Structure

Physi-Chem Properties

Molecular Weight:  100.09
Volume:  112.566
LogP:  1.104
LogD:  0.979
LogS:  -0.635
# Rotatable Bonds:  0
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.486
Synthetic Accessibility Score:  1.818
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.327
MDCK Permeability:  4.2620511521818116e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.729
Human Intestinal Absorption (HIA):  0.01
20% Bioavailability (F20%):  0.047
30% Bioavailability (F30%):  0.654

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.951
Plasma Protein Binding (PPB):  44.389129638671875%
Volume Distribution (VD):  1.259
Pgp-substrate:  57.56501007080078%

ADMET: Metabolism

CYP1A2-inhibitor:  0.249
CYP1A2-substrate:  0.786
CYP2C19-inhibitor:  0.064
CYP2C19-substrate:  0.28
CYP2C9-inhibitor:  0.033
CYP2C9-substrate:  0.675
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.379
CYP3A4-inhibitor:  0.014
CYP3A4-substrate:  0.135

ADMET: Excretion

Clearance (CL):  10.797
Half-life (T1/2):  0.65

ADMET: Toxicity

hERG Blockers:  0.023
Human Hepatotoxicity (H-HT):  0.064
Drug-inuced Liver Injury (DILI):  0.036
AMES Toxicity:  0.014
Rat Oral Acute Toxicity:  0.048
Maximum Recommended Daily Dose:  0.03
Skin Sensitization:  0.6
Carcinogencity:  0.435
Eye Corrosion:  0.965
Eye Irritation:  0.994
Respiratory Toxicity:  0.149

Download Data

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

  Natural Product: NPC325345

Natural Product ID:  NPC325345
Common Name*:   Cyclohexanol
IUPAC Name:   cyclohexanol
Synonyms:   Cyclohexanol
Standard InCHIKey:  HPXRVTGHNJAIIH-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C6H12O/c7-6-4-2-1-3-5-6/h6-7H,1-5H2
SMILES:  C1CCC(CC1)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL32010
PubChem CID:   7966
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0001661] Secondary alcohols
            • [CHEMONTID:0002647] Cyclohexanols

*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
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jep.2005.01.054]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota Fruit n.a. n.a. DOI[10.1016/S0963-9969(99)00095-2]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota Leaves (mother plant) Suwon, Korea 2011-Sep DOI[10.7235/HORT.2013.12200]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota Roots (runner plant) Suwon, Korea 2011-Sep DOI[10.7235/HORT.2013.12200]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota Fruits Suwon, Korea 2012-Nov DOI[10.7235/HORT.2013.12200]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota Leaves Suwon, Korea DOI[10.7235/HORT.2013.12200]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota Runners Suwon, Korea 2011-Sep DOI[10.7235/HORT.2013.12200]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota Leaves (runner plant) Suwon, Korea 2011-Sep DOI[10.7235/HORT.2013.12200]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota Roots (mother plant) Suwon, Korea 2011-Sep DOI[10.7235/HORT.2013.12200]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota n.a. n.a. n.a. PMID[1453178]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota Fruits n.a. n.a. PMID[15568772]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[31181920]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[31418264]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota Fruits n.a. Database[FooDB]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10339 Fragaria x ananassa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10339 Fragaria x ananassa Species Rosaceae 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
NPO10339 NPC325345 n.a. Roots (runner plant) 0.024 n.a. n.a. mg/m3 of FW DOI[10.7235/HORT.2013.12200]

☑ 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
NPT65 Cell Line HepG2 Homo sapiens Potency n.a. 6309.6 nM PMID[557453]
NPT10 Individual Protein Geminin Homo sapiens Potency n.a. 231.1 nM PMID[557453]
NPT27 Others Unspecified EC50 = 1465547840955.91 nM PMID[557450]
NPT419 Organism Oryctolagus cuniculus Oryctolagus cuniculus MES = 8.29 n.a. PMID[557451]
NPT27 Others Unspecified log Ks = 2.67 n.a. PMID[557452]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 18526.0 nM PMID[557453]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 16511.3 nM PMID[557453]
NPT35 Others n.a. LogP = 1.23 n.a. PMID[557454]
NPT1007 Protein Complex GABA-A receptor; alpha-1/beta-2/gamma-2 Homo sapiens Activity = 30.1 % PMID[557455]
NPT2 Others Unspecified Potency n.a. 72021.5 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 9771.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 64765.1 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 38900 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 25554.2 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 NPC325345 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
0.8519 High Similarity NPC560
0.8276 Intermediate Similarity NPC110884
0.8148 Intermediate Similarity NPC213764
0.8148 Intermediate Similarity NPC232554
0.8148 Intermediate Similarity NPC275462
0.7931 Intermediate Similarity NPC159845
0.7857 Intermediate Similarity NPC252154
0.7778 Intermediate Similarity NPC245688
0.7742 Intermediate Similarity NPC267243
0.7742 Intermediate Similarity NPC122962
0.75 Intermediate Similarity NPC193062
0.75 Intermediate Similarity NPC319034
0.75 Intermediate Similarity NPC1748
0.75 Intermediate Similarity NPC72324
0.75 Intermediate Similarity NPC66124
0.7407 Intermediate Similarity NPC39977
0.7407 Intermediate Similarity NPC52403
0.7333 Intermediate Similarity NPC279895
0.7143 Intermediate Similarity NPC199270
0.7059 Intermediate Similarity NPC97967
0.7059 Intermediate Similarity NPC86412
0.7059 Intermediate Similarity NPC192065
0.7059 Intermediate Similarity NPC325034
0.7059 Intermediate Similarity NPC293908
0.7059 Intermediate Similarity NPC66052
0.7037 Intermediate Similarity NPC299484
0.7027 Intermediate Similarity NPC111882
0.7027 Intermediate Similarity NPC88278
0.7027 Intermediate Similarity NPC227707
0.7027 Intermediate Similarity NPC99573
0.7027 Intermediate Similarity NPC102981
0.6897 Remote Similarity NPC88887
0.6875 Remote Similarity NPC24506
0.6875 Remote Similarity NPC112242
0.6875 Remote Similarity NPC147096
0.6875 Remote Similarity NPC163556
0.6875 Remote Similarity NPC185041
0.6875 Remote Similarity NPC225783
0.6875 Remote Similarity NPC236797
0.6857 Remote Similarity NPC474392
0.6857 Remote Similarity NPC474914
0.6667 Remote Similarity NPC149070
0.6667 Remote Similarity NPC127074
0.6667 Remote Similarity NPC294703
0.6667 Remote Similarity NPC126915
0.6667 Remote Similarity NPC187058
0.6667 Remote Similarity NPC197207
0.6667 Remote Similarity NPC182541
0.6579 Remote Similarity NPC266553
0.65 Remote Similarity NPC144891
0.6471 Remote Similarity NPC181516
0.6471 Remote Similarity NPC152759
0.6471 Remote Similarity NPC185538
0.6471 Remote Similarity NPC272998
0.6471 Remote Similarity NPC12231
0.6471 Remote Similarity NPC205141
0.6471 Remote Similarity NPC139131
0.6471 Remote Similarity NPC291158
0.6452 Remote Similarity NPC39869
0.6452 Remote Similarity NPC276332
0.6452 Remote Similarity NPC320326
0.6429 Remote Similarity NPC219266
0.6341 Remote Similarity NPC207656
0.6341 Remote Similarity NPC107091
0.6341 Remote Similarity NPC240994
0.6333 Remote Similarity NPC190797
0.6333 Remote Similarity NPC140389
0.6316 Remote Similarity NPC471282
0.6296 Remote Similarity NPC163707
0.6286 Remote Similarity NPC227267
0.6286 Remote Similarity NPC283682
0.625 Remote Similarity NPC301586
0.625 Remote Similarity NPC52362
0.625 Remote Similarity NPC33415
0.6154 Remote Similarity NPC160261
0.6154 Remote Similarity NPC469759
0.6111 Remote Similarity NPC317203
0.6098 Remote Similarity NPC70756
0.6098 Remote Similarity NPC320240
0.6047 Remote Similarity NPC84030
0.6047 Remote Similarity NPC88638
0.6047 Remote Similarity NPC314613
0.6047 Remote Similarity NPC198540
0.6047 Remote Similarity NPC223468
0.6047 Remote Similarity NPC176309
0.6047 Remote Similarity NPC287550
0.6047 Remote Similarity NPC147343
0.6 Remote Similarity NPC157340
0.6 Remote Similarity NPC114270
0.6 Remote Similarity NPC256186
0.6 Remote Similarity NPC23071
0.5946 Remote Similarity NPC61665
0.5926 Remote Similarity NPC311000
0.5909 Remote Similarity NPC314087
0.5862 Remote Similarity NPC110344
0.5862 Remote Similarity NPC88839
0.5854 Remote Similarity NPC46248
0.5854 Remote Similarity NPC249801
0.5814 Remote Similarity NPC176017
0.5814 Remote Similarity NPC69445
0.5814 Remote Similarity NPC165846
0.5814 Remote Similarity NPC73906
0.5814 Remote Similarity NPC255377
0.5814 Remote Similarity NPC289758
0.5814 Remote Similarity NPC92246
0.5814 Remote Similarity NPC21209
0.5814 Remote Similarity NPC199857
0.5814 Remote Similarity NPC285364
0.5789 Remote Similarity NPC177022
0.5789 Remote Similarity NPC74352
0.5778 Remote Similarity NPC61270
0.5778 Remote Similarity NPC325822
0.5714 Remote Similarity NPC236761
0.5714 Remote Similarity NPC29721
0.5682 Remote Similarity NPC277475
0.5682 Remote Similarity NPC321087
0.5625 Remote Similarity NPC474048

  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 NPC325345 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
1.0 High Similarity NPD8988 Clinical (unspecified phase)
0.7059 Intermediate Similarity NPD9053 Approved
0.7059 Intermediate Similarity NPD9052 Approved
0.7059 Intermediate Similarity NPD9051 Approved
0.7027 Intermediate Similarity NPD8995 Clinical (unspecified phase)
0.7027 Intermediate Similarity NPD8996 Phase 3
0.6667 Remote Similarity NPD8814 Phase 3
0.6471 Remote Similarity NPD2272 Approved
0.6471 Remote Similarity NPD5383 Approved
0.6341 Remote Similarity NPD9219 Approved
0.6341 Remote Similarity NPD9218 Clinical (unspecified phase)
0.6296 Remote Similarity NPD8224 Approved
0.625 Remote Similarity NPD8549 Clinical (unspecified phase)
0.6053 Remote Similarity NPD8976 Approved
0.6053 Remote Similarity NPD8977 Phase 3
0.6047 Remote Similarity NPD384 Approved
0.6047 Remote Similarity NPD385 Approved
0.6 Remote Similarity NPD8226 Approved
0.6 Remote Similarity NPD8225 Phase 3
0.5946 Remote Similarity NPD370 Phase 3
0.5926 Remote Similarity NPD8223 Approved
0.5854 Remote Similarity NPD8958 Phase 2
0.5854 Remote Similarity NPD8957 Approved
0.5814 Remote Similarity NPD8997 Approved
0.5814 Remote Similarity NPD8994 Approved
0.5814 Remote Similarity NPD9000 Phase 3
0.5814 Remote Similarity NPD8993 Phase 1
0.5814 Remote Similarity NPD8998 Phase 2
0.5814 Remote Similarity NPD8999 Phase 3
0.5778 Remote Similarity NPD9061 Clinical (unspecified phase)
0.5714 Remote Similarity NPD9006 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