NPASS Compound

Structure

NPC88193 OpenBabel06302216152D 35 38 0 0 1 0 0 0 0 0999 V2000 10.3572 -1.2665 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.6140 -0.5974 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6630 -0.9064 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.4551 -1.8846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1982 -2.5537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.1493 -2.2447 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5040 -2.1936 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2961 -3.1717 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3450 -3.4807 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1371 -4.4589 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6019 -2.8116 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 6.1019 -1.9456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2064 -0.9511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8974 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2283 0.7431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3147 1.1499 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0 3.3147 1.1499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4012 0.7431 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.4142 1.6137 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1029 2.1463 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9487 1.9399 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.4230 -0.9511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5276 -1.9456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0276 -2.8116 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.8366 -3.3994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8147 -3.6073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7929 -3.3994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5765 -2.2546 0.0000 O 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 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 7 1 0 0 0 0 5 6 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 9 11 1 0 0 0 0 11 28 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 21 1 0 0 0 0 16 17 2 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 18 22 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 22 23 1 0 0 0 0 22 30 1 1 0 0 0 23 24 1 0 0 0 0 24 25 2 3 0 0 0 24 29 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 30 35 2 0 0 0 0 30 31 1 0 0 0 0 31 32 2 0 0 0 0 32 33 1 0 0 0 0 33 34 2 0 0 0 0 34 35 1 0 0 0 0 M CHG 1 16 1 M END $$$$

Physi-Chem Properties

Molecular Weight:	473.29
Volume:	512.435
LogP:	2.359
LogD:	2.773
LogS:	-2.314
# Rotatable Bonds:	4
TPSA:	55.66
# H-Bond Aceptor:	6
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.546
Synthetic Accessibility Score:	5.075
Fsp3:	0.414
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.161
MDCK Permeability:	1.4810391803621314e-05
Pgp-inhibitor:	0.027
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.98
20% Bioavailability (F20%):	0.992
30% Bioavailability (F30%):	0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.744
Plasma Protein Binding (PPB):	89.17713165283203%
Volume Distribution (VD):	1.788
Pgp-substrate:	12.129240989685059%

ADMET: Metabolism

CYP1A2-inhibitor:	0.017
CYP1A2-substrate:	0.067
CYP2C19-inhibitor:	0.054
CYP2C19-substrate:	0.057
CYP2C9-inhibitor:	0.005
CYP2C9-substrate:	0.017
CYP2D6-inhibitor:	0.775
CYP2D6-substrate:	0.186
CYP3A4-inhibitor:	0.092
CYP3A4-substrate:	0.352

ADMET: Excretion

Clearance (CL):	9.526
Half-life (T1/2):	0.853

ADMET: Toxicity

hERG Blockers:	0.09
Human Hepatotoxicity (H-HT):	0.875
Drug-inuced Liver Injury (DILI):	0.36
AMES Toxicity:	0.004
Rat Oral Acute Toxicity:	0.366
Maximum Recommended Daily Dose:	0.932
Skin Sensitization:	0.216
Carcinogencity:	0.027
Eye Corrosion:	0.003
Eye Irritation:	0.019
Respiratory Toxicity:	0.532

Download Data

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

Natural Product: NPC88193

Natural Product ID:	NPC88193
*Common Name:**	SEUKOEKHOYPBJF-VJHGBBPISA-O
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SEUKOEKHOYPBJF-VJHGBBPISA-O
Standard InCHI:	InChI=1S/C29H36N4O2/c34-28-23-27(26-13-5-2-6-14-26)33-22-10-19-31(24-33)18-7-8-20-32(21-9-17-30-28)29(35)16-15-25-11-3-1-4-12-25/h1-6,11-16,24,27H,7-10,17-23H2/p+1/b16-15-/t27-/m0/s1
SMILES:	c1ccc(cc1)/C=CC(=O)N1CCCC[N+]2=CN(CCC2)[C@@H](CC(=NCCC1)O)c1ccccc1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101702772
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000476] Cinnamic 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
NPO11944	Incarvillea sinensis	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10514316]
NPO9878	Dichapetalum gelonioides	Species	Dichapetalaceae	Eukaryota	stem bark	Philippines	n.a.	PMID[16562829]
NPO12054	Holostylis reniformis	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17438049]
NPO12054	Holostylis reniformis	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20961092]
NPO915	Xylaria polymorpha	Species	Xylariaceae	Eukaryota	n.a.	fruit body	n.a.	PMID[21942847]
NPO9878	Dichapetalum gelonioides	Species	Dichapetalaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24597894]
NPO20351	Emericella variecolor	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26394166]
NPO2349	Picrasma excelsa	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11944	Incarvillea sinensis	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7492	Mucuna birdwoodiana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11308	Rohdea japonica	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12054	Holostylis reniformis	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7109	Eugenia edulis	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20351	Emericella variecolor	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11944	Incarvillea sinensis	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2349	Picrasma excelsa	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11308	Rohdea japonica	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7492	Mucuna birdwoodiana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2349	Picrasma excelsa	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7109	Eugenia edulis	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11139	Godmania aesculifolia	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4988	Lavandula stoechas	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9878	Dichapetalum gelonioides	Species	Dichapetalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6900	Koenigia divaricata	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6055	Enkianthus cernuus	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5294	Stemona ovata	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12054	Holostylis reniformis	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8150	Calibrachoa parviflora	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5715	Hyalodendriella betulae	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20351	Emericella variecolor	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2349	Picrasma excelsa	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11470	Sorghum caudatum	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12281	Aleurodiscus amorphus	Species	Stereaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7492	Mucuna birdwoodiana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11308	Rohdea japonica	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4845	Arachniodes standishii	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3700	Frasera speciosa	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12165	Comanthosphace japonica	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11944	Incarvillea sinensis	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO622	Stictina crocata	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO11829	Acacia ehrenbergiana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO915	Xylaria polymorpha	Species	Xylariaceae	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 NPC88193 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	202
0.1-0.2	2014
0.2-0.3	11695
0.3-0.4	17234
0.4-0.5	9200
0.5-0.6	1955
0.6-0.7	373
0.7-0.8	24
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 NPC88193 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	137
0.1-0.2	452
0.2-0.3	928
0.3-0.4	1478
0.4-0.5	3938
0.5-0.6	1919
0.6-0.7	288
0.7-0.8	10
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