Structure

Physi-Chem Properties

Molecular Weight:  400.3
Volume:  454.328
LogP:  7.501
LogD:  5.599
LogS:  -4.693
# Rotatable Bonds:  10
TPSA:  42.6
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.406
Synthetic Accessibility Score:  3.544
Fsp3:  0.615
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.94
MDCK Permeability:  2.0307403246988542e-05
Pgp-inhibitor:  0.731
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.625
30% Bioavailability (F30%):  0.106

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.124
Plasma Protein Binding (PPB):  93.68558502197266%
Volume Distribution (VD):  3.84
Pgp-substrate:  1.2208272218704224%

ADMET: Metabolism

CYP1A2-inhibitor:  0.258
CYP1A2-substrate:  0.442
CYP2C19-inhibitor:  0.329
CYP2C19-substrate:  0.451
CYP2C9-inhibitor:  0.334
CYP2C9-substrate:  0.98
CYP2D6-inhibitor:  0.642
CYP2D6-substrate:  0.896
CYP3A4-inhibitor:  0.711
CYP3A4-substrate:  0.139

ADMET: Excretion

Clearance (CL):  4.898
Half-life (T1/2):  0.121

ADMET: Toxicity

hERG Blockers:  0.003
Human Hepatotoxicity (H-HT):  0.174
Drug-inuced Liver Injury (DILI):  0.05
AMES Toxicity:  0.001
Rat Oral Acute Toxicity:  0.006
Maximum Recommended Daily Dose:  0.714
Skin Sensitization:  0.951
Carcinogencity:  0.032
Eye Corrosion:  0.006
Eye Irritation:  0.135
Respiratory Toxicity:  0.103

Download Data

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

  Natural Product: NPC476489

Natural Product ID:  NPC476489
Common Name*:   2-Methoxy-3-[(3E,7E)-4,8-dimethyl-10-(2,6,6-trimethyl-1-cyclohexenyl)-3,7-decadienyl]furan-5(2H)-one
IUPAC Name:   3-[(3E,7E)-4,8-dimethyl-10-(2,6,6-trimethylcyclohexen-1-yl)deca-3,7-dienyl]-2-methoxy-2H-furan-5-one
Synonyms:   25-O-Methylluffariellolide
Standard InCHIKey:  PFOVLLSEYCTGAF-PFTXGBMHSA-N
Standard InCHI:  InChI=1S/C26H40O3/c1-19(12-8-14-22-18-24(27)29-25(22)28-6)10-7-11-20(2)15-16-23-21(3)13-9-17-26(23,4)5/h11-12,18,25H,7-10,13-17H2,1-6H3/b19-12+,20-11+
SMILES:  CC1=C(C(CCC1)(C)C)CC/C(=C/CC/C(=C/CCC2=CC(=O)OC2OC)/C)/C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   21573065
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001283] Terpene lactones
          • [CHEMONTID:0001538] Diterpene lactones

*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
NPO32957 Acanthodendrilla sp. Species Dictyodendrillidae Eukaryota n.a. n.a. n.a. PMID[14510593]
NPO32957 Acanthodendrilla sp. Species Dictyodendrillidae Eukaryota n.a. Indonesia n.a. PMID[15568767]
NPO32957 Acanthodendrilla sp. Species Dictyodendrillidae Eukaryota n.a. n.a. n.a. PMID[18257533]
NPO32957 Acanthodendrilla sp. Species Dictyodendrillidae Eukaryota n.a. n.a. n.a. PMID[9834155]

☑ 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
NPT1864 Cell Line L5178Y Mus musculus ED50 = 0.7 ug/ml PMID[15568767]
NPT79 Organism Bacillus subtilis Bacillus subtilis IZ = 7 mm PMID[15568767]
NPT20 Organism Candida albicans Candida albicans IZ = 9 mm PMID[15568767]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus IZ = 10 mm PMID[15568767]
NPT79 Organism Bacillus subtilis Bacillus subtilis IZ = 9 mm PMID[15568767]
NPT1780 Organism Davidiella tassiana Davidiella tassiana IZ = 15 mm PMID[15568767]

☑ 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 NPC476489 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
1.0 High Similarity NPC476490
0.9167 High Similarity NPC473756
0.8732 High Similarity NPC257618
0.8701 High Similarity NPC472440
0.8611 High Similarity NPC16349
0.8611 High Similarity NPC222244
0.8571 High Similarity NPC323251
0.8571 High Similarity NPC324170
0.8571 High Similarity NPC471298
0.8481 Intermediate Similarity NPC472442
0.8481 Intermediate Similarity NPC163606
0.8462 Intermediate Similarity NPC471297
0.8354 Intermediate Similarity NPC126518
0.8354 Intermediate Similarity NPC471301
0.8267 Intermediate Similarity NPC27205
0.825 Intermediate Similarity NPC471300
0.825 Intermediate Similarity NPC474860
0.8158 Intermediate Similarity NPC262747
0.8125 Intermediate Similarity NPC471302
0.8052 Intermediate Similarity NPC209135
0.8052 Intermediate Similarity NPC474816
0.8025 Intermediate Similarity NPC42586
0.8025 Intermediate Similarity NPC473251
0.8 Intermediate Similarity NPC469
0.8 Intermediate Similarity NPC226066
0.7949 Intermediate Similarity NPC471299
0.7917 Intermediate Similarity NPC472266
0.7875 Intermediate Similarity NPC471296
0.7821 Intermediate Similarity NPC471220
0.7778 Intermediate Similarity NPC30502
0.775 Intermediate Similarity NPC475944
0.7746 Intermediate Similarity NPC329698
0.7738 Intermediate Similarity NPC474629
0.7711 Intermediate Similarity NPC211892
0.7711 Intermediate Similarity NPC118266
0.7683 Intermediate Similarity NPC470800
0.7683 Intermediate Similarity NPC71626
0.7674 Intermediate Similarity NPC477122
0.7654 Intermediate Similarity NPC471218
0.7647 Intermediate Similarity NPC470734
0.76 Intermediate Similarity NPC469660
0.759 Intermediate Similarity NPC329630
0.7568 Intermediate Similarity NPC276290
0.7561 Intermediate Similarity NPC474193
0.7561 Intermediate Similarity NPC12283
0.7561 Intermediate Similarity NPC477124
0.7561 Intermediate Similarity NPC474809
0.7534 Intermediate Similarity NPC185587
0.7529 Intermediate Similarity NPC472378
0.7529 Intermediate Similarity NPC196407
0.7529 Intermediate Similarity NPC472810
0.7529 Intermediate Similarity NPC472809
0.75 Intermediate Similarity NPC298973
0.75 Intermediate Similarity NPC96663
0.75 Intermediate Similarity NPC477722
0.75 Intermediate Similarity NPC104925
0.7471 Intermediate Similarity NPC65513
0.747 Intermediate Similarity NPC31086
0.747 Intermediate Similarity NPC474865
0.7442 Intermediate Similarity NPC251528
0.7442 Intermediate Similarity NPC293044
0.7436 Intermediate Similarity NPC228978
0.7412 Intermediate Similarity NPC475678
0.7407 Intermediate Similarity NPC268827
0.7381 Intermediate Similarity NPC217394
0.7375 Intermediate Similarity NPC184737
0.7368 Intermediate Similarity NPC64234
0.7368 Intermediate Similarity NPC37929
0.7356 Intermediate Similarity NPC477782
0.7349 Intermediate Similarity NPC42476
0.7349 Intermediate Similarity NPC193198
0.7342 Intermediate Similarity NPC4509
0.7333 Intermediate Similarity NPC325960
0.7333 Intermediate Similarity NPC319692
0.7303 Intermediate Similarity NPC469697
0.7303 Intermediate Similarity NPC324078
0.7297 Intermediate Similarity NPC116013
0.7284 Intermediate Similarity NPC170561
0.7273 Intermediate Similarity NPC141831
0.7273 Intermediate Similarity NPC181587
0.7273 Intermediate Similarity NPC472811
0.7273 Intermediate Similarity NPC477783
0.7262 Intermediate Similarity NPC96055
0.7262 Intermediate Similarity NPC318515
0.726 Intermediate Similarity NPC34883
0.7253 Intermediate Similarity NPC257726
0.7253 Intermediate Similarity NPC204054
0.725 Intermediate Similarity NPC54996
0.725 Intermediate Similarity NPC189206
0.7237 Intermediate Similarity NPC232812
0.7229 Intermediate Similarity NPC200513
0.7229 Intermediate Similarity NPC474439
0.7229 Intermediate Similarity NPC474028
0.7222 Intermediate Similarity NPC473369
0.7209 Intermediate Similarity NPC476600
0.7195 Intermediate Similarity NPC473685
0.7191 Intermediate Similarity NPC472812
0.7176 Intermediate Similarity NPC189311
0.7176 Intermediate Similarity NPC475860
0.7176 Intermediate Similarity NPC30984
0.7176 Intermediate Similarity NPC474694
0.7176 Intermediate Similarity NPC474013
0.7176 Intermediate Similarity NPC473659
0.7162 Intermediate Similarity NPC182794
0.7159 Intermediate Similarity NPC281942
0.7159 Intermediate Similarity NPC232426
0.7143 Intermediate Similarity NPC311070
0.7143 Intermediate Similarity NPC472377
0.7143 Intermediate Similarity NPC112654
0.7143 Intermediate Similarity NPC324243
0.7143 Intermediate Similarity NPC162346
0.7123 Intermediate Similarity NPC217940
0.7111 Intermediate Similarity NPC88507
0.7111 Intermediate Similarity NPC470255
0.7105 Intermediate Similarity NPC476945
0.7097 Intermediate Similarity NPC477721
0.7097 Intermediate Similarity NPC477716
0.7093 Intermediate Similarity NPC471219
0.7093 Intermediate Similarity NPC474062
0.7089 Intermediate Similarity NPC474758
0.7089 Intermediate Similarity NPC477204
0.7083 Intermediate Similarity NPC19241
0.7079 Intermediate Similarity NPC329842
0.7079 Intermediate Similarity NPC179517
0.7079 Intermediate Similarity NPC165904
0.7073 Intermediate Similarity NPC150646
0.7073 Intermediate Similarity NPC242767
0.7067 Intermediate Similarity NPC191233
0.7065 Intermediate Similarity NPC477719
0.7065 Intermediate Similarity NPC477718
0.7059 Intermediate Similarity NPC474693
0.7059 Intermediate Similarity NPC475100
0.7059 Intermediate Similarity NPC149869
0.7037 Intermediate Similarity NPC187568
0.7037 Intermediate Similarity NPC316500
0.7037 Intermediate Similarity NPC473825
0.7037 Intermediate Similarity NPC41780
0.7033 Intermediate Similarity NPC472189
0.7033 Intermediate Similarity NPC471362
0.7033 Intermediate Similarity NPC471372
0.7033 Intermediate Similarity NPC472441
0.7024 Intermediate Similarity NPC268122
0.7021 Intermediate Similarity NPC477717
0.7013 Intermediate Similarity NPC265574
0.7011 Intermediate Similarity NPC312561
0.7 Intermediate Similarity NPC166346
0.7 Intermediate Similarity NPC469939
0.7 Intermediate Similarity NPC242069
0.7 Intermediate Similarity NPC471571
0.7 Intermediate Similarity NPC65650
0.6989 Remote Similarity NPC473154
0.6989 Remote Similarity NPC474440
0.6988 Remote Similarity NPC10636
0.6986 Remote Similarity NPC329416
0.6986 Remote Similarity NPC317025
0.6986 Remote Similarity NPC317177
0.6986 Remote Similarity NPC326645
0.6977 Remote Similarity NPC106416
0.6977 Remote Similarity NPC86316
0.6977 Remote Similarity NPC471795
0.6977 Remote Similarity NPC65661
0.6974 Remote Similarity NPC203335
0.6966 Remote Similarity NPC202886
0.6962 Remote Similarity NPC12680
0.6957 Remote Similarity NPC311166
0.6957 Remote Similarity NPC470801
0.6957 Remote Similarity NPC8954
0.6957 Remote Similarity NPC94905
0.6957 Remote Similarity NPC171598
0.6951 Remote Similarity NPC105197
0.6947 Remote Similarity NPC134077
0.6941 Remote Similarity NPC118423
0.6941 Remote Similarity NPC475714
0.6941 Remote Similarity NPC22611
0.6933 Remote Similarity NPC470688
0.6933 Remote Similarity NPC220766
0.6932 Remote Similarity NPC226863
0.6932 Remote Similarity NPC93411
0.6932 Remote Similarity NPC471956
0.6923 Remote Similarity NPC475572
0.6923 Remote Similarity NPC474554
0.6915 Remote Similarity NPC477720
0.6915 Remote Similarity NPC324841
0.6914 Remote Similarity NPC477202
0.6907 Remote Similarity NPC127790
0.6905 Remote Similarity NPC25554
0.6905 Remote Similarity NPC471552
0.6905 Remote Similarity NPC473339
0.6897 Remote Similarity NPC131813
0.6897 Remote Similarity NPC220478
0.6897 Remote Similarity NPC173917
0.6892 Remote Similarity NPC155849
0.6882 Remote Similarity NPC98112
0.6882 Remote Similarity NPC475709
0.6882 Remote Similarity NPC476768
0.6882 Remote Similarity NPC472188
0.6875 Remote Similarity NPC120009
0.6875 Remote Similarity NPC132395
0.6875 Remote Similarity NPC238146
0.6875 Remote Similarity NPC117746

  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 NPC476489 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
0.8354 Intermediate Similarity NPD6400 Clinical (unspecified phase)
0.8 Intermediate Similarity NPD5325 Clinical (unspecified phase)
0.7436 Intermediate Similarity NPD8039 Approved
0.7397 Intermediate Similarity NPD2685 Clinical (unspecified phase)
0.7229 Intermediate Similarity NPD4752 Clinical (unspecified phase)
0.6986 Remote Similarity NPD4193 Approved
0.6986 Remote Similarity NPD4192 Approved
0.6986 Remote Similarity NPD4194 Approved
0.6986 Remote Similarity NPD4191 Approved
0.66 Remote Similarity NPD6686 Approved
0.6522 Remote Similarity NPD6927 Phase 3
0.6484 Remote Similarity NPD6051 Approved
0.6437 Remote Similarity NPD5209 Approved
0.6404 Remote Similarity NPD1694 Approved
0.6333 Remote Similarity NPD7334 Approved
0.6333 Remote Similarity NPD7521 Approved
0.6333 Remote Similarity NPD6684 Approved
0.6333 Remote Similarity NPD7146 Approved
0.6333 Remote Similarity NPD5330 Approved
0.6333 Remote Similarity NPD6409 Approved
0.6196 Remote Similarity NPD6672 Approved
0.6196 Remote Similarity NPD5737 Approved
0.6196 Remote Similarity NPD7513 Clinical (unspecified phase)
0.6196 Remote Similarity NPD6903 Approved
0.6122 Remote Similarity NPD7638 Approved
0.6081 Remote Similarity NPD4219 Approved
0.6061 Remote Similarity NPD7639 Approved
0.6061 Remote Similarity NPD7640 Approved
0.6055 Remote Similarity NPD7327 Approved
0.6055 Remote Similarity NPD7328 Approved
0.6 Remote Similarity NPD7516 Approved
0.6 Remote Similarity NPD5693 Phase 1
0.596 Remote Similarity NPD8029 Clinical (unspecified phase)
0.596 Remote Similarity NPD4225 Approved
0.5946 Remote Similarity NPD8377 Approved
0.5946 Remote Similarity NPD8294 Approved
0.5895 Remote Similarity NPD5785 Approved
0.5895 Remote Similarity NPD6698 Approved
0.5895 Remote Similarity NPD46 Approved
0.5893 Remote Similarity NPD8033 Approved
0.5893 Remote Similarity NPD7503 Approved
0.5893 Remote Similarity NPD8296 Approved
0.5893 Remote Similarity NPD8380 Approved
0.5893 Remote Similarity NPD8379 Approved
0.5893 Remote Similarity NPD8335 Approved
0.5893 Remote Similarity NPD8378 Approved
0.587 Remote Similarity NPD6082 Clinical (unspecified phase)
0.5833 Remote Similarity NPD7637 Suspended
0.5795 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5789 Remote Similarity NPD6904 Approved
0.5789 Remote Similarity NPD6080 Approved
0.5789 Remote Similarity NPD6673 Approved
0.5729 Remote Similarity NPD7838 Discovery
0.5714 Remote Similarity NPD7901 Clinical (unspecified phase)
0.5714 Remote Similarity NPD7748 Approved
0.5714 Remote Similarity NPD7900 Approved
0.5714 Remote Similarity NPD6412 Phase 2
0.57 Remote Similarity NPD6084 Phase 2
0.57 Remote Similarity NPD6083 Phase 2
0.569 Remote Similarity NPD7507 Approved
0.5684 Remote Similarity NPD5208 Approved
0.567 Remote Similarity NPD6050 Approved
0.5667 Remote Similarity NPD8259 Clinical (unspecified phase)
0.5657 Remote Similarity NPD6356 Clinical (unspecified phase)
0.5657 Remote Similarity NPD5695 Phase 3
0.5652 Remote Similarity NPD7154 Phase 3
0.5638 Remote Similarity NPD6098 Approved
0.5634 Remote Similarity NPD5343 Approved
0.5632 Remote Similarity NPD8264 Approved
0.5625 Remote Similarity NPD689 Discontinued
0.5612 Remote Similarity NPD6399 Phase 3
0.561 Remote Similarity NPD7331 Phase 2

  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