NPASS Compound

Structure

NPC274606 OpenBabel06302215392D 26 27 0 0 0 0 0 0 0 0999 V2000 5.6418 -2.3013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6637 -2.0934 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9945 -2.8366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0000 -2.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5000 -1.8660 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 -1.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0000 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5933 -3.6456 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.3364 -4.3147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2319 -5.3092 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.2024 -3.8147 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 5.9508 -3.2524 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9290 -3.4603 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 7.2380 -4.4114 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5689 -5.1545 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.2161 -4.6193 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.9593 -3.9502 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.8253 -4.4502 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.6174 -5.4283 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.2865 -6.1714 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 8.6229 -5.5328 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 10.7388 -4.0434 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 16 1 0 0 0 0 2 3 2 0 0 0 0 3 15 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 3 0 0 0 4 12 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 2 0 0 0 0 8 10 2 0 0 0 0 8 11 1 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 13 15 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 18 20 1 0 0 0 0 20 25 1 0 0 0 0 20 21 2 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 22 26 1 0 0 0 0 23 24 1 0 0 0 0 23 25 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	509.93
Volume:	358.69
LogP:	-1.066
LogD:	0.815
LogS:	-1.644
# Rotatable Bonds:	9
TPSA:	167.05
# H-Bond Aceptor:	10
# H-Bond Donor:	6
# Rings:	2
# Heavy Atoms:	13

MedChem Properties

QED Drug-Likeness Score:	0.18
Synthetic Accessibility Score:	3.906
Fsp3:	0.308
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.74
MDCK Permeability:	2.4832828785292804e-05
Pgp-inhibitor:	0.033
Pgp-substrate:	0.088
Human Intestinal Absorption (HIA):	0.988
20% Bioavailability (F20%):	0.981
30% Bioavailability (F30%):	0.991

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.251
Plasma Protein Binding (PPB):	75.53962707519531%
Volume Distribution (VD):	0.576
Pgp-substrate:	38.155208587646484%

ADMET: Metabolism

CYP1A2-inhibitor:	0.028
CYP1A2-substrate:	0.918
CYP2C19-inhibitor:	0.28
CYP2C19-substrate:	0.03
CYP2C9-inhibitor:	0.023
CYP2C9-substrate:	0.007
CYP2D6-inhibitor:	0.011
CYP2D6-substrate:	0.034
CYP3A4-inhibitor:	0.085
CYP3A4-substrate:	0.162

ADMET: Excretion

Clearance (CL):	2.808
Half-life (T1/2):	0.878

ADMET: Toxicity

hERG Blockers:	0.027
Human Hepatotoxicity (H-HT):	0.908
Drug-inuced Liver Injury (DILI):	0.681
AMES Toxicity:	0.326
Rat Oral Acute Toxicity:	0.83
Maximum Recommended Daily Dose:	0.246
Skin Sensitization:	0.201
Carcinogencity:	0.926
Eye Corrosion:	0.003
Eye Irritation:	0.042
Respiratory Toxicity:	0.982

Download Data

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

Natural Product: NPC274606

Natural Product ID:	NPC274606
*Common Name:**	RPPSGEYLUBPWMM-WAPJZHGLSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	RPPSGEYLUBPWMM-WAPJZHGLSA-N
Standard InCHI:	InChI=1S/C13H16Br2N6O4S/c14-7-6-9(19-10(7)15)12(22)18-3-1-2-8-11(21-13(16)20-8)17-4-5-26(23,24)25/h2,6,19H,1,3-5H2,(H,18,22)(H,23,24,25)(H3,16,17,20,21)/b8-2-
SMILES:	C(/C=C1/C(=NCCS(=O)(=O)O)NC(=N)N1)CNC(=O)c1cc(c(Br)[nH]1)Br
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10436427
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0001093] Carboxylic acid derivatives [CHEMONTID:0000475] Carboxylic acid amides [CHEMONTID:0004817] 2-heteroaryl carboxamides

*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
NPO27323	Cestrum nocturnum	Species	Solanaceae	Eukaryota	leaves	n.a.	n.a.	PMID[11170659]
NPO27012	Laurencia pannosa	Species	Rhodomelaceae	Eukaryota	n.a.	Malaysian	n.a.	PMID[11374951]
NPO27323	Cestrum nocturnum	Species	Solanaceae	Eukaryota	leaves	n.a.	n.a.	PMID[12502329]
NPO27072	Monochaetum vulcanicum	Species	Melastomataceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15165161]
NPO17223	Agelas oroides	Species	Agelasidae	Eukaryota	n.a.	n.a.	n.a.	PMID[32072810]
NPO27323	Cestrum nocturnum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27725	Artemisia vestita	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27323	Cestrum nocturnum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27725	Artemisia vestita	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27773	Rhododendron ovatum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27323	Cestrum nocturnum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO27725	Artemisia vestita	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO27323	Cestrum nocturnum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27773	Rhododendron ovatum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27262	Dryopteris inaequalis	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27191	Schistochila appendiculata	Species	Schistochilaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27740	Alcantara ekmaniana	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO27725	Artemisia vestita	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7497	Guatteria blepharophylla	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26895	Baccharis bigelovii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11140	Coprinopsis cinerea	Species	Psathyrellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27012	Laurencia pannosa	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22488	Leptosphaeria oraemaris	Species	Leptosphaeriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27569	Archangelica officinalis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27648	Cereus aethiops	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27688	Aeonium goochiae	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27707	Soja hispida	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20208	Rhinogobius brunneus	Species	Gobiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16500	Byssochlamys spectabilis	Species	Thermoascaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17223	Agelas oroides	Species	Agelasidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27072	Monochaetum vulcanicum	Species	Melastomataceae	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 NPC274606 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

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 NPC274606 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

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