NPASS Compound

Structure

NPC96927 OpenBabel06302215192D 35 34 0 0 0 0 0 0 0 0999 V2000 13.8564 -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 C 0 0 0 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 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 -11.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 -10.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -10.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -9.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -10.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -10.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -9.0000 0.0000 O 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 1 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 2 0 0 0 0 16 18 1 0 0 0 0 18 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 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 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 M END $$$$

Physi-Chem Properties

Molecular Weight:	492.49
Volume:	591.632
LogP:	12.052
LogD:	5.699
LogS:	-6.657
# Rotatable Bonds:	30
TPSA:	34.14
# H-Bond Aceptor:	2
# H-Bond Donor:	0
# Rings:	0
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.074
Synthetic Accessibility Score:	1.919
Fsp3:	0.939
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.398
MDCK Permeability:	4.007431925856508e-06
Pgp-inhibitor:	0.0
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.007
20% Bioavailability (F20%):	0.999
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.002
Plasma Protein Binding (PPB):	97.25165557861328%
Volume Distribution (VD):	1.772
Pgp-substrate:	0.5385818481445312%

ADMET: Metabolism

CYP1A2-inhibitor:	0.033
CYP1A2-substrate:	0.14
CYP2C19-inhibitor:	0.108
CYP2C19-substrate:	0.04
CYP2C9-inhibitor:	0.03
CYP2C9-substrate:	0.986
CYP2D6-inhibitor:	0.032
CYP2D6-substrate:	0.011
CYP3A4-inhibitor:	0.196
CYP3A4-substrate:	0.014

ADMET: Excretion

Clearance (CL):	5.101
Half-life (T1/2):	0.166

ADMET: Toxicity

hERG Blockers:	0.409
Human Hepatotoxicity (H-HT):	0.018
Drug-inuced Liver Injury (DILI):	0.84
AMES Toxicity:	0.009
Rat Oral Acute Toxicity:	0.01
Maximum Recommended Daily Dose:	0.033
Skin Sensitization:	0.967
Carcinogencity:	0.024
Eye Corrosion:	0.985
Eye Irritation:	0.916
Respiratory Toxicity:	0.977

Download Data

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

Natural Product: NPC96927

Natural Product ID:	NPC96927
*Common Name:**	BYKYTXUAKJDVPV-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	BYKYTXUAKJDVPV-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C33H64O2/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-32(34)31-33(35)30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h3-31H2,1-2H3
SMILES:	CCCCCCCCCCCCCCCC(=O)CC(=O)CCCCCCCCCCCCCCC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	154874
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0001831] Carbonyl compounds [CHEMONTID:0000133] 1,3-dicarbonyl compounds [CHEMONTID:0003926] Beta-diketones

*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
NPO15388	Eucalyptus globulus	Species	Myrtaceae	Eukaryota	n.a.	fruit	n.a.	PMID[18020353]
NPO16886	Amorpha fruticosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18841906]
NPO25518	Hedychium coronarium	Species	Zingiberaceae	Eukaryota	rhizomes	n.a.	n.a.	PMID[21106458]
NPO20414	Ocimum basilicum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21574561]
NPO15388	Eucalyptus globulus	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22934600]
NPO15388	Eucalyptus globulus	Species	Myrtaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[23678820]
NPO20414	Ocimum basilicum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23747095]
NPO7175	Eucalyptus robusta	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27142786]
NPO16886	Amorpha fruticosa	Species	Fabaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[28075580]
NPO20414	Ocimum basilicum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29192771]
NPO15388	Eucalyptus globulus	Species	Myrtaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[30543429]
NPO15388	Eucalyptus globulus	Species	Myrtaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[30848923]
NPO16886	Amorpha fruticosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8326318]
NPO16886	Amorpha fruticosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8350086]
NPO15388	Eucalyptus globulus	Species	Myrtaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[8864235]
NPO20414	Ocimum basilicum	Species	Lamiaceae	Eukaryota	Stem	n.a.	n.a.	Database[FooDB]
NPO20414	Ocimum basilicum	Species	Lamiaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO20414	Ocimum basilicum	Species	Lamiaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO20414	Ocimum basilicum	Species	Lamiaceae	Eukaryota	Flower	n.a.	n.a.	Database[FooDB]
NPO20414	Ocimum basilicum	Species	Lamiaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO20414	Ocimum basilicum	Species	Lamiaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO20414	Ocimum basilicum	Species	Lamiaceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO20414	Ocimum basilicum	Species	Lamiaceae	Eukaryota	Shoot Essent. Oil	n.a.	n.a.	Database[FooDB]
NPO20414	Ocimum basilicum	Species	Lamiaceae	Eukaryota	Sprout Seedling	n.a.	n.a.	Database[FooDB]
NPO15069	Csitus ladaniferus	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[HerDing]
NPO11583	Calycanthus floridus	Species	Calycanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20414	Ocimum basilicum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16886	Amorpha fruticosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6479	Melaleuca leucadendra	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO31130	Eucalyptus sp	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7175	Eucalyptus robusta	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25518	Hedychium coronarium	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO473	Artemisia maritima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4307	Canarium album	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15388	Eucalyptus globulus	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20414	Ocimum basilicum	Species	Lamiaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO22269	Eucalyptus sp.	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7175	Eucalyptus robusta	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15388	Eucalyptus globulus	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25518	Hedychium coronarium	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO473	Artemisia maritima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15069	Csitus ladaniferus	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO20414	Ocimum basilicum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4307	Canarium album	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16886	Amorpha fruticosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11583	Calycanthus floridus	Species	Calycanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6479	Melaleuca leucadendra	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO473	Artemisia maritima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4307	Canarium album	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO6479	Melaleuca leucadendra	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15388	Eucalyptus globulus	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16886	Amorpha fruticosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20414	Ocimum basilicum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO25518	Hedychium coronarium	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11583	Calycanthus floridus	Species	Calycanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7175	Eucalyptus robusta	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4307	Canarium album	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO11583	Calycanthus floridus	Species	Calycanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20414	Ocimum basilicum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25518	Hedychium coronarium	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO473	Artemisia maritima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15388	Eucalyptus globulus	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16886	Amorpha fruticosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7175	Eucalyptus robusta	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4307	Canarium album	Species	Burseraceae	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 NPC96927 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	2068
0.1-0.2	23704
0.2-0.3	12617
0.3-0.4	3596
0.4-0.5	500
0.5-0.6	130
0.6-0.7	55
0.7-0.8	6
0.8-0.85	5
0.85-0.9	15
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 NPC96927 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	2446
0.1-0.2	5214
0.2-0.3	1134
0.3-0.4	286
0.4-0.5	46
0.5-0.6	19
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