NPASS Compound

Structure

NPC58696 OpenBabel06302215082D 62 61 0 0 1 0 0 0 0 0999 V2000 21.6506 19.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 21.6506 20.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 20.7846 21.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 19.9186 20.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 19.0526 21.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 18.1865 20.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 17.3205 21.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 16.4545 20.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 15.5885 21.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 14.7224 20.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 14.7224 19.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.8564 19.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.8564 18.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.9904 17.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.9904 16.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.1244 16.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.1244 15.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 14.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 13.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 15.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 14.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 13.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 10.3923 13.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 12.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 11.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 10.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 12.1244 12.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.9904 11.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.9904 10.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.8564 10.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.8564 9.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 14.7224 8.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 14.7224 7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 15.5885 7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 15.5885 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 16.4545 5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 16.4545 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 17.3205 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 17.3205 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 18.1865 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 18.1865 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 13.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 12.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 11.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 10.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 12.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 11.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 10.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 10.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 9.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 8.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 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 0.0000 1.0000 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 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 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 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 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 22 42 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 25 27 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 30 31 1 0 0 0 0 31 32 1 0 0 0 0 32 33 1 0 0 0 0 33 34 1 0 0 0 0 34 35 1 0 0 0 0 35 36 1 0 0 0 0 36 37 1 0 0 0 0 37 38 1 0 0 0 0 38 39 1 0 0 0 0 39 40 1 0 0 0 0 40 41 1 0 0 0 0 42 43 1 0 0 0 0 43 44 1 0 0 0 0 44 45 2 0 0 0 0 44 46 1 0 0 0 0 46 47 1 0 0 0 0 47 48 1 0 0 0 0 48 49 1 0 0 0 0 49 50 1 0 0 0 0 50 51 1 0 0 0 0 51 52 1 0 0 0 0 52 53 1 0 0 0 0 53 54 1 0 0 0 0 54 55 1 0 0 0 0 55 56 1 0 0 0 0 56 57 1 0 0 0 0 57 58 1 0 0 0 0 58 59 1 0 0 0 0 59 60 1 0 0 0 0 60 61 1 0 0 0 0 61 62 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	874.8
Volume:	1019.327
LogP:	17.302
LogD:	6.975
LogS:	-3.563
# Rotatable Bonds:	54
TPSA:	78.9
# H-Bond Aceptor:	6
# H-Bond Donor:	0
# Rings:	0
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.034
Synthetic Accessibility Score:	3.472
Fsp3:	0.911
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:	-5.459
MDCK Permeability:	1.0066194136015838e-06
Pgp-inhibitor:	0.0
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.009
20% Bioavailability (F20%):	0.991
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0
Plasma Protein Binding (PPB):	109.18293762207031%
Volume Distribution (VD):	2.85
Pgp-substrate:	0.17415542900562286%

ADMET: Metabolism

CYP1A2-inhibitor:	0.004
CYP1A2-substrate:	0.091
CYP2C19-inhibitor:	0.039
CYP2C19-substrate:	0.029
CYP2C9-inhibitor:	0.003
CYP2C9-substrate:	0.966
CYP2D6-inhibitor:	0.01
CYP2D6-substrate:	0.006
CYP3A4-inhibitor:	0.113
CYP3A4-substrate:	0.005

ADMET: Excretion

Clearance (CL):	4.176
Half-life (T1/2):	0.039

ADMET: Toxicity

hERG Blockers:	0.321
Human Hepatotoxicity (H-HT):	0.053
Drug-inuced Liver Injury (DILI):	0.201
AMES Toxicity:	0.065
Rat Oral Acute Toxicity:	0.009
Maximum Recommended Daily Dose:	0.025
Skin Sensitization:	0.992
Carcinogencity:	0.026
Eye Corrosion:	0.095
Eye Irritation:	0.887
Respiratory Toxicity:	0.306

Download Data

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

Natural Product: NPC58696

Natural Product ID:	NPC58696
*Common Name:**	JOHGUOMDFLEFNX-RFBIWTDZSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JOHGUOMDFLEFNX-RFBIWTDZSA-N
Standard InCHI:	InChI=1S/C56H106O6/c1-4-7-10-13-16-19-22-25-27-30-32-35-38-41-44-47-53(57)50-60-54(51-61-55(58)48-45-42-39-36-33-29-24-21-18-15-12-9-6-3)52-62-56(59)49-46-43-40-37-34-31-28-26-23-20-17-14-11-8-5-2/h25,27,54H,4-24,26,28-52H2,1-3H3/b27-25-
SMILES:	CCCCCCCC/C=CCCCCCCCC(=O)COC(COC(=O)CCCCCCCCCCCCCCC)COC(=O)CCCCCCCCCCCCCCCCC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	6850730
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000175] Glycerolipids [CHEMONTID:0003815] Triradylcglycerols [CHEMONTID:0003814] Alkyldiacylglycerols

*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
NPO18030	Herba acalyphae	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]

☑ 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 NPC58696 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	201
0.1-0.2	2568
0.2-0.3	10915
0.3-0.4	16155
0.4-0.5	8586
0.5-0.6	3428
0.6-0.7	728
0.7-0.8	90
0.8-0.85	17
0.85-0.9	8
0.9-0.95	1
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 NPC58696 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	177
0.1-0.2	3326
0.2-0.3	3664
0.3-0.4	1382
0.4-0.5	439
0.5-0.6	126
0.6-0.7	26
0.7-0.8	10
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