-28-19-13-14(17(26)16(25)12(15(13)24)11(2)10-23)22(5)9-7-8-21(3,4)20(22)18(19)27/h11,18-20,23,25,27H,6-10H2,1-5H3/t11-,18-,19+,20+,22-/m1/s1
SMILES:	CCO[C@H]1C2=C(C(=O)C(=C([C@H](C)CO)C2=O)O)[C@@]2(C)CCCC(C)(C)[C@@H]2[C@@H]1O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids

*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
NPO19645	Chironia krebsii	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/0031-9422(91)80080-K]
NPO16538	Stylophorum diphyllum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22029392]
NPO18135	Clausena vestita	Species	Rutaceae	Eukaryota	whole plants	Yunnan Province, China	2008-JAN	PMID[22093759]
NPO12583	Sauromatum giganteum	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28394604]
NPO18319	Fraxinus japonica	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16538	Stylophorum diphyllum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16703	Isodon lophanthoides	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18319	Fraxinus japonica	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16538	Stylophorum diphyllum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12583	Sauromatum giganteum	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO16771	Amomum mindanaense	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18135	Clausena vestita	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18319	Fraxinus japonica	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16538	Stylophorum diphyllum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16354	Allium scorodoprasum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12583	Sauromatum giganteum	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19645	Chironia krebsii	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17735	Acinetobacter genospecies	Species	Moraxellaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO16703	Isodon lophanthoides	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6896	Haliclona fulva	Species	Chalinidae	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 NPC302124 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	223
0.1-0.2	1429
0.2-0.3	4536
0.3-0.4	8634
0.4-0.5	14144
0.5-0.6	8042
0.6-0.7	4819
0.7-0.8	833
0.8-0.85	30
0.85-0.9	4
0.9-0.95	3
0.95-1	0

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 NPC302124 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	212
0.1-0.2	1838
0.2-0.3	3706
0.3-0.4	2213
0.4-0.5	768
0.5-0.6	230
0.6-0.7	176
0.7-0.8	7
0.8-0.85	0
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