NPASS Compound

Structure

NPC199024 OpenBabel06302216022D 32 31 0 0 0 0 0 0 0 0999 V2000 12.1244 -21.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.9904 -20.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.9904 -19.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.1244 -19.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.1244 -18.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 -17.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 -16.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 -16.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 -15.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 -14.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 -13.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -13.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -12.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -11.5000 0.0000 C 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 1 0 0 0 0 20 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 M END $$$$

Physi-Chem Properties

Molecular Weight:	450.48
Volume:	550.886
LogP:	12.57
LogD:	5.415
LogS:	-7.516
# Rotatable Bonds:	28
TPSA:	17.07
# H-Bond Aceptor:	1
# H-Bond Donor:	0
# Rings:	0
# Heavy Atoms:	1

MedChem Properties

QED Drug-Likeness Score:	0.108
Synthetic Accessibility Score:	1.699
Fsp3:	0.968
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.338
MDCK Permeability:	3.267025476816343e-06
Pgp-inhibitor:	0.0
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.833
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.002
Plasma Protein Binding (PPB):	98.60210418701172%
Volume Distribution (VD):	3.615
Pgp-substrate:	0.6334262490272522%

ADMET: Metabolism

CYP1A2-inhibitor:	0.032
CYP1A2-substrate:	0.133
CYP2C19-inhibitor:	0.101
CYP2C19-substrate:	0.045
CYP2C9-inhibitor:	0.02
CYP2C9-substrate:	0.979
CYP2D6-inhibitor:	0.038
CYP2D6-substrate:	0.026
CYP3A4-inhibitor:	0.159
CYP3A4-substrate:	0.012

ADMET: Excretion

Clearance (CL):	4.675
Half-life (T1/2):	0.033

ADMET: Toxicity

hERG Blockers:	0.598
Human Hepatotoxicity (H-HT):	0.021
Drug-inuced Liver Injury (DILI):	0.256
AMES Toxicity:	0.005
Rat Oral Acute Toxicity:	0.01
Maximum Recommended Daily Dose:	0.034
Skin Sensitization:	0.965
Carcinogencity:	0.017
Eye Corrosion:	0.958
Eye Irritation:	0.91
Respiratory Toxicity:	0.778

Download Data

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

Natural Product: NPC199024

Natural Product ID:	NPC199024
*Common Name:**	UNRFDARCMOHDBJ-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	UNRFDARCMOHDBJ-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C31H62O/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-31(32)30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h3-30H2,1-2H3
SMILES:	CCCCCCCCCCCCCCCC(=O)CCCCCCCCCCCCCCC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	94741
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0001831] Carbonyl compounds [CHEMONTID:0000118] Ketones

*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
NPO21707	Trichosanthes kirilowii	Species	Cucurbitaceae	Eukaryota	n.a.	seed	n.a.	DOI[10.1016/S0031-9422(00)97029-8]
NPO4795	Prunus armeniaca	Species	Rosaceae	Eukaryota	n.a.	kernel	n.a.	PMID[10670815]
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	n.a.	fruit	n.a.	PMID[15577254]
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15621610]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	fruit	n.a.	PMID[16417304]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	branch	n.a.	PMID[17202693]
NPO4795	Prunus armeniaca	Species	Rosaceae	Eukaryota	Fruits	Malatya Fruit Research Institute	between the first and third weeks of 2005-Jul.	PMID[18038980]
NPO21707	Trichosanthes kirilowii	Species	Cucurbitaceae	Eukaryota	seeds	n.a.	n.a.	PMID[18603435]
NPO21707	Trichosanthes kirilowii	Species	Cucurbitaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[20469887]
NPO8101	Rehmannia glutinosa	Species	Orobanchaceae	Eukaryota	Roots	n.a.	n.a.	PMID[22916954]
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	fruits	n.a.	n.a.	PMID[23327905]
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[28453270]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO4795	Prunus armeniaca	Species	Rosaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO4795	Prunus armeniaca	Species	Rosaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO4795	Prunus armeniaca	Species	Rosaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	Bark	n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO4795	Prunus armeniaca	Species	Rosaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO4795	Prunus armeniaca	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[FooDB]
NPO11578.1	Aloe vera var. chinensis	Varieties	Xanthorrhoeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO963	Litsea pungens	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4795	Prunus armeniaca	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21707	Trichosanthes kirilowii	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8101	Rehmannia glutinosa	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4702	Trichosanthes rosthornii	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4795	Prunus armeniaca	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[Phenol-Explorer]
NPO4795	Prunus armeniaca	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4702	Trichosanthes rosthornii	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8101	Rehmannia glutinosa	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21707	Trichosanthes kirilowii	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO963	Litsea pungens	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11578.1	Aloe vera var. chinensis	Varieties	Xanthorrhoeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8101	Rehmannia glutinosa	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4795	Prunus armeniaca	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4702	Trichosanthes rosthornii	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21707	Trichosanthes kirilowii	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO963	Litsea pungens	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4702	Trichosanthes rosthornii	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO21707	Trichosanthes kirilowii	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4795	Prunus armeniaca	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO8101	Rehmannia glutinosa	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4795	Prunus armeniaca	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8101	Rehmannia glutinosa	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4702	Trichosanthes rosthornii	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO963	Litsea pungens	Species	Lauraceae	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 NPC199024 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	2589
0.1-0.2	24461
0.2-0.3	11876
0.3-0.4	3052
0.4-0.5	484
0.5-0.6	143
0.6-0.7	58
0.7-0.8	12
0.8-0.85	2
0.85-0.9	1
0.9-0.95	5
0.95-1	14

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 NPC199024 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	2714
0.1-0.2	5047
0.2-0.3	1058
0.3-0.4	265
0.4-0.5	45
0.5-0.6	16
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