Structure

Physi-Chem Properties

Molecular Weight:  373.24
Volume:  414.365
LogP:  5.084
LogD:  4.414
LogS:  -4.937
# Rotatable Bonds:  12
TPSA:  21.59
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.225
Synthetic Accessibility Score:  4.847
Fsp3:  0.609
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.639
MDCK Permeability:  1.9739873096114025e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.211
30% Bioavailability (F30%):  0.978

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.291
Plasma Protein Binding (PPB):  99.15986633300781%
Volume Distribution (VD):  2.215
Pgp-substrate:  0.9449504613876343%

ADMET: Metabolism

CYP1A2-inhibitor:  0.333
CYP1A2-substrate:  0.928
CYP2C19-inhibitor:  0.806
CYP2C19-substrate:  0.909
CYP2C9-inhibitor:  0.707
CYP2C9-substrate:  0.879
CYP2D6-inhibitor:  0.548
CYP2D6-substrate:  0.926
CYP3A4-inhibitor:  0.957
CYP3A4-substrate:  0.76

ADMET: Excretion

Clearance (CL):  4.018
Half-life (T1/2):  0.327

ADMET: Toxicity

hERG Blockers:  0.39
Human Hepatotoxicity (H-HT):  0.927
Drug-inuced Liver Injury (DILI):  0.476
AMES Toxicity:  0.882
Rat Oral Acute Toxicity:  0.032
Maximum Recommended Daily Dose:  0.955
Skin Sensitization:  0.95
Carcinogencity:  0.387
Eye Corrosion:  0.004
Eye Irritation:  0.046
Respiratory Toxicity:  0.587

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General Info & Identifiers & Properties  
Structure MOL file  
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  Natural Product: NPC311369

Natural Product ID:  NPC311369
Common Name*:   Curacin A
IUPAC Name:   (4R)-4-[(1Z,5E,7E,11R)-11-methoxy-8-methyltetradeca-1,5,7,13-tetraenyl]-2-[(1R,2S)-2-methylcyclopropyl]-4,5-dihydro-1,3-thiazole
Synonyms:   Curacin A
Standard InCHIKey:  LUEYTMPPCOCKBX-KWYHTCOPSA-N
Standard InCHI:  InChI=1S/C23H35NOS/c1-5-11-21(25-4)15-14-18(2)12-9-7-6-8-10-13-20-17-26-23(24-20)22-16-19(22)3/h5,7,9-10,12-13,19-22H,1,6,8,11,14-17H2,2-4H3/b9-7+,13-10-,18-12+/t19-,20+,21-,22+/m0/s1
SMILES:  C=CC[C@@H](CC/C(=C/C=C/CC/C=C[C@@H]1CSC(=N1)[C@@H]1C[C@@H]1C)/C)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL89138
PubChem CID:   5281967
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000004] Organosulfur compounds
      • [CHEMONTID:0001094] Imidothioesters
        • [CHEMONTID:0003885] Imidothiolactones

*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
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[10514329]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[10654420]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[10691708]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. palauan n.a. PMID[10691729]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[10843570]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[10924172]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[10978206]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11076571]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11076573]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11076574]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11277744]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11389621]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11430000]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11473443]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11922791]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[12762816]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. Papua New Guinea n.a. PMID[12828459]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[14575437]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[1517734]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. Papua New Guinea n.a. PMID[16643028]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[17125217]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[17441769]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[18444683]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. Singapore n.a. PMID[19093843]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[19489598]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. eastern Caribbean n.a. PMID[19739598]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[19839606]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[20030365]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. panamanian n.a. PMID[20158242]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. Floridian n.a. PMID[20166701]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[20936843]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[21138309]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[2128518]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[21341718]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[21539315]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[21806011]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[21999614]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[22035372]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[29792428]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[3924698]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. Caribbean n.a. PMID[7623050]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. Caribbean n.a. PMID[8699186]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[9584405]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[9599278]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[9599279]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[9784156]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae 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
NPT179 Cell Line A2780 Homo sapiens Inhibition = 94.0 % PMID[506664]
NPT179 Cell Line A2780 Homo sapiens Inhibition = 78.0 % PMID[506664]
NPT179 Cell Line A2780 Homo sapiens TPI = 98.0 % PMID[506664]
NPT83 Cell Line MCF7 Homo sapiens GI50 = 40.0 nM PMID[506664]
NPT306 Cell Line PC-3 Homo sapiens GI50 = 50.0 nM PMID[506664]
NPT82 Cell Line MDA-MB-231 Homo sapiens GI50 = 96.0 nM PMID[506664]
NPT1719 Cell Line 2008 Homo sapiens GI50 = 35.0 nM PMID[506664]
NPT1396 Cell Line NCI-H69 Homo sapiens IC50 = 0.89 ug.mL-1 PMID[506666]
NPT3377 Cell Line PC-9 IC50 = 19.6 ug.mL-1 PMID[506666]
NPT1183 Cell Line WiDr Homo sapiens IC50 < 0.2 ug.mL-1 PMID[506666]
NPT76 Cell Line C6 Rattus norvegicus LC50 = 11.0 nM PMID[506668]
NPT518 Protein Complex Tubulin Homo sapiens IC50 = 720.0 nM PMID[506664]
NPT781 Individual Protein Tubulin alpha chain Sus scrofa IC50 = 2500.0 nM PMID[506665]
NPT781 Individual Protein Tubulin alpha chain Sus scrofa IC50 = 2500.0 nM PMID[506666]
NPT2 Others Unspecified IC50 = 1400.0 nM PMID[506667]
NPT2 Others Unspecified Inhibition = 96.0 % PMID[506667]
NPT140 Organism Artemia Artemia LD50 = 8.0 nM PMID[506667]
NPT2 Others Unspecified EC50 = 510.0 nM PMID[506668]
NPT176 Organism Artemia salina Artemia salina LC50 = 0.0025 ug.mL-1 PMID[506669]
NPT782 Protein Family Tubulin Bos taurus IC50 = 900.0 nM PMID[506670]
NPT782 Protein Family Tubulin Bos taurus IC50 = 600.0 nM PMID[506670]
NPT782 Protein Family Tubulin Bos taurus IC50 = 780.0 nM PMID[506670]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. GI50 = 96.0 nM PMID[506670]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. GI50 = 50.0 nM PMID[506670]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. GI50 = 35.0 nM PMID[506670]
NPT782 Protein Family Tubulin Bos taurus Inhibition = 84.9 % PMID[506670]
NPT782 Protein Family Tubulin Bos taurus Inhibition = 96.2 % PMID[506670]
NPT782 Protein Family Tubulin Bos taurus Inhibition = 97.9 % PMID[506670]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. GI50 = 64.0 nM PMID[506670]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. GI50 = 48.0 nM PMID[506670]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. GI50 = 26.0 nM PMID[506670]
NPT782 Protein Family Tubulin Bos taurus Inhibition = 87.0 % PMID[506670]
NPT782 Protein Family Tubulin Bos taurus Inhibition = 78.0 % PMID[506670]
NPT782 Protein Family Tubulin Bos taurus Inhibition = 97.0 % PMID[506670]
NPT782 Protein Family Tubulin Bos taurus Inhibition = 99.0 % PMID[506670]
NPT782 Protein Family Tubulin Bos taurus IC50 = 520.0 nM PMID[506670]

☑ 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 NPC311369 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
0.6224 Remote Similarity NPC319473
0.6058 Remote Similarity NPC474873
0.6023 Remote Similarity NPC314678
0.6019 Remote Similarity NPC471636
0.6019 Remote Similarity NPC287572
0.6019 Remote Similarity NPC132931
0.5963 Remote Similarity NPC474891
0.5882 Remote Similarity NPC129995
0.5882 Remote Similarity NPC315141
0.5877 Remote Similarity NPC201968
0.5872 Remote Similarity NPC474969
0.5872 Remote Similarity NPC476034
0.5849 Remote Similarity NPC72401
0.5849 Remote Similarity NPC325339
0.5841 Remote Similarity NPC50694
0.5833 Remote Similarity NPC477199
0.5833 Remote Similarity NPC101106
0.5833 Remote Similarity NPC135216
0.5804 Remote Similarity NPC279383
0.5804 Remote Similarity NPC273215
0.5804 Remote Similarity NPC268327
0.5804 Remote Similarity NPC295444
0.5789 Remote Similarity NPC477554
0.578 Remote Similarity NPC250187
0.5765 Remote Similarity NPC477525
0.5758 Remote Similarity NPC316186
0.5752 Remote Similarity NPC475988
0.5739 Remote Similarity NPC477553
0.569 Remote Similarity NPC477555
0.5682 Remote Similarity NPC291196
0.5682 Remote Similarity NPC103712
0.5625 Remote Similarity NPC242930
0.5625 Remote Similarity NPC297020
0.5625 Remote Similarity NPC127578
0.561 Remote Similarity NPC321030
0.56 Remote Similarity NPC34754

  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 NPC311369 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
0.5833 Remote Similarity NPD4211 Phase 1

  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