Structure

Physi-Chem Properties

Molecular Weight:  110.07
Volume:  124.589
LogP:  1.478
LogD:  1.107
LogS:  -1.246
# Rotatable Bonds:  1
TPSA:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.369
Synthetic Accessibility Score:  3.56
Fsp3:  0.571
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.403
MDCK Permeability:  2.70135988102993e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.111

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.984
Plasma Protein Binding (PPB):  24.952184677124023%
Volume Distribution (VD):  1.4
Pgp-substrate:  67.43377685546875%

ADMET: Metabolism

CYP1A2-inhibitor:  0.195
CYP1A2-substrate:  0.467
CYP2C19-inhibitor:  0.043
CYP2C19-substrate:  0.266
CYP2C9-inhibitor:  0.008
CYP2C9-substrate:  0.501
CYP2D6-inhibitor:  0.052
CYP2D6-substrate:  0.426
CYP3A4-inhibitor:  0.067
CYP3A4-substrate:  0.18

ADMET: Excretion

Clearance (CL):  11.742
Half-life (T1/2):  0.791

ADMET: Toxicity

hERG Blockers:  0.022
Human Hepatotoxicity (H-HT):  0.021
Drug-inuced Liver Injury (DILI):  0.026
AMES Toxicity:  0.151
Rat Oral Acute Toxicity:  0.007
Maximum Recommended Daily Dose:  0.291
Skin Sensitization:  0.975
Carcinogencity:  0.413
Eye Corrosion:  0.994
Eye Irritation:  0.995
Respiratory Toxicity:  0.712

Download Data

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

  Natural Product: NPC114841

Natural Product ID:  NPC114841
Common Name*:   Cyclohex-3-Ene-1-Carbaldehyde
IUPAC Name:   cyclohex-3-ene-1-carbaldehyde
Synonyms:  
Standard InCHIKey:  DCFDVJPDXYGCOK-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H10O/c8-6-7-4-2-1-3-5-7/h1-2,6-7H,3-5H2
SMILES:  O=CC1CCC=CC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3188123
PubChem CID:   7508
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0003940] Organic oxides

*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
NPO15730.2 Citrus medica var. sarcodactylis Varieties Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15730.2 Citrus medica var. sarcodactylis Varieties Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15730.2 Citrus medica var. sarcodactylis Varieties Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]

☑ 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. 67962.3 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 5398.4 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 NPC114841 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
0.8261 Intermediate Similarity NPC276009
0.8261 Intermediate Similarity NPC195246
0.8261 Intermediate Similarity NPC22098
0.8 Intermediate Similarity NPC106819
0.7843 Intermediate Similarity NPC209431
0.7843 Intermediate Similarity NPC100809
0.76 Intermediate Similarity NPC30433
0.7347 Intermediate Similarity NPC91962
0.7234 Intermediate Similarity NPC269862
0.717 Intermediate Similarity NPC95581
0.7059 Intermediate Similarity NPC32351
0.7059 Intermediate Similarity NPC163984
0.7059 Intermediate Similarity NPC58970
0.7059 Intermediate Similarity NPC176819
0.6957 Remote Similarity NPC113082
0.6939 Remote Similarity NPC239754
0.68 Remote Similarity NPC110234
0.68 Remote Similarity NPC163751
0.68 Remote Similarity NPC44363
0.6792 Remote Similarity NPC22182
0.6739 Remote Similarity NPC33761
0.6727 Remote Similarity NPC46151
0.6727 Remote Similarity NPC188789
0.6667 Remote Similarity NPC279300
0.6667 Remote Similarity NPC37644
0.6667 Remote Similarity NPC324812
0.6667 Remote Similarity NPC268564
0.661 Remote Similarity NPC269737
0.6604 Remote Similarity NPC64866
0.66 Remote Similarity NPC166788
0.6596 Remote Similarity NPC48930
0.6596 Remote Similarity NPC101147
0.6557 Remote Similarity NPC268039
0.6545 Remote Similarity NPC250539
0.6531 Remote Similarity NPC292463
0.6522 Remote Similarity NPC92863
0.6522 Remote Similarity NPC155880
0.6491 Remote Similarity NPC22019
0.6491 Remote Similarity NPC208749
0.6491 Remote Similarity NPC321568
0.6491 Remote Similarity NPC281986
0.6481 Remote Similarity NPC170167
0.6481 Remote Similarity NPC216407
0.6458 Remote Similarity NPC33489
0.6444 Remote Similarity NPC75204
0.64 Remote Similarity NPC25771
0.6379 Remote Similarity NPC311852
0.6349 Remote Similarity NPC193770
0.6349 Remote Similarity NPC4370
0.6349 Remote Similarity NPC290350
0.6327 Remote Similarity NPC67920
0.6327 Remote Similarity NPC287397
0.6327 Remote Similarity NPC298710
0.6327 Remote Similarity NPC208936
0.6316 Remote Similarity NPC473733
0.6304 Remote Similarity NPC254764
0.6296 Remote Similarity NPC27438
0.6296 Remote Similarity NPC244452
0.6296 Remote Similarity NPC48162
0.6296 Remote Similarity NPC234829
0.625 Remote Similarity NPC155198
0.625 Remote Similarity NPC323278
0.625 Remote Similarity NPC18205
0.625 Remote Similarity NPC12319
0.6226 Remote Similarity NPC234597
0.6222 Remote Similarity NPC72258
0.6154 Remote Similarity NPC236355
0.6154 Remote Similarity NPC8610
0.6154 Remote Similarity NPC262558
0.6154 Remote Similarity NPC14917
0.6154 Remote Similarity NPC4079
0.614 Remote Similarity NPC477984
0.6129 Remote Similarity NPC52449
0.6129 Remote Similarity NPC169275
0.6111 Remote Similarity NPC289388
0.6111 Remote Similarity NPC15325
0.6111 Remote Similarity NPC118788
0.6102 Remote Similarity NPC308108
0.6102 Remote Similarity NPC170799
0.6087 Remote Similarity NPC38497
0.6071 Remote Similarity NPC14002
0.6071 Remote Similarity NPC23117
0.6034 Remote Similarity NPC252860
0.6 Remote Similarity NPC244038
0.6 Remote Similarity NPC276764
0.6 Remote Similarity NPC472304
0.597 Remote Similarity NPC304983
0.597 Remote Similarity NPC474562
0.5968 Remote Similarity NPC202118
0.5968 Remote Similarity NPC197238
0.5965 Remote Similarity NPC63396
0.5965 Remote Similarity NPC5626
0.5965 Remote Similarity NPC202850
0.5962 Remote Similarity NPC191337
0.5962 Remote Similarity NPC210560
0.5962 Remote Similarity NPC165651
0.5962 Remote Similarity NPC24824
0.5957 Remote Similarity NPC76145
0.5957 Remote Similarity NPC190810
0.5957 Remote Similarity NPC185839
0.5957 Remote Similarity NPC8416
0.5957 Remote Similarity NPC34764
0.5952 Remote Similarity NPC287782
0.5932 Remote Similarity NPC115385
0.5918 Remote Similarity NPC183670
0.5909 Remote Similarity NPC199557
0.5902 Remote Similarity NPC127582
0.5893 Remote Similarity NPC471751
0.5873 Remote Similarity NPC34883
0.5873 Remote Similarity NPC469662
0.587 Remote Similarity NPC218357
0.5862 Remote Similarity NPC275472
0.5849 Remote Similarity NPC471752
0.5849 Remote Similarity NPC100380
0.5846 Remote Similarity NPC106613
0.5833 Remote Similarity NPC48638
0.5833 Remote Similarity NPC229262
0.5833 Remote Similarity NPC45727
0.5833 Remote Similarity NPC27610
0.5833 Remote Similarity NPC180840
0.5833 Remote Similarity NPC139717
0.5833 Remote Similarity NPC329819
0.5833 Remote Similarity NPC56905
0.5833 Remote Similarity NPC297643
0.5818 Remote Similarity NPC116906
0.5818 Remote Similarity NPC228776
0.5806 Remote Similarity NPC213152
0.58 Remote Similarity NPC144023
0.5797 Remote Similarity NPC211641
0.5797 Remote Similarity NPC128346
0.5797 Remote Similarity NPC219232
0.5789 Remote Similarity NPC474141
0.5789 Remote Similarity NPC45283
0.5781 Remote Similarity NPC183422
0.5781 Remote Similarity NPC251118
0.5778 Remote Similarity NPC213749
0.5769 Remote Similarity NPC477686
0.5745 Remote Similarity NPC282119
0.5714 Remote Similarity NPC288253
0.5714 Remote Similarity NPC165695
0.5692 Remote Similarity NPC323005
0.5692 Remote Similarity NPC477982
0.5686 Remote Similarity NPC187922
0.5686 Remote Similarity NPC177470
0.5672 Remote Similarity NPC162867
0.5672 Remote Similarity NPC61702
0.5672 Remote Similarity NPC261398
0.5667 Remote Similarity NPC193695
0.5667 Remote Similarity NPC165808
0.5667 Remote Similarity NPC230823
0.5667 Remote Similarity NPC49575
0.5667 Remote Similarity NPC267626
0.5667 Remote Similarity NPC55004
0.5652 Remote Similarity NPC186042
0.5652 Remote Similarity NPC271437
0.5645 Remote Similarity NPC19241
0.5636 Remote Similarity NPC477789
0.5636 Remote Similarity NPC163345
0.5634 Remote Similarity NPC469796
0.5634 Remote Similarity NPC19907
0.5634 Remote Similarity NPC242722
0.5634 Remote Similarity NPC469793
0.5625 Remote Similarity NPC212210
0.5625 Remote Similarity NPC285371
0.5625 Remote Similarity NPC24833
0.5625 Remote Similarity NPC4638
0.5625 Remote Similarity NPC475124
0.5625 Remote Similarity NPC150162
0.5625 Remote Similarity NPC6697
0.5614 Remote Similarity NPC151919
0.5614 Remote Similarity NPC294358
0.5614 Remote Similarity NPC40417
0.5606 Remote Similarity NPC269985
0.5606 Remote Similarity NPC472875
0.56 Remote Similarity NPC111474

  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 NPC114841 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
0.6102 Remote Similarity NPD287 Approved
0.5957 Remote Similarity NPD319 Phase 1
0.5741 Remote Similarity NPD5343 Approved
0.5714 Remote Similarity NPD5783 Phase 3
0.566 Remote Similarity NPD3174 Discontinued

  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