NPASS Compound

Structure

NPC80804 OpenBabel06302215112D 25 28 0 0 1 0 0 0 0 0999 V2000 1.3360 2.1680 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3360 2.1680 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1640 3.0340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1640 1.3019 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0675 0.9010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1640 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6270 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0193 1.2631 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6270 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.4088 -1.1235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3837 -0.9010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8176 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.8086 0.1342 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9871 1.1182 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1065 1.5920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3837 0.9010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4088 1.1235 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.0702 1.8735 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7514 2.8213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7712 3.0191 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1098 2.2691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4524 3.9670 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6270 1.3019 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0000 0.8019 0.0000 N 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 4 2 1 6 0 0 0 4 5 1 0 0 0 0 4 23 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 17 1 0 0 0 0 7 8 1 1 0 0 0 7 9 1 0 0 0 0 9 10 1 6 0 0 0 9 25 1 0 0 0 0 10 11 1 0 0 0 0 12 11 1 6 0 0 0 12 13 1 0 0 0 0 12 16 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 17 18 1 1 0 0 0 17 23 1 0 0 0 0 18 19 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 23 24 1 6 0 0 0 24 25 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	345.27
Volume:	378.147
LogP:	3.517
LogD:	3.664
LogS:	-4.122
# Rotatable Bonds:	4
TPSA:	49.33
# H-Bond Aceptor:	3
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.731
Synthetic Accessibility Score:	5.792
Fsp3:	0.864
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:	-5.275
MDCK Permeability:	2.3954330572451e-06
Pgp-inhibitor:	0.056
Pgp-substrate:	0.007
Human Intestinal Absorption (HIA):	0.007
20% Bioavailability (F20%):	0.15
30% Bioavailability (F30%):	0.526

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.803
Plasma Protein Binding (PPB):	88.35698699951172%
Volume Distribution (VD):	0.547
Pgp-substrate:	5.373461723327637%

ADMET: Metabolism

CYP1A2-inhibitor:	0.042
CYP1A2-substrate:	0.422
CYP2C19-inhibitor:	0.027
CYP2C19-substrate:	0.893
CYP2C9-inhibitor:	0.121
CYP2C9-substrate:	0.897
CYP2D6-inhibitor:	0.092
CYP2D6-substrate:	0.853
CYP3A4-inhibitor:	0.414
CYP3A4-substrate:	0.288

ADMET: Excretion

Clearance (CL):	2.612
Half-life (T1/2):	0.483

ADMET: Toxicity

hERG Blockers:	0.186
Human Hepatotoxicity (H-HT):	0.391
Drug-inuced Liver Injury (DILI):	0.02
AMES Toxicity:	0.007
Rat Oral Acute Toxicity:	0.718
Maximum Recommended Daily Dose:	0.9
Skin Sensitization:	0.489
Carcinogencity:	0.235
Eye Corrosion:	0.004
Eye Irritation:	0.012
Respiratory Toxicity:	0.958

Download Data

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

Natural Product: NPC80804

Natural Product ID:	NPC80804
*Common Name:**	RVEHXCTUKLDIGQ-IUSKLVQGSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	RVEHXCTUKLDIGQ-IUSKLVQGSA-N
Standard InCHI:	InChI=1S/C22H35NO2/c1-14(2)17-9-11-21(3)16-8-7-15-5-4-6-18(15)22(21,12-10-19(24)25)20(17)23-13-16/h6,14-17,20,23H,4-5,7-13H2,1-3H3,(H,24,25)/t15-,16-,17-,20+,21+,22+/m0/s1
SMILES:	CC(C)[C@@H]1CC[C@]2(C)[C@H]3CC[C@@H]4CCC=C4[C@]2(CCC(=O)O)[C@@H]1NC3
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:0001550] Sesquiterpenoids

*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
NPO2863	Macaranga mappa	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11170679]
NPO1284	Neocheiropteris palmatopedata	Species	Polypodiaceae	Eukaryota	n.a.	root	n.a.	PMID[20100622]
NPO19849.1	Melilotus officinalis subsp. suaveolens	Subspecies	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4333	Neorautanenia edulis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2863	Macaranga mappa	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3332	Rhaponticum integrifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19849.1	Melilotus officinalis subsp. suaveolens	Subspecies	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1284	Neocheiropteris palmatopedata	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14943	Aphanamixis rohituka	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8017	Tonduzia pittieri	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9584	Delphinium zalil	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9341	Chaetomium abuense	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10259	Aralia cordata	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7405	Candelaria medians	Species	Candelariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4333	Neorautanenia edulis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2005	Rungia repens	Species	Acanthaceae	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 NPC80804 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	92
0.1-0.2	857
0.2-0.3	10926
0.3-0.4	16631
0.4-0.5	10722
0.5-0.6	3224
0.6-0.7	240
0.7-0.8	5
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
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 NPC80804 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	87
0.1-0.2	547
0.2-0.3	2994
0.3-0.4	3896
0.4-0.5	1311
0.5-0.6	310
0.6-0.7	5
0.7-0.8	0
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