NPASS Compound

Structure

NPC137900 OpenBabel06302215392D 26 28 0 0 1 0 0 0 0 0999 V2000 -0.0257 -1.8624 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3810 -2.7760 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2067 -3.5850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3756 -2.8805 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7823 -3.7941 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9634 -2.0715 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5566 -1.1580 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9420 -1.2226 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4067 -0.9135 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.4388 -1.4474 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4013 -0.8090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6092 0.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7431 0.6691 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.3578 0.7337 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8930 0.4247 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1444 -0.1399 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.0159 -0.7444 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5511 -1.0534 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6557 -2.0480 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0104 -0.6399 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9886 -0.8478 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7591 -0.0753 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5657 1.7119 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1878 1.5008 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0704 -1.5522 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 2 4 1 0 0 0 0 4 5 2 0 0 0 0 4 6 1 0 0 0 0 7 6 1 6 0 0 0 7 8 1 0 0 0 0 7 17 1 0 0 0 0 8 9 1 0 0 0 0 9 25 1 0 0 0 0 9 10 1 6 0 0 0 9 11 1 0 0 0 0 11 12 1 0 0 0 0 11 26 1 6 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 13 24 1 6 0 0 0 13 25 1 0 0 0 0 14 15 2 0 0 0 0 14 23 1 0 0 0 0 16 15 1 1 0 0 0 16 17 1 0 0 0 0 16 22 1 0 0 0 0 17 18 1 6 0 0 0 18 19 2 0 0 0 0 18 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	366.17
Volume:	362.497
LogP:	1.024
LogD:	1.015
LogS:	-2.462
# Rotatable Bonds:	3
TPSA:	102.29
# H-Bond Aceptor:	7
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.43
Synthetic Accessibility Score:	5.972
Fsp3:	0.684
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	2
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.963
MDCK Permeability:	6.498602306237444e-05
Pgp-inhibitor:	0.087
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.016
20% Bioavailability (F20%):	0.023
30% Bioavailability (F30%):	0.895

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.221
Plasma Protein Binding (PPB):	69.4474105834961%
Volume Distribution (VD):	1.208
Pgp-substrate:	37.8549690246582%

ADMET: Metabolism

CYP1A2-inhibitor:	0.029
CYP1A2-substrate:	0.181
CYP2C19-inhibitor:	0.039
CYP2C19-substrate:	0.805
CYP2C9-inhibitor:	0.033
CYP2C9-substrate:	0.044
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.083
CYP3A4-inhibitor:	0.325
CYP3A4-substrate:	0.624

ADMET: Excretion

Clearance (CL):	7.443
Half-life (T1/2):	0.75

ADMET: Toxicity

hERG Blockers:	0.03
Human Hepatotoxicity (H-HT):	0.801
Drug-inuced Liver Injury (DILI):	0.921
AMES Toxicity:	0.087
Rat Oral Acute Toxicity:	0.926
Maximum Recommended Daily Dose:	0.839
Skin Sensitization:	0.323
Carcinogencity:	0.208
Eye Corrosion:	0.007
Eye Irritation:	0.018
Respiratory Toxicity:	0.839

Download Data

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

Natural Product: NPC137900

Natural Product ID:	NPC137900
*Common Name:**	RHVYFOFKEZHFKR-GIKWLFIVSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	RHVYFOFKEZHFKR-GIKWLFIVSA-N
Standard InCHI:	InChI=1S/C19H26O7/c1-9(2)16(21)25-13-7-18(5)14(20)8-19(23,26-18)10(3)6-12-15(13)11(4)17(22)24-12/h6,9,12-15,20,23H,4,7-8H2,1-3,5H3/b10-6-/t12-,13-,14+,15+,18-,19-/m1/s1
SMILES:	CC(C)C(=O)O[C@@H]1C[C@]2(C)[C@H](C[C@@](/C(=C[C@@H]3[C@@H]1C(=C)C(=O)O3)/C)(O)O2)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	5281491
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones

*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
NPO19629	Laurencia scoparia	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11754610]
NPO11074	Mycale izuensis	Species	Mycalidae	Eukaryota	n.a.	n.a.	n.a.	PMID[12088446]
NPO18159	Crypteronia paniculata	Species	Crypteroniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12502343]
NPO340	Orixa japonica	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15568765]
NPO18159	Crypteronia paniculata	Species	Crypteroniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15787463]
NPO19629	Laurencia scoparia	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16872159]
NPO15112	Premna oligotricha	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8450316]
NPO17110	Barleria prionitis	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9784173]
NPO340	Orixa japonica	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17989	Astragalus falcatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO340	Orixa japonica	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17989	Astragalus falcatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO340	Orixa japonica	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18837	Ulva rigida	Species	Ulvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15112	Premna oligotricha	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO340	Orixa japonica	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19433	Trichocline caulescens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9841	Picramnia hirsuta	Species	Picramniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16972	Penicillium spiculisporum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19629	Laurencia scoparia	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17110	Barleria prionitis	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11074	Mycale izuensis	Species	Mycalidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19081	Iris halophila	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17486	Alpinia javanica	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18159	Crypteronia paniculata	Species	Crypteroniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23391	Nidula niveotomentosa	Species	Nidulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19007	Lycopodium fastigiatum	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17989	Astragalus falcatus	Species	Fabaceae	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 NPC137900 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	1202
0.2-0.3	4578
0.3-0.4	9680
0.4-0.5	13862
0.5-0.6	7761
0.6-0.7	4145
0.7-0.8	1058
0.8-0.85	151
0.85-0.9	29
0.9-0.95	6
0.95-1	2

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 NPC137900 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	205
0.1-0.2	1844
0.2-0.3	3721
0.3-0.4	2299
0.4-0.5	715
0.5-0.6	286
0.6-0.7	66
0.7-0.8	14
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