Structure

Physi-Chem Properties

Molecular Weight:  218.17
Volume:  251.764
LogP:  4.044
LogD:  3.662
LogS:  -4.247
# Rotatable Bonds:  1
TPSA:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.61
Synthetic Accessibility Score:  4.158
Fsp3:  0.667
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:  -4.643
MDCK Permeability:  1.6250793123617768e-05
Pgp-inhibitor:  0.94
Pgp-substrate:  0.007
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.803
30% Bioavailability (F30%):  0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.843
Plasma Protein Binding (PPB):  90.00040435791016%
Volume Distribution (VD):  2.435
Pgp-substrate:  4.630887031555176%

ADMET: Metabolism

CYP1A2-inhibitor:  0.128
CYP1A2-substrate:  0.529
CYP2C19-inhibitor:  0.15
CYP2C19-substrate:  0.809
CYP2C9-inhibitor:  0.14
CYP2C9-substrate:  0.652
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.681
CYP3A4-inhibitor:  0.308
CYP3A4-substrate:  0.392

ADMET: Excretion

Clearance (CL):  10.787
Half-life (T1/2):  0.392

ADMET: Toxicity

hERG Blockers:  0.014
Human Hepatotoxicity (H-HT):  0.333
Drug-inuced Liver Injury (DILI):  0.736
AMES Toxicity:  0.059
Rat Oral Acute Toxicity:  0.078
Maximum Recommended Daily Dose:  0.499
Skin Sensitization:  0.596
Carcinogencity:  0.674
Eye Corrosion:  0.88
Eye Irritation:  0.949
Respiratory Toxicity:  0.888

Download Data

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

  Natural Product: NPC20603

Natural Product ID:  NPC20603
Common Name*:   4,11-Guaiadien-3-One
IUPAC Name:   (5R,8S,8aS)-3,8-dimethyl-5-prop-1-en-2-yl-4,5,6,7,8,8a-hexahydro-1H-azulen-2-one
Synonyms:  
Standard InCHIKey:  CESATEXQMONATC-UHTWSYAYSA-N
Standard InCHI:  InChI=1S/C15H22O/c1-9(2)12-6-5-10(3)13-8-15(16)11(4)14(13)7-12/h10,12-13H,1,5-8H2,2-4H3/t10-,12+,13-/m0/s1
SMILES:  C=C(C)[C@@H]1CC[C@H](C)[C@@H]2CC(=O)C(=C2C1)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1096220
PubChem CID:   10082128
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0002874] Guaianes

*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
NPO2035 Daphne aurantiaca Species Thymelaeaceae Eukaryota n.a. n.a. n.a. PMID[20192236]
NPO29532 Vigna angularis Species Fabaceae Eukaryota Leaf Diffusate n.a. n.a. Database[FooDB]
NPO29532 Vigna angularis Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO29532 Vigna angularis Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO29532 Vigna angularis Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO29532 Vigna angularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29532 Vigna angularis Species Fabaceae Eukaryota Seeds n.a. Database[Phenol-Explorer]
NPO29532 Vigna angularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3998 Neolitsea pulchella Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17495 Isodon amethystoides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29532 Vigna angularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10765 Dracaena concinna Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10542 Liparis keitaoensis Species Liparidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14335 Ophiorrhiza kuroiwae Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1787 Agathis lanceolata Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13009 Laurencia saitoi Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3998 Neolitsea pulchella Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29532 Vigna angularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2035 Daphne aurantiaca Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3426 Pseudocyphellaria hirsuta Species Lobariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17495 Isodon amethystoides Species Lamiaceae 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
NPT113 Cell Line RAW264.7 Mus musculus IC50 > 400.0 nM PMID[509200]

☑ 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 NPC20603 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
0.9057 High Similarity NPC474141
0.8596 High Similarity NPC94991
0.8596 High Similarity NPC266295
0.8448 Intermediate Similarity NPC259261
0.8448 Intermediate Similarity NPC143834
0.8421 Intermediate Similarity NPC193695
0.8305 Intermediate Similarity NPC25853
0.8167 Intermediate Similarity NPC97322
0.8103 Intermediate Similarity NPC55004
0.8103 Intermediate Similarity NPC267626
0.8103 Intermediate Similarity NPC230823
0.8103 Intermediate Similarity NPC49575
0.807 Intermediate Similarity NPC275472
0.8036 Intermediate Similarity NPC45283
0.8036 Intermediate Similarity NPC268564
0.8033 Intermediate Similarity NPC165695
0.8 Intermediate Similarity NPC27438
0.7966 Intermediate Similarity NPC30215
0.7963 Intermediate Similarity NPC145311
0.7903 Intermediate Similarity NPC473902
0.7903 Intermediate Similarity NPC6697
0.7903 Intermediate Similarity NPC212210
0.7895 Intermediate Similarity NPC63396
0.7895 Intermediate Similarity NPC202850
0.7879 Intermediate Similarity NPC29328
0.7869 Intermediate Similarity NPC213152
0.7857 Intermediate Similarity NPC471751
0.7833 Intermediate Similarity NPC276764
0.7833 Intermediate Similarity NPC285594
0.7833 Intermediate Similarity NPC96551
0.7833 Intermediate Similarity NPC472304
0.7818 Intermediate Similarity NPC32351
0.7812 Intermediate Similarity NPC476626
0.7797 Intermediate Similarity NPC115385
0.7742 Intermediate Similarity NPC32285
0.7742 Intermediate Similarity NPC472306
0.7742 Intermediate Similarity NPC167256
0.7727 Intermediate Similarity NPC151045
0.7727 Intermediate Similarity NPC246722
0.7719 Intermediate Similarity NPC296311
0.7705 Intermediate Similarity NPC127582
0.7667 Intermediate Similarity NPC56905
0.7667 Intermediate Similarity NPC27610
0.7647 Intermediate Similarity NPC7382
0.7612 Intermediate Similarity NPC469737
0.7593 Intermediate Similarity NPC100380
0.7593 Intermediate Similarity NPC236355
0.7593 Intermediate Similarity NPC14917
0.7593 Intermediate Similarity NPC4079
0.7581 Intermediate Similarity NPC475795
0.7576 Intermediate Similarity NPC61702
0.7576 Intermediate Similarity NPC162867
0.7538 Intermediate Similarity NPC475523
0.75 Intermediate Similarity NPC474304
0.75 Intermediate Similarity NPC192427
0.75 Intermediate Similarity NPC474329
0.7463 Intermediate Similarity NPC280256
0.7368 Intermediate Similarity NPC236623
0.7344 Intermediate Similarity NPC475124
0.7344 Intermediate Similarity NPC285371
0.7333 Intermediate Similarity NPC473733
0.7324 Intermediate Similarity NPC472014
0.7313 Intermediate Similarity NPC256846
0.7313 Intermediate Similarity NPC139397
0.7273 Intermediate Similarity NPC8610
0.7273 Intermediate Similarity NPC262558
0.7246 Intermediate Similarity NPC300940
0.7231 Intermediate Similarity NPC251118
0.7206 Intermediate Similarity NPC251929
0.7206 Intermediate Similarity NPC307176
0.7206 Intermediate Similarity NPC265782
0.7206 Intermediate Similarity NPC159577
0.7206 Intermediate Similarity NPC260040
0.7206 Intermediate Similarity NPC2634
0.7206 Intermediate Similarity NPC282593
0.7206 Intermediate Similarity NPC35734
0.7193 Intermediate Similarity NPC163984
0.7193 Intermediate Similarity NPC176819
0.7193 Intermediate Similarity NPC58970
0.7193 Intermediate Similarity NPC116906
0.7188 Intermediate Similarity NPC288253
0.7164 Intermediate Similarity NPC469679
0.7164 Intermediate Similarity NPC469688
0.7164 Intermediate Similarity NPC476614
0.7143 Intermediate Similarity NPC91962
0.7123 Intermediate Similarity NPC476624
0.7123 Intermediate Similarity NPC472013
0.7101 Intermediate Similarity NPC181204
0.7101 Intermediate Similarity NPC54123
0.7101 Intermediate Similarity NPC115023
0.7097 Intermediate Similarity NPC170799
0.7097 Intermediate Similarity NPC308108
0.7097 Intermediate Similarity NPC311852
0.7083 Intermediate Similarity NPC195785
0.7083 Intermediate Similarity NPC15975
0.7077 Intermediate Similarity NPC150162
0.7069 Intermediate Similarity NPC64866
0.7059 Intermediate Similarity NPC67608
0.7042 Intermediate Similarity NPC469669
0.7042 Intermediate Similarity NPC89374
0.7042 Intermediate Similarity NPC475771
0.7042 Intermediate Similarity NPC469678
0.7042 Intermediate Similarity NPC77501
0.7042 Intermediate Similarity NPC473171
0.7031 Intermediate Similarity NPC60565
0.7027 Intermediate Similarity NPC69271
0.7027 Intermediate Similarity NPC74673
0.7 Intermediate Similarity NPC303613
0.7 Intermediate Similarity NPC470045
0.7 Intermediate Similarity NPC470044
0.7 Intermediate Similarity NPC474228
0.7 Intermediate Similarity NPC95581
0.7 Intermediate Similarity NPC251705
0.697 Remote Similarity NPC470329
0.6964 Remote Similarity NPC471752
0.6944 Remote Similarity NPC182848
0.6923 Remote Similarity NPC202118
0.6923 Remote Similarity NPC197238
0.6912 Remote Similarity NPC87141
0.6912 Remote Similarity NPC310992
0.6912 Remote Similarity NPC20610
0.6912 Remote Similarity NPC260474
0.6912 Remote Similarity NPC155198
0.6912 Remote Similarity NPC188292
0.6909 Remote Similarity NPC25771
0.6901 Remote Similarity NPC329866
0.6901 Remote Similarity NPC309852
0.6901 Remote Similarity NPC474797
0.6901 Remote Similarity NPC167049
0.6901 Remote Similarity NPC469691
0.6901 Remote Similarity NPC474796
0.6892 Remote Similarity NPC229204
0.6885 Remote Similarity NPC188789
0.6885 Remote Similarity NPC200258
0.6875 Remote Similarity NPC270042
0.6866 Remote Similarity NPC197089
0.6866 Remote Similarity NPC323005
0.6857 Remote Similarity NPC234707
0.6857 Remote Similarity NPC5701
0.6833 Remote Similarity NPC23117
0.6818 Remote Similarity NPC469662
0.6812 Remote Similarity NPC296522
0.6812 Remote Similarity NPC182815
0.6812 Remote Similarity NPC144511
0.6812 Remote Similarity NPC469677
0.6806 Remote Similarity NPC474011
0.6806 Remote Similarity NPC293803
0.6806 Remote Similarity NPC251435
0.6806 Remote Similarity NPC216791
0.6769 Remote Similarity NPC260573
0.6757 Remote Similarity NPC299235
0.6757 Remote Similarity NPC476627
0.6727 Remote Similarity NPC301972
0.6727 Remote Similarity NPC292463
0.6721 Remote Similarity NPC209431
0.6721 Remote Similarity NPC250539
0.6721 Remote Similarity NPC100809
0.6716 Remote Similarity NPC183422
0.6714 Remote Similarity NPC477856
0.6714 Remote Similarity NPC18543
0.6714 Remote Similarity NPC214770
0.6712 Remote Similarity NPC69408
0.6712 Remote Similarity NPC469796
0.6712 Remote Similarity NPC124289
0.6712 Remote Similarity NPC25908
0.6712 Remote Similarity NPC141346
0.6712 Remote Similarity NPC469646
0.6712 Remote Similarity NPC142759
0.6712 Remote Similarity NPC469793
0.6712 Remote Similarity NPC472967
0.6712 Remote Similarity NPC473437
0.6712 Remote Similarity NPC215481
0.6712 Remote Similarity NPC266159
0.6712 Remote Similarity NPC115719
0.6712 Remote Similarity NPC473223
0.6711 Remote Similarity NPC255580
0.6711 Remote Similarity NPC136150
0.6711 Remote Similarity NPC39411
0.6667 Remote Similarity NPC471890
0.6667 Remote Similarity NPC469641
0.6667 Remote Similarity NPC255021
0.6667 Remote Similarity NPC84185
0.6667 Remote Similarity NPC469643
0.6667 Remote Similarity NPC66677
0.6667 Remote Similarity NPC22098
0.6667 Remote Similarity NPC195246
0.6667 Remote Similarity NPC276009
0.662 Remote Similarity NPC304983
0.662 Remote Similarity NPC190035
0.662 Remote Similarity NPC470078
0.662 Remote Similarity NPC133253
0.662 Remote Similarity NPC305501
0.662 Remote Similarity NPC223187
0.662 Remote Similarity NPC21944
0.662 Remote Similarity NPC288667
0.662 Remote Similarity NPC474562
0.6618 Remote Similarity NPC304665
0.6618 Remote Similarity NPC126899
0.6618 Remote Similarity NPC154728
0.661 Remote Similarity NPC228776

  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 NPC20603 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
0.7313 Intermediate Similarity NPD4137 Phase 3
0.7206 Intermediate Similarity NPD4747 Approved
0.7206 Intermediate Similarity NPD4691 Approved
0.7101 Intermediate Similarity NPD5276 Approved
0.7097 Intermediate Similarity NPD287 Approved
0.6912 Remote Similarity NPD3621 Clinical (unspecified phase)
0.6901 Remote Similarity NPD4687 Approved
0.6901 Remote Similarity NPD5733 Approved
0.6901 Remote Similarity NPD4058 Approved
0.6618 Remote Similarity NPD7331 Phase 2
0.6471 Remote Similarity NPD7341 Phase 2
0.6203 Remote Similarity NPD4221 Approved
0.6203 Remote Similarity NPD4223 Phase 3
0.6125 Remote Similarity NPD3527 Clinical (unspecified phase)
0.6104 Remote Similarity NPD3617 Approved
0.6102 Remote Similarity NPD343 Approved
0.6102 Remote Similarity NPD345 Approved
0.6102 Remote Similarity NPD344 Approved
0.6094 Remote Similarity NPD4627 Clinical (unspecified phase)
0.6049 Remote Similarity NPD3666 Approved
0.6049 Remote Similarity NPD3133 Approved
0.6049 Remote Similarity NPD3665 Phase 1
0.6049 Remote Similarity NPD4197 Approved
0.6 Remote Similarity NPD5783 Phase 3
0.5976 Remote Similarity NPD5329 Approved
0.5949 Remote Similarity NPD4695 Discontinued
0.5904 Remote Similarity NPD3618 Phase 1
0.5904 Remote Similarity NPD4689 Approved
0.5904 Remote Similarity NPD7334 Approved
0.5904 Remote Similarity NPD5205 Approved
0.5904 Remote Similarity NPD7521 Approved
0.5904 Remote Similarity NPD5279 Phase 3
0.5904 Remote Similarity NPD4690 Approved
0.5904 Remote Similarity NPD6684 Approved
0.5904 Remote Similarity NPD4138 Approved
0.5904 Remote Similarity NPD4693 Phase 3
0.5904 Remote Similarity NPD5280 Approved
0.5904 Remote Similarity NPD7146 Approved
0.5904 Remote Similarity NPD4688 Approved
0.5904 Remote Similarity NPD5330 Approved
0.5904 Remote Similarity NPD6409 Approved
0.5904 Remote Similarity NPD4519 Discontinued
0.5904 Remote Similarity NPD4694 Approved
0.5904 Remote Similarity NPD5690 Phase 2
0.5904 Remote Similarity NPD4623 Approved
0.5897 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5882 Remote Similarity NPD1695 Approved
0.5802 Remote Similarity NPD3667 Approved
0.5802 Remote Similarity NPD4800 Clinical (unspecified phase)
0.5783 Remote Similarity NPD5363 Approved
0.5765 Remote Similarity NPD6672 Approved
0.5765 Remote Similarity NPD7513 Clinical (unspecified phase)
0.5765 Remote Similarity NPD5737 Approved
0.5765 Remote Similarity NPD4518 Approved
0.5765 Remote Similarity NPD6903 Approved
0.5765 Remote Similarity NPD5208 Approved
0.575 Remote Similarity NPD5368 Approved
0.5732 Remote Similarity NPD5362 Discontinued
0.573 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5714 Remote Similarity NPD3574 Clinical (unspecified phase)
0.5714 Remote Similarity NPD2664 Clinical (unspecified phase)
0.5698 Remote Similarity NPD4753 Phase 2
0.5698 Remote Similarity NPD5328 Approved
0.5698 Remote Similarity NPD6080 Approved
0.5698 Remote Similarity NPD6904 Approved
0.5698 Remote Similarity NPD6673 Approved
0.5694 Remote Similarity NPD6108 Clinical (unspecified phase)
0.5679 Remote Similarity NPD5369 Approved
0.5679 Remote Similarity NPD8028 Phase 2
0.5663 Remote Similarity NPD4786 Approved
0.5663 Remote Similarity NPD3668 Phase 3
0.5632 Remote Similarity NPD4096 Approved
0.5632 Remote Similarity NPD5207 Approved
0.5632 Remote Similarity NPD5692 Phase 3
0.561 Remote Similarity NPD5209 Approved
0.561 Remote Similarity NPD4270 Approved
0.561 Remote Similarity NPD4269 Approved
0.561 Remote Similarity NPD6435 Approved
0.561 Remote Similarity NPD4752 Clinical (unspecified phase)

  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