NPASS Compound

Structure

NPC69855 OpenBabel06302216202D 27 29 0 0 1 0 0 0 0 0999 V2000 4.5493 2.0255 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8061 1.3563 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.9401 1.8563 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9456 1.7518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2024 1.0827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3364 1.5827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9945 0.1045 0.0000 C 0 0 2 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 2.2673 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2618 -1.2045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0050 -0.5354 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2129 0.4428 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.1264 0.0361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0219 1.0306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9354 0.6238 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0400 -0.3707 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9060 -0.8707 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6981 -1.8488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7035 -1.9534 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2968 -1.0398 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6581 -1.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2079 -0.9781 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.9890 0.2091 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5768 -0.6000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3958 1.1226 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3903 1.2271 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 7 23 1 0 0 0 0 7 8 1 0 0 0 0 7 24 1 1 0 0 0 8 9 1 6 0 0 0 8 21 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 11 12 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 20 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 21 22 2 0 0 0 0 22 23 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	522.21
Volume:	504.9
LogP:	0.585
LogD:	0.912
LogS:	-2.857
# Rotatable Bonds:	10
TPSA:	167.53
# H-Bond Aceptor:	11
# H-Bond Donor:	6
# Rings:	4
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.239
Synthetic Accessibility Score:	4.276
Fsp3:	0.538
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.975
MDCK Permeability:	1.879348565125838e-05
Pgp-inhibitor:	0.02
Pgp-substrate:	0.961
Human Intestinal Absorption (HIA):	0.763
20% Bioavailability (F20%):	0.009
30% Bioavailability (F30%):	0.486

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.209
Plasma Protein Binding (PPB):	70.30870056152344%
Volume Distribution (VD):	0.383
Pgp-substrate:	16.12054443359375%

ADMET: Metabolism

CYP1A2-inhibitor:	0.016
CYP1A2-substrate:	0.23
CYP2C19-inhibitor:	0.013
CYP2C19-substrate:	0.783
CYP2C9-inhibitor:	0.01
CYP2C9-substrate:	0.276
CYP2D6-inhibitor:	0.014
CYP2D6-substrate:	0.173
CYP3A4-inhibitor:	0.092
CYP3A4-substrate:	0.611

ADMET: Excretion

Clearance (CL):	5.432
Half-life (T1/2):	0.678

ADMET: Toxicity

hERG Blockers:	0.359
Human Hepatotoxicity (H-HT):	0.249
Drug-inuced Liver Injury (DILI):	0.119
AMES Toxicity:	0.254
Rat Oral Acute Toxicity:	0.033
Maximum Recommended Daily Dose:	0.018
Skin Sensitization:	0.664
Carcinogencity:	0.035
Eye Corrosion:	0.003
Eye Irritation:	0.012
Respiratory Toxicity:	0.014

Download Data

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

Natural Product: NPC69855

Natural Product ID:	NPC69855
*Common Name:**	KYFFDWMRQAXSTR-IPICDUNHSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	KYFFDWMRQAXSTR-IPICDUNHSA-N
Standard InCHI:	InChI=1S/C22H30N2O3/c1-16-7-8-17(2)22(20(25)26-4)19(14-23-24-22)6-5-11-21(16,3)12-9-18-10-13-27-15-18/h5-6,10,13-16,19,24H,2,7-9,11-12H2,1,3-4H3/b6-5-/t16-,19-,21-,22-/m1/s1
SMILES:	C[C@@H]1CCC(=C)[C@@]2([C@H](/C=CC[C@]1(C)CCc1ccoc1)C=NN2)C(=O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0000013] Amino acids, peptides, and analogues [CHEMONTID:0000347] Amino acids and derivatives [CHEMONTID:0000060] Alpha amino acids 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
NPO3544	Sophora mollis	Species	Fabaceae	Eukaryota	roots	n.a.	n.a.	PMID[19572738]
NPO6431	Strophioblachia fimbricalyx	Species	Euphorbiaceae	Eukaryota	roots	n.a.	n.a.	PMID[19778068]
NPO27656	Lotus edulis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22014228]
NPO27656	Lotus edulis	Species	Fabaceae	Eukaryota	n.a.	leaf	n.a.	PMID[22014228]
NPO27656	Lotus edulis	Species	Fabaceae	Eukaryota	n.a.	branch	n.a.	PMID[22014228]
NPO6431	Strophioblachia fimbricalyx	Species	Euphorbiaceae	Eukaryota	Roots	n.a.	n.a.	PMID[23806014]
NPO4546	Evodiella muelleri	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27656	Lotus edulis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO257	Aplophyllum griffithianum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO6100	Senecio pleistocephalus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2394	Myoporum tenuifolium	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18646	Rubus rosifolius	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1679	Plagiogyria dunnii	Species	Plagiogyriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3544	Sophora mollis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO700	Cassia multijuga	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5245	Angiopteris palmiformis	Species	Marattiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6431	Strophioblachia fimbricalyx	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5574	Schelhammera undulata	Species	Colchicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO65	Geranium palustre	Species	Geraniaceae	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 NPC69855 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	1527
0.2-0.3	5812
0.3-0.4	13323
0.4-0.5	17010
0.5-0.6	4453
0.6-0.7	335
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	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 NPC69855 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	156
0.1-0.2	683
0.2-0.3	1481
0.3-0.4	3014
0.4-0.5	2962
0.5-0.6	835
0.6-0.7	19
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