Structure

Physi-Chem Properties

Molecular Weight:  234.16
Volume:  266.474
LogP:  1.948
LogD:  2.188
LogS:  -3.493
# Rotatable Bonds:  5
TPSA:  34.14
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.681
Synthetic Accessibility Score:  3.238
Fsp3:  0.6
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.587
MDCK Permeability:  2.7999496523989365e-05
Pgp-inhibitor:  0.88
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.049
30% Bioavailability (F30%):  0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.694
Plasma Protein Binding (PPB):  69.61322784423828%
Volume Distribution (VD):  0.382
Pgp-substrate:  31.87363052368164%

ADMET: Metabolism

CYP1A2-inhibitor:  0.076
CYP1A2-substrate:  0.576
CYP2C19-inhibitor:  0.609
CYP2C19-substrate:  0.842
CYP2C9-inhibitor:  0.417
CYP2C9-substrate:  0.855
CYP2D6-inhibitor:  0.065
CYP2D6-substrate:  0.874
CYP3A4-inhibitor:  0.036
CYP3A4-substrate:  0.338

ADMET: Excretion

Clearance (CL):  6.087
Half-life (T1/2):  0.856

ADMET: Toxicity

hERG Blockers:  0.021
Human Hepatotoxicity (H-HT):  0.062
Drug-inuced Liver Injury (DILI):  0.163
AMES Toxicity:  0.184
Rat Oral Acute Toxicity:  0.035
Maximum Recommended Daily Dose:  0.177
Skin Sensitization:  0.947
Carcinogencity:  0.623
Eye Corrosion:  0.926
Eye Irritation:  0.952
Respiratory Toxicity:  0.37

Download Data

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

  Natural Product: NPC296311

Natural Product ID:  NPC296311
Common Name*:   Capillosanane O
IUPAC Name:   4,4-dimethyl-2-[(Z)-2-methyl-6-oxohept-2-enyl]cyclopent-2-en-1-one
Synonyms:  
Standard InCHIKey:  WSAXCZSLPACXPU-WDZFZDKYSA-N
Standard InCHI:  InChI=1S/C15H22O2/c1-11(6-5-7-12(2)16)8-13-9-15(3,4)10-14(13)17/h6,9H,5,7-8,10H2,1-4H3/b11-6-
SMILES:  CC(=O)CC/C=C(CC1=CC(CC1=O)(C)C)/C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2419327
PubChem CID:   73356775
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones
            • [CHEMONTID:0003487] Cyclic ketones

*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
NPO22108 Sinularia capillosa Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[11087604]
NPO22108 Sinularia capillosa Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[20155971]
NPO22108 Sinularia capillosa Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[23964704]
NPO22108 Sinularia capillosa Species Alcyoniidae 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
NPT146 Cell Line SK-OV-3 Homo sapiens IC50 > 10.0 ug.mL-1 PMID[473878]
NPT81 Cell Line A549 Homo sapiens IC50 > 10.0 ug.mL-1 PMID[473878]
NPT547 Cell Line BGC-823 Homo sapiens IC50 > 10.0 ug.mL-1 PMID[473878]
NPT65 Cell Line HepG2 Homo sapiens IC50 > 10.0 ug.mL-1 PMID[473878]
NPT180 Cell Line HCT-8 Homo sapiens IC50 > 10.0 ug.mL-1 PMID[473878]

☑ 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 NPC296311 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
0.8654 High Similarity NPC471751
0.8627 High Similarity NPC228776
0.8596 High Similarity NPC260573
0.8596 High Similarity NPC97322
0.8491 Intermediate Similarity NPC474141
0.8491 Intermediate Similarity NPC45283
0.8448 Intermediate Similarity NPC167256
0.8431 Intermediate Similarity NPC145311
0.84 Intermediate Similarity NPC100380
0.8246 Intermediate Similarity NPC259261
0.8136 Intermediate Similarity NPC32285
0.8103 Intermediate Similarity NPC25853
0.807 Intermediate Similarity NPC266295
0.807 Intermediate Similarity NPC30215
0.807 Intermediate Similarity NPC94991
0.8039 Intermediate Similarity NPC8610
0.8039 Intermediate Similarity NPC262558
0.8039 Intermediate Similarity NPC471752
0.8 Intermediate Similarity NPC212210
0.7966 Intermediate Similarity NPC475795
0.7931 Intermediate Similarity NPC285594
0.7931 Intermediate Similarity NPC96551
0.7925 Intermediate Similarity NPC118788
0.7857 Intermediate Similarity NPC275472
0.7833 Intermediate Similarity NPC165695
0.7833 Intermediate Similarity NPC288253
0.7818 Intermediate Similarity NPC37644
0.78 Intermediate Similarity NPC216921
0.7778 Intermediate Similarity NPC64866
0.7759 Intermediate Similarity NPC311852
0.7719 Intermediate Similarity NPC20603
0.7705 Intermediate Similarity NPC473902
0.7667 Intermediate Similarity NPC213152
0.7656 Intermediate Similarity NPC256846
0.7619 Intermediate Similarity NPC475523
0.7593 Intermediate Similarity NPC163984
0.7593 Intermediate Similarity NPC32351
0.7593 Intermediate Similarity NPC176819
0.7593 Intermediate Similarity NPC58970
0.7586 Intermediate Similarity NPC230823
0.7586 Intermediate Similarity NPC267626
0.7586 Intermediate Similarity NPC49575
0.7586 Intermediate Similarity NPC55004
0.7586 Intermediate Similarity NPC193695
0.7586 Intermediate Similarity NPC115385
0.7581 Intermediate Similarity NPC251118
0.75 Intermediate Similarity NPC23117
0.75 Intermediate Similarity NPC166788
0.75 Intermediate Similarity NPC69898
0.75 Intermediate Similarity NPC295777
0.75 Intermediate Similarity NPC268564
0.75 Intermediate Similarity NPC127582
0.75 Intermediate Similarity NPC191337
0.7458 Intermediate Similarity NPC56905
0.7458 Intermediate Similarity NPC27610
0.7455 Intermediate Similarity NPC27438
0.7451 Intermediate Similarity NPC301972
0.7419 Intermediate Similarity NPC4638
0.7385 Intermediate Similarity NPC61702
0.7385 Intermediate Similarity NPC162867
0.7377 Intermediate Similarity NPC294304
0.7377 Intermediate Similarity NPC228574
0.7368 Intermediate Similarity NPC63396
0.7368 Intermediate Similarity NPC202850
0.7333 Intermediate Similarity NPC143834
0.7308 Intermediate Similarity NPC25771
0.7308 Intermediate Similarity NPC471753
0.7308 Intermediate Similarity NPC477686
0.7302 Intermediate Similarity NPC470329
0.7288 Intermediate Similarity NPC192427
0.7273 Intermediate Similarity NPC265782
0.7273 Intermediate Similarity NPC15325
0.7273 Intermediate Similarity NPC251929
0.7273 Intermediate Similarity NPC2634
0.7273 Intermediate Similarity NPC116906
0.7231 Intermediate Similarity NPC469679
0.7231 Intermediate Similarity NPC469688
0.7231 Intermediate Similarity NPC87141
0.7231 Intermediate Similarity NPC155198
0.7231 Intermediate Similarity NPC260474
0.7231 Intermediate Similarity NPC188292
0.7193 Intermediate Similarity NPC14002
0.7167 Intermediate Similarity NPC60772
0.7167 Intermediate Similarity NPC170799
0.7167 Intermediate Similarity NPC308108
0.7164 Intermediate Similarity NPC54123
0.7143 Intermediate Similarity NPC475124
0.7143 Intermediate Similarity NPC150162
0.7143 Intermediate Similarity NPC6697
0.7143 Intermediate Similarity NPC285371
0.7121 Intermediate Similarity NPC139397
0.7119 Intermediate Similarity NPC473733
0.7115 Intermediate Similarity NPC292463
0.7097 Intermediate Similarity NPC60565
0.7069 Intermediate Similarity NPC5626
0.7059 Intermediate Similarity NPC303613
0.7059 Intermediate Similarity NPC474228
0.7049 Intermediate Similarity NPC472304
0.7049 Intermediate Similarity NPC276764
0.7037 Intermediate Similarity NPC236355
0.7037 Intermediate Similarity NPC14917
0.7037 Intermediate Similarity NPC4079
0.7031 Intermediate Similarity NPC183422
0.7031 Intermediate Similarity NPC474304
0.7031 Intermediate Similarity NPC474329
0.7015 Intermediate Similarity NPC246722
0.7015 Intermediate Similarity NPC260040
0.7015 Intermediate Similarity NPC151045
0.7015 Intermediate Similarity NPC307176
0.7 Intermediate Similarity NPC217923
0.7 Intermediate Similarity NPC192843
0.7 Intermediate Similarity NPC281230
0.6984 Remote Similarity NPC472306
0.6984 Remote Similarity NPC322457
0.697 Remote Similarity NPC476614
0.697 Remote Similarity NPC310992
0.6964 Remote Similarity NPC474391
0.6957 Remote Similarity NPC474796
0.6957 Remote Similarity NPC329866
0.6957 Remote Similarity NPC474797
0.6957 Remote Similarity NPC309852
0.6949 Remote Similarity NPC188789
0.6939 Remote Similarity NPC185839
0.6912 Remote Similarity NPC21944
0.6912 Remote Similarity NPC5701
0.6912 Remote Similarity NPC181204
0.6912 Remote Similarity NPC474562
0.6909 Remote Similarity NPC324812
0.6909 Remote Similarity NPC91962
0.6875 Remote Similarity NPC169275
0.6875 Remote Similarity NPC52449
0.6866 Remote Similarity NPC250928
0.6866 Remote Similarity NPC473603
0.6866 Remote Similarity NPC476059
0.6866 Remote Similarity NPC67608
0.6866 Remote Similarity NPC10758
0.6863 Remote Similarity NPC111474
0.6857 Remote Similarity NPC474011
0.6857 Remote Similarity NPC469669
0.6857 Remote Similarity NPC469678
0.6857 Remote Similarity NPC216791
0.6857 Remote Similarity NPC473171
0.6857 Remote Similarity NPC475771
0.6857 Remote Similarity NPC251435
0.6842 Remote Similarity NPC477458
0.6842 Remote Similarity NPC234829
0.6842 Remote Similarity NPC236623
0.6825 Remote Similarity NPC64985
0.6818 Remote Similarity NPC290350
0.6818 Remote Similarity NPC4370
0.6812 Remote Similarity NPC251705
0.6812 Remote Similarity NPC470045
0.6812 Remote Similarity NPC470044
0.68 Remote Similarity NPC155880
0.68 Remote Similarity NPC92863
0.68 Remote Similarity NPC180840
0.678 Remote Similarity NPC95581
0.678 Remote Similarity NPC250539
0.6774 Remote Similarity NPC38455
0.6765 Remote Similarity NPC318766
0.6765 Remote Similarity NPC159577
0.6765 Remote Similarity NPC35734
0.6765 Remote Similarity NPC282593
0.6761 Remote Similarity NPC27205
0.6761 Remote Similarity NPC469793
0.6761 Remote Similarity NPC469796
0.6761 Remote Similarity NPC69408
0.6735 Remote Similarity NPC38497
0.6721 Remote Similarity NPC321568
0.6721 Remote Similarity NPC208749
0.6721 Remote Similarity NPC281986
0.6721 Remote Similarity NPC22019
0.6719 Remote Similarity NPC202118
0.6719 Remote Similarity NPC190049
0.6719 Remote Similarity NPC197238
0.6714 Remote Similarity NPC20025
0.6714 Remote Similarity NPC255021
0.6714 Remote Similarity NPC167049
0.6714 Remote Similarity NPC469691
0.6667 Remote Similarity NPC176171
0.6667 Remote Similarity NPC234707
0.6667 Remote Similarity NPC92327
0.6667 Remote Similarity NPC267514
0.6667 Remote Similarity NPC304983
0.6667 Remote Similarity NPC257618
0.6667 Remote Similarity NPC305501
0.6667 Remote Similarity NPC133253
0.6667 Remote Similarity NPC200258
0.6667 Remote Similarity NPC145755
0.6667 Remote Similarity NPC115023
0.6667 Remote Similarity NPC29328
0.6667 Remote Similarity NPC86917
0.6667 Remote Similarity NPC474539
0.6667 Remote Similarity NPC474884
0.6667 Remote Similarity NPC197089
0.6667 Remote Similarity NPC190035
0.6667 Remote Similarity NPC106309
0.662 Remote Similarity NPC255650
0.662 Remote Similarity NPC476346
0.662 Remote Similarity NPC77501

  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 NPC296311 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
0.7273 Intermediate Similarity NPD4691 Approved
0.7167 Intermediate Similarity NPD287 Approved
0.7121 Intermediate Similarity NPD4137 Phase 3
0.7015 Intermediate Similarity NPD4747 Approved
0.6957 Remote Similarity NPD4058 Approved
0.6912 Remote Similarity NPD5276 Approved
0.6714 Remote Similarity NPD4687 Approved
0.6714 Remote Similarity NPD5733 Approved
0.6667 Remote Similarity NPD7331 Phase 2
0.6667 Remote Similarity NPD5783 Phase 3
0.6471 Remote Similarity NPD3621 Clinical (unspecified phase)
0.6308 Remote Similarity NPD4193 Approved
0.6308 Remote Similarity NPD4192 Approved
0.6308 Remote Similarity NPD4194 Approved
0.6308 Remote Similarity NPD4191 Approved
0.6234 Remote Similarity NPD5209 Approved
0.6212 Remote Similarity NPD2664 Clinical (unspecified phase)
0.6184 Remote Similarity NPD4695 Discontinued
0.6176 Remote Similarity NPD6108 Clinical (unspecified phase)
0.6154 Remote Similarity NPD3527 Clinical (unspecified phase)
0.6129 Remote Similarity NPD4627 Clinical (unspecified phase)
0.6029 Remote Similarity NPD7341 Phase 2
0.6026 Remote Similarity NPD4221 Approved
0.6026 Remote Similarity NPD4223 Phase 3
0.6 Remote Similarity NPD1696 Phase 3
0.5974 Remote Similarity NPD8259 Clinical (unspecified phase)
0.5968 Remote Similarity NPD539 Approved
0.5926 Remote Similarity NPD4623 Approved
0.5926 Remote Similarity NPD5690 Phase 2
0.5926 Remote Similarity NPD4519 Discontinued
0.5897 Remote Similarity NPD8028 Phase 2
0.5875 Remote Similarity NPD4197 Approved
0.5875 Remote Similarity NPD3666 Approved
0.5875 Remote Similarity NPD3133 Approved
0.5875 Remote Similarity NPD3665 Phase 1
0.5844 Remote Similarity NPD4195 Approved
0.5823 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5802 Remote Similarity NPD5329 Approved
0.5802 Remote Similarity NPD1694 Approved
0.5797 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5738 Remote Similarity NPD29 Approved
0.5738 Remote Similarity NPD28 Approved
0.5732 Remote Similarity NPD5280 Approved
0.5732 Remote Similarity NPD3618 Phase 1
0.5732 Remote Similarity NPD4693 Phase 3
0.5732 Remote Similarity NPD7146 Approved
0.5732 Remote Similarity NPD4690 Approved
0.5732 Remote Similarity NPD5205 Approved
0.5732 Remote Similarity NPD3574 Clinical (unspecified phase)
0.5732 Remote Similarity NPD4689 Approved
0.5732 Remote Similarity NPD4688 Approved
0.5732 Remote Similarity NPD7334 Approved
0.5732 Remote Similarity NPD5279 Phase 3
0.5732 Remote Similarity NPD4138 Approved
0.5732 Remote Similarity NPD7521 Approved
0.5732 Remote Similarity NPD6684 Approved
0.5732 Remote Similarity NPD5330 Approved
0.5732 Remote Similarity NPD4694 Approved
0.5732 Remote Similarity NPD6409 Approved
0.5714 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5714 Remote Similarity NPD3617 Approved
0.5692 Remote Similarity NPD8779 Phase 3
0.569 Remote Similarity NPD3174 Discontinued
0.5663 Remote Similarity NPD3573 Approved
0.5652 Remote Similarity NPD5325 Clinical (unspecified phase)
0.5634 Remote Similarity NPD3709 Clinical (unspecified phase)
0.5625 Remote Similarity NPD3667 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