NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	133.02
Volume:	119.554
LogP:	0.896
LogD:	0.492
LogS:	-1.358
# Rotatable Bonds:	3
TPSA:	49.66
# H-Bond Aceptor:	3
# H-Bond Donor:	1
# Rings:	0
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.344
Synthetic Accessibility Score:	3.615
Fsp3:	0.5
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.711
MDCK Permeability:	1.2593910469149705e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.006
Human Intestinal Absorption (HIA):	0.072
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.49

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.998
Plasma Protein Binding (PPB):	51.67668914794922%
Volume Distribution (VD):	0.635
Pgp-substrate:	59.459228515625%

ADMET: Metabolism

CYP1A2-inhibitor:	0.239
CYP1A2-substrate:	0.348
CYP2C19-inhibitor:	0.129
CYP2C19-substrate:	0.064
CYP2C9-inhibitor:	0.012
CYP2C9-substrate:	0.181
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.165
CYP3A4-inhibitor:	0.035
CYP3A4-substrate:	0.153

ADMET: Excretion

Clearance (CL):	4.88
Half-life (T1/2):	0.84

ADMET: Toxicity

hERG Blockers:	0.031
Human Hepatotoxicity (H-HT):	0.114
Drug-inuced Liver Injury (DILI):	0.481
AMES Toxicity:	0.777
Rat Oral Acute Toxicity:	0.96
Maximum Recommended Daily Dose:	0.023
Skin Sensitization:	0.85
Carcinogencity:	0.898
Eye Corrosion:	0.971
Eye Irritation:	0.987
Respiratory Toxicity:	0.954

Download Data

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

Natural Product: NPC235432

Natural Product ID:	NPC235432
*Common Name:**	3-Methylsulfanyl-2-Oxo-Propionaldehyde Oxime
IUPAC Name:	(1E)-1-hydroxyimino-3-methylsulfanylpropan-2-one
Synonyms:
Standard InCHIKey:	UJQBJDWFMFBDLF-GORDUTHDSA-N
Standard InCHI:	InChI=1S/C4H7NO2S/c1-8-3-4(6)2-5-7/h2,7H,3H2,1H3/b5-2+
SMILES:	CSCC(=O)/C=N/O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL167567
PubChem CID:	44377758
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004707] Organic nitrogen compounds [CHEMONTID:0000278] Organonitrogen compounds [CHEMONTID:0000411] Oximes [CHEMONTID:0003078] Aldoximes

*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
NPO11045	Paederia scandens	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11045	Paederia scandens	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11045	Paederia scandens	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11045	Paederia scandens	Species	Rubiaceae	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

Activity Type	# Activity
LD50	1
Others	12

Activity Type	# Activity
NON-MOLECULAR	1
Organism	2
Others	10

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT35	Others	n.a.		pKa	=	8.16	n.a.	PMID[454393]
NPT938	Organism	Cavia porcellus	Cavia porcellus	pKb	>	13.0	n.a.	PMID[454393]
NPT35	Others	n.a.		LogD	=	8.16	n.a.	PMID[454393]
NPT27	Others	Unspecified		K1	=	24.5	M-1 s-1	PMID[454393]
NPT27	Others	Unspecified		K2	=	192.7	M-1 min-1	PMID[454393]
NPT27	Others	Unspecified		K eff	=	79.2	M-1 min-1	PMID[454393]
NPT27	Others	Unspecified		K2	=	160.0	M-1 min-1	PMID[454393]
NPT27	Others	Unspecified		K eff	=	66.0	M-1 min-1	PMID[454393]
NPT27	Others	Unspecified		K2	=	162.1	M-1 min-1	PMID[454393]
NPT27	Others	Unspecified		K eff	=	66.6	M-1 min-1	PMID[454393]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	LD50	>	1000.0	mg.kg-1	PMID[454393]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Sign free dose	=	50.0	mg kg-1	PMID[454393]
NPT27	Others	Unspecified		Protective index	=	8.4	n.a.	PMID[454393]

☑ 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 NPC235432 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	12365
0.1-0.2	27547
0.2-0.3	2294
0.3-0.4	423
0.4-0.5	49
0.5-0.6	17
0.6-0.7	1
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.6098	Remote Similarity	NPC60250

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 NPC235432 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	891
0.1-0.2	7115
0.2-0.3	857
0.3-0.4	247
0.4-0.5	28
0.5-0.6	12
0.6-0.7	0
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
0.5714	Remote Similarity	NPD8869	Approved

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