Structure

Physi-Chem Properties

Molecular Weight:  594.16
Volume:  555.367
LogP:  0.151
LogD:  -0.261
LogS:  -2.349
# Rotatable Bonds:  13
TPSA:  249.97
# H-Bond Aceptor:  15
# H-Bond Donor:  8
# Rings:  3
# Heavy Atoms:  15

MedChem Properties

QED Drug-Likeness Score:  0.104
Synthetic Accessibility Score:  4.417
Fsp3:  0.37
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.372
MDCK Permeability:  4.29343490395695e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.79
Human Intestinal Absorption (HIA):  0.808
20% Bioavailability (F20%):  0.905
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.076
Plasma Protein Binding (PPB):  81.3215103149414%
Volume Distribution (VD):  0.339
Pgp-substrate:  11.434985160827637%

ADMET: Metabolism

CYP1A2-inhibitor:  0.095
CYP1A2-substrate:  0.012
CYP2C19-inhibitor:  0.022
CYP2C19-substrate:  0.043
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.735
CYP2D6-inhibitor:  0.042
CYP2D6-substrate:  0.115
CYP3A4-inhibitor:  0.068
CYP3A4-substrate:  0.004

ADMET: Excretion

Clearance (CL):  1.373
Half-life (T1/2):  0.908

ADMET: Toxicity

hERG Blockers:  0.039
Human Hepatotoxicity (H-HT):  0.102
Drug-inuced Liver Injury (DILI):  0.864
AMES Toxicity:  0.02
Rat Oral Acute Toxicity:  0.008
Maximum Recommended Daily Dose:  0.0
Skin Sensitization:  0.073
Carcinogencity:  0.03
Eye Corrosion:  0.003
Eye Irritation:  0.012
Respiratory Toxicity:  0.004

Download Data

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

  Natural Product: NPC223315

Natural Product ID:  NPC223315
Common Name*:   2-Heptylcyclopentan-1-One
IUPAC Name:   2-heptylcyclopentan-1-one
Synonyms:  
Standard InCHIKey:  PJXHBTZLHITWFX-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C12H22O/c1-2-3-4-5-6-8-11-9-7-10-12(11)13/h11H,2-10H2,1H3
SMILES:  CCCCCCCC1CCCC1=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3185887
PubChem CID:   8710
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
NPO23256 Mentha arvensis Species Lamiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO23256 Mentha arvensis Species Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO13857 Mentha canadensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13857 Mentha canadensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23256 Mentha arvensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13857 Mentha canadensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23256 Mentha arvensis 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
NPT2 Others Unspecified Potency n.a. 6113.1 nM PubChem BioAssay data set

☑ 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 NPC223315 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
0.8974 High Similarity NPC18397
0.8462 Intermediate Similarity NPC45270
0.8462 Intermediate Similarity NPC215118
0.8462 Intermediate Similarity NPC135077
0.8462 Intermediate Similarity NPC59570
0.8205 Intermediate Similarity NPC141634
0.814 Intermediate Similarity NPC285814
0.814 Intermediate Similarity NPC83187
0.814 Intermediate Similarity NPC131981
0.814 Intermediate Similarity NPC173996
0.814 Intermediate Similarity NPC98246
0.814 Intermediate Similarity NPC40249
0.8 Intermediate Similarity NPC321646
0.7955 Intermediate Similarity NPC294440
0.7838 Intermediate Similarity NPC248190
0.7778 Intermediate Similarity NPC293343
0.7778 Intermediate Similarity NPC258672
0.7778 Intermediate Similarity NPC247786
0.7714 Intermediate Similarity NPC29561
0.7714 Intermediate Similarity NPC4962
0.7714 Intermediate Similarity NPC196434
0.7714 Intermediate Similarity NPC42403
0.7714 Intermediate Similarity NPC222997
0.7714 Intermediate Similarity NPC221192
0.7714 Intermediate Similarity NPC79887
0.7714 Intermediate Similarity NPC153439
0.7692 Intermediate Similarity NPC69245
0.7632 Intermediate Similarity NPC121215
0.7556 Intermediate Similarity NPC20017
0.75 Intermediate Similarity NPC168982
0.7447 Intermediate Similarity NPC274182
0.7442 Intermediate Similarity NPC171783
0.7429 Intermediate Similarity NPC198118
0.7429 Intermediate Similarity NPC295442
0.7429 Intermediate Similarity NPC38859
0.7297 Intermediate Similarity NPC268596
0.7297 Intermediate Similarity NPC76608
0.7297 Intermediate Similarity NPC149101
0.7297 Intermediate Similarity NPC225318
0.7297 Intermediate Similarity NPC16578
0.7179 Intermediate Similarity NPC218357
0.7143 Intermediate Similarity NPC100997
0.7 Intermediate Similarity NPC319589
0.7 Intermediate Similarity NPC288296
0.7 Intermediate Similarity NPC53245
0.6863 Remote Similarity NPC184819
0.6809 Remote Similarity NPC13105
0.68 Remote Similarity NPC474141
0.6757 Remote Similarity NPC158107
0.6739 Remote Similarity NPC314679
0.6735 Remote Similarity NPC236623
0.6731 Remote Similarity NPC143597
0.6731 Remote Similarity NPC151464
0.6731 Remote Similarity NPC474105
0.6604 Remote Similarity NPC267626
0.6604 Remote Similarity NPC49575
0.6604 Remote Similarity NPC230823
0.6604 Remote Similarity NPC55004
0.6585 Remote Similarity NPC301919
0.6571 Remote Similarity NPC66624
0.6571 Remote Similarity NPC227197
0.6571 Remote Similarity NPC307594
0.6531 Remote Similarity NPC116906
0.6531 Remote Similarity NPC305182
0.6522 Remote Similarity NPC55023
0.6481 Remote Similarity NPC266295
0.6481 Remote Similarity NPC94991
0.6481 Remote Similarity NPC30215
0.6458 Remote Similarity NPC324793
0.6458 Remote Similarity NPC477878
0.6415 Remote Similarity NPC20603
0.641 Remote Similarity NPC49151
0.641 Remote Similarity NPC254713
0.641 Remote Similarity NPC261991
0.641 Remote Similarity NPC262505
0.641 Remote Similarity NPC179831
0.64 Remote Similarity NPC27438
0.6389 Remote Similarity NPC79591
0.6364 Remote Similarity NPC259261
0.6364 Remote Similarity NPC143834
0.6346 Remote Similarity NPC63396
0.6346 Remote Similarity NPC202850
0.6286 Remote Similarity NPC91093
0.625 Remote Similarity NPC4079
0.625 Remote Similarity NPC14917
0.625 Remote Similarity NPC236355
0.625 Remote Similarity NPC270042
0.625 Remote Similarity NPC21844
0.625 Remote Similarity NPC25853
0.6226 Remote Similarity NPC200258
0.6226 Remote Similarity NPC307063
0.6226 Remote Similarity NPC275472
0.6222 Remote Similarity NPC325452
0.6222 Remote Similarity NPC248763
0.614 Remote Similarity NPC213152
0.614 Remote Similarity NPC475795
0.6136 Remote Similarity NPC3531
0.6098 Remote Similarity NPC49615
0.6078 Remote Similarity NPC314084
0.6034 Remote Similarity NPC165695
0.6034 Remote Similarity NPC472306
0.6 Remote Similarity NPC192427
0.6 Remote Similarity NPC193695
0.6 Remote Similarity NPC254524
0.6 Remote Similarity NPC115385
0.5932 Remote Similarity NPC212210
0.5932 Remote Similarity NPC128608
0.5932 Remote Similarity NPC473902
0.5893 Remote Similarity NPC27610
0.5893 Remote Similarity NPC127798
0.5893 Remote Similarity NPC56905
0.5882 Remote Similarity NPC32351
0.5862 Remote Similarity NPC97322
0.5849 Remote Similarity NPC268564
0.5849 Remote Similarity NPC72722
0.5849 Remote Similarity NPC45283
0.5833 Remote Similarity NPC30338
0.5833 Remote Similarity NPC157518
0.5814 Remote Similarity NPC328441
0.58 Remote Similarity NPC91962
0.5789 Remote Similarity NPC276764
0.5789 Remote Similarity NPC472304
0.5789 Remote Similarity NPC285594
0.5789 Remote Similarity NPC96551
0.5763 Remote Similarity NPC167256
0.5763 Remote Similarity NPC32285
0.5738 Remote Similarity NPC43300
0.5738 Remote Similarity NPC96812
0.5738 Remote Similarity NPC107704
0.5738 Remote Similarity NPC168824
0.5738 Remote Similarity NPC323005
0.5738 Remote Similarity NPC39462
0.5738 Remote Similarity NPC189917
0.5714 Remote Similarity NPC32603
0.5714 Remote Similarity NPC308301
0.5714 Remote Similarity NPC282440
0.5714 Remote Similarity NPC83723
0.569 Remote Similarity NPC40206
0.569 Remote Similarity NPC127582
0.569 Remote Similarity NPC478126
0.5686 Remote Similarity NPC145311
0.5676 Remote Similarity NPC172053
0.5676 Remote Similarity NPC129976
0.566 Remote Similarity NPC22182
0.566 Remote Similarity NPC471751
0.5645 Remote Similarity NPC475523
0.5641 Remote Similarity NPC32279
0.5641 Remote Similarity NPC287782
0.5625 Remote Similarity NPC317128
0.5625 Remote Similarity NPC76051
0.5625 Remote Similarity NPC74845
0.56 Remote Similarity NPC249754

  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 NPC223315 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
0.814 Intermediate Similarity NPD343 Approved
0.814 Intermediate Similarity NPD344 Approved
0.814 Intermediate Similarity NPD345 Approved
0.6739 Remote Similarity NPD634 Phase 3
0.6444 Remote Similarity NPD387 Clinical (unspecified phase)
0.6429 Remote Similarity NPD9449 Clinical (unspecified phase)
0.6346 Remote Similarity NPD615 Clinical (unspecified phase)
0.6341 Remote Similarity NPD9447 Approved
0.6136 Remote Similarity NPD77 Approved
0.6136 Remote Similarity NPD9450 Approved
0.6071 Remote Similarity NPD3198 Approved
0.5962 Remote Similarity NPD3186 Phase 1
0.5833 Remote Similarity NPD3171 Clinical (unspecified phase)
0.5738 Remote Similarity NPD4224 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