NPASS Compound

Structure

NPC139738 OpenBabel06302215112D 25 25 0 0 1 0 0 0 0 0999 V2000 -2.5981 -4.5000 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 -1.7321 -3.0000 0.0000 N 0 0 0 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 -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 -1.7321 1.0000 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 -0.0000 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 -2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 3.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 4.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 4.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 3 0 0 0 2 25 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 6 0 0 0 4 12 1 0 0 0 0 5 6 1 0 0 0 0 6 11 2 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 12 13 2 3 0 0 0 12 24 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 6 0 0 0 14 22 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 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 22 23 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	347.2
Volume:	356.931
LogP:	-0.402
LogD:	-0.64
LogS:	-1.624
# Rotatable Bonds:	12
TPSA:	139.67
# H-Bond Aceptor:	8
# H-Bond Donor:	6
# Rings:	1
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.195
Synthetic Accessibility Score:	3.034
Fsp3:	0.412
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.832
MDCK Permeability:	0.00015923114551696926
Pgp-inhibitor:	0.002
Pgp-substrate:	0.988
Human Intestinal Absorption (HIA):	0.058
20% Bioavailability (F20%):	0.007
30% Bioavailability (F30%):	0.02

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.15
Plasma Protein Binding (PPB):	29.888872146606445%
Volume Distribution (VD):	1.223
Pgp-substrate:	75.34088134765625%

ADMET: Metabolism

CYP1A2-inhibitor:	0.008
CYP1A2-substrate:	0.06
CYP2C19-inhibitor:	0.023
CYP2C19-substrate:	0.046
CYP2C9-inhibitor:	0.006
CYP2C9-substrate:	0.015
CYP2D6-inhibitor:	0.032
CYP2D6-substrate:	0.174
CYP3A4-inhibitor:	0.017
CYP3A4-substrate:	0.113

ADMET: Excretion

Clearance (CL):	3.17
Half-life (T1/2):	0.395

ADMET: Toxicity

hERG Blockers:	0.193
Human Hepatotoxicity (H-HT):	0.107
Drug-inuced Liver Injury (DILI):	0.039
AMES Toxicity:	0.065
Rat Oral Acute Toxicity:	0.05
Maximum Recommended Daily Dose:	0.403
Skin Sensitization:	0.421
Carcinogencity:	0.028
Eye Corrosion:	0.003
Eye Irritation:	0.011
Respiratory Toxicity:	0.037

Download Data

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

Natural Product: NPC139738

Natural Product ID:	NPC139738
*Common Name:**	ZXZKRYZJMLNJBU-GJZGRUSLSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ZXZKRYZJMLNJBU-GJZGRUSLSA-N
Standard InCHI:	InChI=1S/C17H25N5O3/c1-12(24)21-15(10-13-6-3-2-4-7-13)16(25)22-14(11-23)8-5-9-20-17(18)19/h2-4,6-7,11,14-15H,5,8-10H2,1H3,(H,21,24)(H,22,25)(H4,18,19,20)/t14-,15-/m0/s1
SMILES:	CC(=N[C@@H](Cc1ccccc1)C(=N[C@@H](CCCNC(=N)N)C=O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0002279] Benzene and substituted derivatives [CHEMONTID:0000186] Phenethylamines [CHEMONTID:0000188] Amphetamines and derivatives

*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
NPO1520	Callyspongia pseudoreticulata	Species	Callyspongiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[12828480]
NPO24252	Uvaria hamiltonii	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[14552774]
NPO24252	Uvaria hamiltonii	Species	Annonaceae	Eukaryota	leaf and stem	n.a.	n.a.	PMID[9584399]
NPO23277	Lobophora papenfussii	Species	Dictyotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24585	Ocotea macropoda	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24252	Uvaria hamiltonii	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28694	Sanguisorba tenuifolia	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23819	Baccharis peruviana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1520	Callyspongia pseudoreticulata	Species	Callyspongiidae	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 NPC139738 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	82
0.1-0.2	1095
0.2-0.3	8692
0.3-0.4	20043
0.4-0.5	10407
0.5-0.6	1762
0.6-0.7	484
0.7-0.8	126
0.8-0.85	5
0.85-0.9	1
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 NPC139738 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	82
0.1-0.2	331
0.2-0.3	832
0.3-0.4	2168
0.4-0.5	3823
0.5-0.6	1550
0.6-0.7	323
0.7-0.8	39
0.8-0.85	2
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