Structure

Physi-Chem Properties

Molecular Weight:  328.07
Volume:  296.353
LogP:  -0.29
LogD:  -0.589
LogS:  -1.329
# Rotatable Bonds:  7
TPSA:  124.01
# H-Bond Aceptor:  8
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.586
Synthetic Accessibility Score:  3.235
Fsp3:  0.538
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.187
MDCK Permeability:  9.53047447183053e-07
Pgp-inhibitor:  0.0
Pgp-substrate:  0.93
Human Intestinal Absorption (HIA):  0.598
20% Bioavailability (F20%):  0.095
30% Bioavailability (F30%):  0.676

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.042
Plasma Protein Binding (PPB):  41.42298126220703%
Volume Distribution (VD):  0.214
Pgp-substrate:  61.34534454345703%

ADMET: Metabolism

CYP1A2-inhibitor:  0.003
CYP1A2-substrate:  0.041
CYP2C19-inhibitor:  0.031
CYP2C19-substrate:  0.042
CYP2C9-inhibitor:  0.021
CYP2C9-substrate:  0.856
CYP2D6-inhibitor:  0.068
CYP2D6-substrate:  0.107
CYP3A4-inhibitor:  0.013
CYP3A4-substrate:  0.028

ADMET: Excretion

Clearance (CL):  2.344
Half-life (T1/2):  0.964

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.147
Drug-inuced Liver Injury (DILI):  0.974
AMES Toxicity:  0.006
Rat Oral Acute Toxicity:  0.01
Maximum Recommended Daily Dose:  0.004
Skin Sensitization:  0.67
Carcinogencity:  0.031
Eye Corrosion:  0.003
Eye Irritation:  0.016
Respiratory Toxicity:  0.012

Download Data

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

  Natural Product: NPC144780

Natural Product ID:  NPC144780
Common Name*:   (6R,7R)-7-(4-Carboxybutanoylamino)-3-Methyl-8-Oxo-5-Thia-1-Azabicyclo[4.2.0]Oct-2-Ene-2-Carboxylic Acid
IUPAC Name:   (6R,7R)-7-(4-carboxybutanoylamino)-3-methyl-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid
Synonyms:  
Standard InCHIKey:  KFAZOAVBYQAACA-BXKDBHETSA-N
Standard InCHI:  InChI=1S/C13H16N2O6S/c1-6-5-22-12-9(11(19)15(12)10(6)13(20)21)14-7(16)3-2-4-8(17)18/h9,12H,2-5H2,1H3,(H,14,16)(H,17,18)(H,20,21)/t9-,12-/m1/s1
SMILES:  OC(=N[C@@H]1C(=O)N2[C@@H]1SCC(=C2C(=O)O)C)CCCC(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1426785
PubChem CID:   6351451
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000160] Lactams
        • [CHEMONTID:0000162] Beta lactams
          • [CHEMONTID:0000168] Cephems
            • [CHEMONTID:0000173] Cephalosporins

*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
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. root n.a. PMID[10364842]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. root n.a. PMID[12392098]
NPO16914 Abacopteris penangiana n.a. n.a. n.a. n.a. rhizome n.a. PMID[16499328]
NPO16914 Abacopteris penangiana n.a. n.a. n.a. Rhizomes n.a. n.a. PMID[16499328]
NPO16914 Abacopteris penangiana n.a. n.a. n.a. aerial parts Jiangxi Province, China 2004-JUN PMID[17922550]
NPO21717 Acremonium chrysogenum Species n.a. Eukaryota n.a. n.a. n.a. PMID[23089729]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23501116]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[24996657]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. root n.a. PMID[25767328]
NPO1816 Pterogorgia citrina Species Gorgoniidae Eukaryota n.a. Caribbean n.a. PMID[7911157]
NPO12178 Pinellia pedatisecta Species Araceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17598 Maytenus mossambicensis Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12178 Pinellia pedatisecta Species Araceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12178 Pinellia pedatisecta Species Araceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12400 Cereus gummosus Species Sagartiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14792 Abies grandis Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16689 Corydalis clavicula Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21717 Acremonium chrysogenum Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10736 Teucrium kotschyanum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17137 Nymania capensis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16208 Viguiera pinnatiloba Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1816 Pterogorgia citrina Species Gorgoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16914 Abacopteris penangiana n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO814 Acipenser sturio Species Acipenseridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22249 Senecio leptolobus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3210 Polyporus arcularius Species Polyporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO309 Phyla canescens Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21752.1 Bauhinia forficata subsp. pruinosa Subspecies Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16559 Darwinia grandiflora Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15728 Prunus nipponica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17598 Maytenus mossambicensis Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12178 Pinellia pedatisecta Species Araceae 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
NPT53 Individual Protein 4'-phosphopantetheinyl transferase ffp Bacillus subtilis Potency = 5011.9 nM PMID[463440]
NPT135 Individual Protein Chromobox protein homolog 1 Homo sapiens Potency n.a. 11220.2 nM PMID[463440]
NPT3937 Protein-Protein Interaction Voltage-gated N-type calcium channel alpha-1B subunit/Amyloid beta A4 precursor protein-binding family A member 1 Homo sapiens IC50 = 34000.0 nM PMID[463440]
NPT3937 Protein-Protein Interaction Voltage-gated N-type calcium channel alpha-1B subunit/Amyloid beta A4 precursor protein-binding family A member 1 Homo sapiens IC50 > 50000.0 nM PMID[463440]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 5221.3 nM PMID[463440]

☑ 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 NPC144780 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
0.8056 Intermediate Similarity NPC288109
0.7019 Intermediate Similarity NPC117829
0.6466 Remote Similarity NPC59249
0.619 Remote Similarity NPC473495
0.6028 Remote Similarity NPC13470
0.5769 Remote Similarity NPC284456
0.5769 Remote Similarity NPC53858
0.5769 Remote Similarity NPC84128
0.5769 Remote Similarity NPC184473
0.5769 Remote Similarity NPC6902
0.5758 Remote Similarity NPC256312
0.5758 Remote Similarity NPC209156
0.5758 Remote Similarity NPC161774
0.5758 Remote Similarity NPC266888
0.5743 Remote Similarity NPC59867
0.5714 Remote Similarity NPC214532
0.5714 Remote Similarity NPC76297
0.5714 Remote Similarity NPC313265
0.5714 Remote Similarity NPC196007
0.5688 Remote Similarity NPC155230
0.5631 Remote Similarity NPC312315
0.56 Remote Similarity NPC477862

  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 NPC144780 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
0.8265 Intermediate Similarity NPD982 Approved
0.7944 Intermediate Similarity NPD2090 Approved
0.7589 Intermediate Similarity NPD2099 Approved
0.7321 Intermediate Similarity NPD2100 Approved
0.7 Intermediate Similarity NPD2147 Approved
0.6875 Remote Similarity NPD9578 Clinical (unspecified phase)
0.6807 Remote Similarity NPD1665 Approved
0.6792 Remote Similarity NPD1784 Approved
0.6752 Remote Similarity NPD1604 Approved
0.6752 Remote Similarity NPD1605 Approved
0.6695 Remote Similarity NPD1263 Approved
0.6694 Remote Similarity NPD2025 Approved
0.6694 Remote Similarity NPD2065 Discontinued
0.6667 Remote Similarity NPD985 Approved
0.664 Remote Similarity NPD4616 Suspended
0.6612 Remote Similarity NPD2023 Approved
0.6612 Remote Similarity NPD3572 Approved
0.6612 Remote Similarity NPD3571 Approved
0.66 Remote Similarity NPD9577 Approved
0.6581 Remote Similarity NPD984 Approved
0.6532 Remote Similarity NPD2153 Approved
0.6532 Remote Similarity NPD4073 Discontinued
0.6529 Remote Similarity NPD1667 Approved
0.6529 Remote Similarity NPD1666 Approved
0.6446 Remote Similarity NPD2024 Approved
0.64 Remote Similarity NPD4088 Approved
0.6385 Remote Similarity NPD5234 Approved
0.6381 Remote Similarity NPD1782 Approved
0.6341 Remote Similarity NPD1748 Approved
0.6328 Remote Similarity NPD2858 Approved
0.632 Remote Similarity NPD1959 Approved
0.6316 Remote Similarity NPD777 Phase 3
0.6311 Remote Similarity NPD2645 Approved
0.6279 Remote Similarity NPD5664 Approved
0.625 Remote Similarity NPD2857 Approved
0.6224 Remote Similarity NPD9389 Approved
0.621 Remote Similarity NPD1806 Approved
0.619 Remote Similarity NPD967 Approved
0.619 Remote Similarity NPD2148 Clinical (unspecified phase)
0.6183 Remote Similarity NPD4444 Discontinued
0.6183 Remote Similarity NPD3544 Discontinued
0.6183 Remote Similarity NPD2419 Approved
0.6179 Remote Similarity NPD805 Approved
0.6179 Remote Similarity NPD806 Approved
0.6165 Remote Similarity NPD3045 Approved
0.6165 Remote Similarity NPD3044 Approved
0.6154 Remote Similarity NPD4653 Approved
0.6148 Remote Similarity NPD1773 Discontinued
0.6136 Remote Similarity NPD3285 Discontinued
0.6124 Remote Similarity NPD1278 Approved
0.6124 Remote Similarity NPD1277 Approved
0.6107 Remote Similarity NPD2418 Approved
0.6098 Remote Similarity NPD3159 Discontinued
0.609 Remote Similarity NPD3970 Phase 3
0.6071 Remote Similarity NPD1979 Approved
0.6045 Remote Similarity NPD5767 Discontinued
0.6028 Remote Similarity NPD2016 Approved
0.6028 Remote Similarity NPD2013 Approved
0.6028 Remote Similarity NPD2014 Approved
0.6 Remote Similarity NPD778 Phase 2
0.6 Remote Similarity NPD2027 Approved
0.6 Remote Similarity NPD20 Approved
0.5963 Remote Similarity NPD161 Discontinued
0.594 Remote Similarity NPD3969 Clinical (unspecified phase)
0.5929 Remote Similarity NPD1978 Approved
0.5926 Remote Similarity NPD6000 Clinical (unspecified phase)
0.5918 Remote Similarity NPD9387 Approved
0.5918 Remote Similarity NPD9388 Approved
0.5876 Remote Similarity NPD2262 Clinical (unspecified phase)
0.5818 Remote Similarity NPD1749 Approved
0.5814 Remote Similarity NPD3677 Clinical (unspecified phase)
0.5804 Remote Similarity NPD1581 Approved
0.5804 Remote Similarity NPD1582 Approved
0.5782 Remote Similarity NPD2891 Approved
0.5766 Remote Similarity NPD2252 Approved
0.5766 Remote Similarity NPD2251 Approved
0.5746 Remote Similarity NPD2048 Approved
0.5746 Remote Similarity NPD2044 Approved
0.5746 Remote Similarity NPD2047 Approved
0.5746 Remote Similarity NPD2043 Approved
0.5746 Remote Similarity NPD2046 Approved
0.5746 Remote Similarity NPD2045 Approved
0.5746 Remote Similarity NPD2051 Approved
0.5746 Remote Similarity NPD21 Approved
0.5746 Remote Similarity NPD2050 Clinical (unspecified phase)
0.5746 Remote Similarity NPD2049 Clinical (unspecified phase)
0.5714 Remote Similarity NPD2495 Phase 3
0.5693 Remote Similarity NPD1676 Phase 3
0.5676 Remote Similarity NPD2020 Approved
0.5667 Remote Similarity NPD3649 Discontinued
0.5652 Remote Similarity NPD4798 Approved
0.5652 Remote Similarity NPD4797 Approved
0.5619 Remote Similarity NPD1125 Discovery
0.5608 Remote Similarity NPD2018 Approved
0.5608 Remote Similarity NPD2019 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