NPASS Compound

Structure

NPC74493 OpenBabel06302215562D 24 27 0 0 1 0 0 0 0 0999 V2000 -2.1321 1.4798 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9631 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.8766 1.5274 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7900 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7900 -0.0547 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.4170 -0.7006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4170 -1.5181 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7899 -2.1640 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.7031 -1.6366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7032 -0.5821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6164 -0.0549 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6625 -0.1887 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.2093 0.9179 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 -3.8765 -1.6366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8766 -0.5821 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.9631 -0.0547 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4833 -0.8858 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0035 -0.0547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5237 0.7764 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5641 0.7764 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.5527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9127 1.2562 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9127 0.2965 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 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 16 1 0 0 0 0 3 4 1 0 0 0 0 5 4 1 1 0 0 0 5 10 1 0 0 0 0 5 15 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 6 0 0 0 8 14 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 11 13 1 0 0 0 0 15 14 1 1 0 0 0 15 16 1 0 0 0 0 16 17 1 1 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 24 2 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 M CHG 1 13 -1 M END $$$$

Physi-Chem Properties

Molecular Weight:	330.18
Volume:	344.865
LogP:	3.806
LogD:	3.805
LogS:	-4.139
# Rotatable Bonds:	4
TPSA:	59.67
# H-Bond Aceptor:	4
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.895
Synthetic Accessibility Score:	5.953
Fsp3:	0.65
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.447
MDCK Permeability:	1.9864104615407996e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	0.051
Human Intestinal Absorption (HIA):	0.014
20% Bioavailability (F20%):	0.219
30% Bioavailability (F30%):	0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.084
Plasma Protein Binding (PPB):	97.12236022949219%
Volume Distribution (VD):	1.141
Pgp-substrate:	2.9312922954559326%

ADMET: Metabolism

CYP1A2-inhibitor:	0.034
CYP1A2-substrate:	0.156
CYP2C19-inhibitor:	0.109
CYP2C19-substrate:	0.522
CYP2C9-inhibitor:	0.246
CYP2C9-substrate:	0.224
CYP2D6-inhibitor:	0.019
CYP2D6-substrate:	0.444
CYP3A4-inhibitor:	0.272
CYP3A4-substrate:	0.154

ADMET: Excretion

Clearance (CL):	17.553
Half-life (T1/2):	0.753

ADMET: Toxicity

hERG Blockers:	0.041
Human Hepatotoxicity (H-HT):	0.76
Drug-inuced Liver Injury (DILI):	0.024
AMES Toxicity:	0.005
Rat Oral Acute Toxicity:	0.845
Maximum Recommended Daily Dose:	0.859
Skin Sensitization:	0.133
Carcinogencity:	0.711
Eye Corrosion:	0.009
Eye Irritation:	0.313
Respiratory Toxicity:	0.976

Download Data

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

Natural Product: NPC74493

Natural Product ID:	NPC74493
*Common Name:**	YNNJQADRYQOWDM-SYOYXXOUSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YNNJQADRYQOWDM-SYOYXXOUSA-N
Standard InCHI:	InChI=1S/C20H26O4/c1-13-3-7-20-12-24-15(9-16(20)18(21)22)10-17(20)19(13,2)6-4-14-5-8-23-11-14/h5,8-9,11,13,15,17H,3-4,6-7,10,12H2,1-2H3,(H,21,22)/p-1/t13-,15+,17-,19+,20-/m1/s1
SMILES:	C[C@@H]1CC[C@@]23CO[C@@H](C=C2C(=O)[O-])C[C@@H]3[C@@]1(C)CCc1ccoc1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	6325080
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0001757] Colensane and clerodane 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
NPO16484	Muraltia heisteria	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11858755]
NPO17691	Santalum album	Species	Santalaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15974602]
NPO17462	Pouteria sapota	Species	Sapotaceae	Eukaryota	n.a.	ripe fruit	n.a.	PMID[21214217]
NPO2286	Fischerella muscicola	Species	Hapalosiphonaceae	Bacteria	n.a.	n.a.	n.a.	PMID[22863526]
NPO17620	Rhodopirellula baltica	Species	Planctomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[23826385]
NPO17462	Pouteria sapota	Species	Sapotaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26057604]
NPO17462	Pouteria sapota	Species	Sapotaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO17691	Santalum album	Species	Santalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17691	Santalum album	Species	Santalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14039	Leucaena leucocephala	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15771	Polygonatum prattii	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17691	Santalum album	Species	Santalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO17691	Santalum album	Species	Santalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO2286	Fischerella muscicola	Species	Hapalosiphonaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO16352	Peperomia villipetiola	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17620	Rhodopirellula baltica	Species	Planctomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO14039	Leucaena leucocephala	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17462	Pouteria sapota	Species	Sapotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9405	Siphocampylus foliosus	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15031	Senecio microglossus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15771	Polygonatum prattii	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17155	Selaginella apoda	Species	Selaginellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16484	Muraltia heisteria	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17691	Santalum album	Species	Santalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO669	Crepis pygmaea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16065	Micromeria japonica	Species	Lamiaceae	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 NPC74493 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	310
0.1-0.2	1368
0.2-0.3	2708
0.3-0.4	6026
0.4-0.5	12275
0.5-0.6	12270
0.6-0.7	6706
0.7-0.8	776
0.8-0.85	188
0.85-0.9	62
0.9-0.95	8
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 NPC74493 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	279
0.1-0.2	961
0.2-0.3	1671
0.3-0.4	2709
0.4-0.5	2093
0.5-0.6	1163
0.6-0.7	263
0.7-0.8	11
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