Structure

Physi-Chem Properties

Molecular Weight:  275.09
Volume:  255.091
LogP:  1.452
LogD:  0.98
LogS:  -3.063
# Rotatable Bonds:  4
TPSA:  75.63
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.576
Synthetic Accessibility Score:  4.603
Fsp3:  0.833
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.163
MDCK Permeability:  4.6243785618571565e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.025
Human Intestinal Absorption (HIA):  0.034
20% Bioavailability (F20%):  0.093
30% Bioavailability (F30%):  0.923

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.993
Plasma Protein Binding (PPB):  62.02620315551758%
Volume Distribution (VD):  0.675
Pgp-substrate:  45.587684631347656%

ADMET: Metabolism

CYP1A2-inhibitor:  0.021
CYP1A2-substrate:  0.818
CYP2C19-inhibitor:  0.028
CYP2C19-substrate:  0.811
CYP2C9-inhibitor:  0.019
CYP2C9-substrate:  0.073
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.167
CYP3A4-inhibitor:  0.065
CYP3A4-substrate:  0.45

ADMET: Excretion

Clearance (CL):  8.496
Half-life (T1/2):  0.733

ADMET: Toxicity

hERG Blockers:  0.01
Human Hepatotoxicity (H-HT):  0.175
Drug-inuced Liver Injury (DILI):  0.042
AMES Toxicity:  0.141
Rat Oral Acute Toxicity:  0.926
Maximum Recommended Daily Dose:  0.216
Skin Sensitization:  0.319
Carcinogencity:  0.959
Eye Corrosion:  0.012
Eye Irritation:  0.015
Respiratory Toxicity:  0.535

Download Data

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

  Natural Product: NPC226513

Natural Product ID:  NPC226513
Common Name*:   Antiprotealide
IUPAC Name:   (1S,2R,5R)-2-(2-chloroethyl)-5-[(1S)-1-hydroxy-2-methylpropyl]-1-methyl-7-oxa-4-azabicyclo[3.2.0]heptane-3,6-dione
Synonyms:   Antiprotealide
Standard InCHIKey:  ISOLNHGTJDCQNQ-OSTYVCCYSA-N
Standard InCHI:  InChI=1S/C12H18ClNO4/c1-6(2)8(15)12-10(17)18-11(12,3)7(4-5-13)9(16)14-12/h6-8,15H,4-5H2,1-3H3,(H,14,16)/t7-,8-,11-,12-/m0/s1
SMILES:  CC(C)[C@@H]([C@]12C(=O)O[C@@]1(C)[C@@H](CCCl)C(=N2)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL561240
PubChem CID:   11173422
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
NPO4320 Salinispora tropica Species Micromonosporaceae Bacteria n.a. n.a. n.a. PMID[12548698]
NPO4320 Salinispora tropica Species Micromonosporaceae Bacteria n.a. n.a. n.a. PMID[15916417]
NPO4320 Salinispora tropica Species Micromonosporaceae Bacteria n.a. n.a. n.a. PMID[17243724]
NPO4320 Salinispora tropica Species Micromonosporaceae Bacteria n.a. n.a. n.a. PMID[19133779]
NPO4320 Salinispora tropica Species Micromonosporaceae Bacteria 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
NPT389 Cell Line RPMI-8226 Homo sapiens IC50 = 220.0 nM PMID[517974]
NPT389 Cell Line RPMI-8226 Homo sapiens IC50 = 283.0 nM PMID[517975]
NPT393 Cell Line HCT-116 Homo sapiens IC50 = 777.0 nM PMID[517976]
NPT2 Others Unspecified IC50 = 27.0 nM PMID[517974]
NPT2 Others Unspecified IC50 = 31.0 nM PMID[517975]
NPT2 Others Unspecified IC50 = 211.0 nM PMID[517974]
NPT2 Others Unspecified IC50 = 262.0 nM PMID[517975]
NPT2 Others Unspecified IC50 > 10000.0 nM PMID[517974]
NPT2 Others Unspecified IC50 > 20000.0 nM PMID[517975]
NPT2 Others Unspecified IC50 = 101.0 nM PMID[517976]

☑ 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 NPC226513 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
0.8431 Intermediate Similarity NPC12270
0.767 Intermediate Similarity NPC14537
0.7596 Intermediate Similarity NPC473252
0.7184 Intermediate Similarity NPC234542
0.7157 Intermediate Similarity NPC123141
0.7115 Intermediate Similarity NPC473224
0.7053 Intermediate Similarity NPC47135
0.697 Remote Similarity NPC193386
0.6496 Remote Similarity NPC201968
0.6458 Remote Similarity NPC473984
0.6452 Remote Similarity NPC43219
0.6429 Remote Similarity NPC42590
0.6408 Remote Similarity NPC477729
0.64 Remote Similarity NPC227051
0.6389 Remote Similarity NPC474952
0.6383 Remote Similarity NPC86064
0.6354 Remote Similarity NPC316242
0.6325 Remote Similarity NPC50694
0.63 Remote Similarity NPC145748
0.63 Remote Similarity NPC95478
0.63 Remote Similarity NPC155670
0.6289 Remote Similarity NPC478017
0.6289 Remote Similarity NPC315131
0.6289 Remote Similarity NPC315535
0.6129 Remote Similarity NPC477642
0.6129 Remote Similarity NPC478256
0.6122 Remote Similarity NPC200085
0.6122 Remote Similarity NPC51695
0.6122 Remote Similarity NPC253703
0.6122 Remote Similarity NPC314858
0.6121 Remote Similarity NPC92829
0.6117 Remote Similarity NPC477728
0.6106 Remote Similarity NPC259476
0.6082 Remote Similarity NPC472594
0.6022 Remote Similarity NPC475808
0.6022 Remote Similarity NPC474299
0.6022 Remote Similarity NPC473985
0.6022 Remote Similarity NPC28348
0.6022 Remote Similarity NPC474298
0.6 Remote Similarity NPC477641
0.6 Remote Similarity NPC320865
0.6 Remote Similarity NPC477643
0.5966 Remote Similarity NPC122404
0.5948 Remote Similarity NPC168733
0.5917 Remote Similarity NPC24462
0.5882 Remote Similarity NPC477730
0.5876 Remote Similarity NPC472595
0.5833 Remote Similarity NPC208537
0.5833 Remote Similarity NPC270005
0.575 Remote Similarity NPC7797
0.5678 Remote Similarity NPC70235
0.5673 Remote Similarity NPC320936
0.567 Remote Similarity NPC474403
0.5664 Remote Similarity NPC220234
0.5641 Remote Similarity NPC475637
0.563 Remote Similarity NPC474725
0.5625 Remote Similarity NPC476291
0.5625 Remote Similarity NPC476285
0.5603 Remote Similarity NPC215988
0.56 Remote Similarity NPC474020

  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 NPC226513 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
0.8431 Intermediate Similarity NPD1719 Phase 1
0.7053 Intermediate Similarity NPD7345 Approved
0.6598 Remote Similarity NPD1448 Clinical (unspecified phase)
0.6289 Remote Similarity NPD7918 Clinical (unspecified phase)
0.6289 Remote Similarity NPD7917 Clinical (unspecified phase)
0.605 Remote Similarity NPD7916 Approved
0.605 Remote Similarity NPD7915 Approved
0.6 Remote Similarity NPD4264 Clinical (unspecified phase)
0.6 Remote Similarity NPD2256 Clinical (unspecified phase)
0.5872 Remote Similarity NPD8394 Approved
0.5714 Remote Similarity NPD619 Phase 3
0.563 Remote Similarity NPD8306 Approved
0.563 Remote Similarity NPD8305 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