NPASS Compound

Structure

NPC118626 OpenBabel06302215142D 24 26 0 0 1 0 0 0 0 0999 V2000 1.7321 1.0000 0.0000 C 0 0 0 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 2.2321 -0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 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 -2.0000 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 -0.8660 -0.5000 0.0000 C 0 0 0 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 -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 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 C 0 0 1 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 -1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.9641 -1.1340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9641 -1.1340 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9641 -2.8660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9641 -2.8660 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 2.7321 -0.0000 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 2 24 1 0 0 0 0 4 23 2 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 6 7 1 0 0 0 0 7 12 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 8 23 1 0 0 0 0 9 10 1 0 0 0 0 11 10 1 6 0 0 0 11 12 1 0 0 0 0 11 17 1 0 0 0 0 12 13 1 6 0 0 0 12 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 6 0 0 0 17 19 1 0 0 0 0 19 20 2 0 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	330.22
Volume:	361.928
LogP:	3.727
LogD:	3.008
LogS:	-4.628
# Rotatable Bonds:	3
TPSA:	46.53
# H-Bond Aceptor:	3
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.831
Synthetic Accessibility Score:	3.63
Fsp3:	0.667
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:	-4.811
MDCK Permeability:	1.9955545212724246e-05
Pgp-inhibitor:	0.941
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.937
30% Bioavailability (F30%):	0.903

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.081
Plasma Protein Binding (PPB):	90.63502502441406%
Volume Distribution (VD):	0.965
Pgp-substrate:	8.3385009765625%

ADMET: Metabolism

CYP1A2-inhibitor:	0.146
CYP1A2-substrate:	0.76
CYP2C19-inhibitor:	0.338
CYP2C19-substrate:	0.933
CYP2C9-inhibitor:	0.251
CYP2C9-substrate:	0.76
CYP2D6-inhibitor:	0.103
CYP2D6-substrate:	0.843
CYP3A4-inhibitor:	0.733
CYP3A4-substrate:	0.616

ADMET: Excretion

Clearance (CL):	6.487
Half-life (T1/2):	0.128

ADMET: Toxicity

hERG Blockers:	0.172
Human Hepatotoxicity (H-HT):	0.223
Drug-inuced Liver Injury (DILI):	0.217
AMES Toxicity:	0.012
Rat Oral Acute Toxicity:	0.052
Maximum Recommended Daily Dose:	0.608
Skin Sensitization:	0.464
Carcinogencity:	0.055
Eye Corrosion:	0.004
Eye Irritation:	0.066
Respiratory Toxicity:	0.05

Download Data

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

Natural Product: NPC118626

Natural Product ID:	NPC118626
*Common Name:**	IGUDTNVZIOWVIV-DUXKGJEZSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	IGUDTNVZIOWVIV-DUXKGJEZSA-N
Standard InCHI:	InChI=1S/C21H30O3/c1-19(2,23)15-8-9-16-14(13-15)7-10-17-20(16,3)11-6-12-21(17,4)18(22)24-5/h8-9,13,17,23H,6-7,10-12H2,1-5H3/t17-,20-,21-/m1/s1
SMILES:	CC(C)(c1ccc2c(CC[C@@H]3[C@]2(C)CCC[C@@]3(C)C(=O)OC)c1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11573479
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
NPO25880	Sarcococca coriacea	Species	Buxaceae	Eukaryota	leaves	Nepalese	n.a.	PMID[11421762]
NPO7869	Peritassa campestris	Species	Celastraceae	Eukaryota	n.a.	root	n.a.	PMID[11738408]
NPO8513	Pseudomonas fluorescens	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[15826166]
NPO9829	Arnica chamissonis	Species	Asteraceae	Eukaryota	n.a.	rhizome	n.a.	PMID[16644542]
NPO9829	Arnica chamissonis	Species	Asteraceae	Eukaryota	n.a.	root	n.a.	PMID[16644542]
NPO8513	Pseudomonas fluorescens	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[17924666]
NPO8513	Pseudomonas fluorescens	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[20979386]
NPO9829	Arnica chamissonis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23501116]
NPO8513	Pseudomonas fluorescens	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[23688329]
NPO8513	Pseudomonas fluorescens	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[23897464]
NPO8513	Pseudomonas fluorescens	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[7798954]
NPO8513	Pseudomonas fluorescens	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[8626242]
NPO24299	Litsea laurifolia	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24299	Litsea laurifolia	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25421	Stemodia viscosa	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6478	Tubifera ferruginosa	Species	Reticulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8513	Pseudomonas fluorescens	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO8086	Lepechinia caulescens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24479	Phaseolus atropurpureus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO195	Maprounea guianensis	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17593.1	Pinus sylvestris var. hamata	Varieties	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25483	Croton cortesianus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7869	Peritassa campestris	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24568	Spongia zimocca	Species	Spongiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26279	Premna schimperi	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9829	Arnica chamissonis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1325	Bonnemaisonia asparagoides	Species	Bonnemaisoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26582	Erigeron sumatrensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25880	Sarcococca coriacea	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6851	Aplysilla pallida	Species	Darwinellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26464	Macaranga indica	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10310	Cutaneotrichosporon cutaneum	Species	Trichosporonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26799	Vitis heyneana	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24299	Litsea laurifolia	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16067.1	Pseudotsuga sinensis var. wilsoniana	Varieties	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20800	Pholiota nameko	Species	Strophariaceae	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 NPC118626 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	195
0.1-0.2	1055
0.2-0.3	1846
0.3-0.4	5663
0.4-0.5	12576
0.5-0.6	15886
0.6-0.7	4771
0.7-0.8	611
0.8-0.85	57
0.85-0.9	25
0.9-0.95	8
0.95-1	4

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 NPC118626 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	188
0.1-0.2	806
0.2-0.3	1059
0.3-0.4	2533
0.4-0.5	2551
0.5-0.6	1459
0.6-0.7	467
0.7-0.8	82
0.8-0.85	4
0.85-0.9	1
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