Structure

Physi-Chem Properties

Molecular Weight:  112.09
Volume:  127.226
LogP:  1.617
LogD:  1.127
LogS:  -1.013
# Rotatable Bonds:  1
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.507
Synthetic Accessibility Score:  3.105
Fsp3:  0.714
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:  -4.211
MDCK Permeability:  0.0002177993446821347
Pgp-inhibitor:  0.0
Pgp-substrate:  0.012
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.22

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.967
Plasma Protein Binding (PPB):  42.20117950439453%
Volume Distribution (VD):  0.77
Pgp-substrate:  56.93796157836914%

ADMET: Metabolism

CYP1A2-inhibitor:  0.43
CYP1A2-substrate:  0.532
CYP2C19-inhibitor:  0.043
CYP2C19-substrate:  0.574
CYP2C9-inhibitor:  0.011
CYP2C9-substrate:  0.435
CYP2D6-inhibitor:  0.014
CYP2D6-substrate:  0.527
CYP3A4-inhibitor:  0.023
CYP3A4-substrate:  0.154

ADMET: Excretion

Clearance (CL):  10.15
Half-life (T1/2):  0.766

ADMET: Toxicity

hERG Blockers:  0.012
Human Hepatotoxicity (H-HT):  0.032
Drug-inuced Liver Injury (DILI):  0.019
AMES Toxicity:  0.022
Rat Oral Acute Toxicity:  0.011
Maximum Recommended Daily Dose:  0.252
Skin Sensitization:  0.932
Carcinogencity:  0.867
Eye Corrosion:  0.918
Eye Irritation:  0.992
Respiratory Toxicity:  0.143

Download Data

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

  Natural Product: NPC269862

Natural Product ID:  NPC269862
Common Name*:   Cyclohex-3-En-1-Ylmethanol
IUPAC Name:   cyclohex-3-en-1-ylmethanol
Synonyms:  
Standard InCHIKey:  VEIYJWQZNGASMA-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H12O/c8-6-7-4-2-1-3-5-7/h1-2,7-8H,3-6H2
SMILES:  C1=CCC(CC1)CO
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3188995
PubChem CID:   15512
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0000286] Primary alcohols

*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
NPO19935 Evodia rutaecarpa Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[7463094]
NPO19935 Evodia rutaecarpa Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[8201313]
NPO19935 Evodia rutaecarpa Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[8699182]
NPO19935 Evodia rutaecarpa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4877 Euodia officinalis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8314 Euodia ruticarpa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16845 Euodia bodinieri Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19935 Evodia rutaecarpa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19935 Evodia rutaecarpa Species Rutaceae 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
NPT153 Individual Protein Androgen Receptor Homo sapiens Potency n.a. 1096.4 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 1380.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 27306 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 61130.6 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 68589.6 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 21689.9 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 54482.7 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 NPC269862 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
0.8222 Intermediate Similarity NPC165651
0.8222 Intermediate Similarity NPC24824
0.8222 Intermediate Similarity NPC210560
0.75 Intermediate Similarity NPC148216
0.75 Intermediate Similarity NPC148163
0.75 Intermediate Similarity NPC251666
0.75 Intermediate Similarity NPC232247
0.75 Intermediate Similarity NPC130209
0.7442 Intermediate Similarity NPC40434
0.7442 Intermediate Similarity NPC34873
0.74 Intermediate Similarity NPC244038
0.7347 Intermediate Similarity NPC62755
0.7234 Intermediate Similarity NPC114841
0.7059 Intermediate Similarity NPC214584
0.7059 Intermediate Similarity NPC26906
0.7037 Intermediate Similarity NPC48891
0.7021 Intermediate Similarity NPC252978
0.7018 Intermediate Similarity NPC269737
0.6957 Remote Similarity NPC188596
0.6923 Remote Similarity NPC306195
0.6923 Remote Similarity NPC157781
0.6923 Remote Similarity NPC179169
0.6923 Remote Similarity NPC177112
0.6923 Remote Similarity NPC35519
0.6923 Remote Similarity NPC71506
0.6923 Remote Similarity NPC181255
0.6852 Remote Similarity NPC298299
0.6842 Remote Similarity NPC66020
0.6786 Remote Similarity NPC10017
0.6735 Remote Similarity NPC87439
0.6735 Remote Similarity NPC76976
0.6731 Remote Similarity NPC200772
0.6724 Remote Similarity NPC68679
0.6724 Remote Similarity NPC207007
0.6724 Remote Similarity NPC321867
0.6667 Remote Similarity NPC63121
0.6667 Remote Similarity NPC197356
0.6604 Remote Similarity NPC294358
0.6604 Remote Similarity NPC40417
0.6604 Remote Similarity NPC35756
0.6557 Remote Similarity NPC267027
0.6557 Remote Similarity NPC476039
0.6557 Remote Similarity NPC222366
0.6557 Remote Similarity NPC286669
0.6552 Remote Similarity NPC240506
0.6545 Remote Similarity NPC227135
0.6538 Remote Similarity NPC26960
0.6538 Remote Similarity NPC182102
0.6538 Remote Similarity NPC474460
0.6538 Remote Similarity NPC329773
0.6531 Remote Similarity NPC108195
0.6522 Remote Similarity NPC15934
0.65 Remote Similarity NPC290367
0.65 Remote Similarity NPC107540
0.6491 Remote Similarity NPC181872
0.6491 Remote Similarity NPC155025
0.6491 Remote Similarity NPC226848
0.6458 Remote Similarity NPC51758
0.6458 Remote Similarity NPC68889
0.6458 Remote Similarity NPC108494
0.6458 Remote Similarity NPC209279
0.6458 Remote Similarity NPC180871
0.6458 Remote Similarity NPC67761
0.6458 Remote Similarity NPC88079
0.6458 Remote Similarity NPC194586
0.6452 Remote Similarity NPC197805
0.6441 Remote Similarity NPC475251
0.6441 Remote Similarity NPC225342
0.6429 Remote Similarity NPC249645
0.6429 Remote Similarity NPC55412
0.6415 Remote Similarity NPC48162
0.64 Remote Similarity NPC140501
0.64 Remote Similarity NPC276825
0.6393 Remote Similarity NPC471200
0.6393 Remote Similarity NPC473722
0.6393 Remote Similarity NPC163678
0.6383 Remote Similarity NPC329762
0.6383 Remote Similarity NPC103236
0.6383 Remote Similarity NPC27444
0.6379 Remote Similarity NPC122239
0.6379 Remote Similarity NPC475931
0.6364 Remote Similarity NPC58957
0.6349 Remote Similarity NPC117804
0.6346 Remote Similarity NPC234597
0.6327 Remote Similarity NPC15162
0.6296 Remote Similarity NPC68014
0.629 Remote Similarity NPC326310
0.629 Remote Similarity NPC202017
0.629 Remote Similarity NPC149680
0.6271 Remote Similarity NPC99487
0.625 Remote Similarity NPC329686
0.625 Remote Similarity NPC281590
0.625 Remote Similarity NPC471560
0.623 Remote Similarity NPC323424
0.623 Remote Similarity NPC225415
0.623 Remote Similarity NPC96793
0.623 Remote Similarity NPC300593
0.6226 Remote Similarity NPC289388
0.6222 Remote Similarity NPC79544
0.6207 Remote Similarity NPC475830
0.619 Remote Similarity NPC45782
0.619 Remote Similarity NPC106613
0.619 Remote Similarity NPC114651
0.619 Remote Similarity NPC171225
0.619 Remote Similarity NPC476650
0.617 Remote Similarity NPC182840
0.617 Remote Similarity NPC255042
0.617 Remote Similarity NPC103213
0.617 Remote Similarity NPC29091
0.6167 Remote Similarity NPC274704
0.6154 Remote Similarity NPC145498
0.614 Remote Similarity NPC473865
0.614 Remote Similarity NPC274396
0.614 Remote Similarity NPC474643
0.6136 Remote Similarity NPC250734
0.6129 Remote Similarity NPC308844
0.6122 Remote Similarity NPC46248
0.6122 Remote Similarity NPC304151
0.6122 Remote Similarity NPC249801
0.6122 Remote Similarity NPC149668
0.6111 Remote Similarity NPC129263
0.6111 Remote Similarity NPC474495
0.6111 Remote Similarity NPC244452
0.6111 Remote Similarity NPC473672
0.6102 Remote Similarity NPC473866
0.6094 Remote Similarity NPC471238
0.6094 Remote Similarity NPC216460
0.6094 Remote Similarity NPC32055
0.6094 Remote Similarity NPC208999
0.6094 Remote Similarity NPC96484
0.6087 Remote Similarity NPC76145
0.6087 Remote Similarity NPC190810
0.6087 Remote Similarity NPC34764
0.6066 Remote Similarity NPC211291
0.6066 Remote Similarity NPC473759
0.6066 Remote Similarity NPC474155
0.6066 Remote Similarity NPC174956
0.6066 Remote Similarity NPC473508
0.6066 Remote Similarity NPC133368
0.6066 Remote Similarity NPC279200
0.6061 Remote Similarity NPC95863
0.6061 Remote Similarity NPC242001
0.6042 Remote Similarity NPC183670
0.6038 Remote Similarity NPC302310
0.6034 Remote Similarity NPC121034
0.6034 Remote Similarity NPC11130
0.6034 Remote Similarity NPC52012
0.6032 Remote Similarity NPC250977
0.6 Remote Similarity NPC471081
0.6 Remote Similarity NPC135648
0.6 Remote Similarity NPC116934
0.6 Remote Similarity NPC170167
0.6 Remote Similarity NPC474248
0.6 Remote Similarity NPC473893
0.597 Remote Similarity NPC471799
0.597 Remote Similarity NPC186042
0.597 Remote Similarity NPC182717
0.5968 Remote Similarity NPC110241
0.5968 Remote Similarity NPC309300
0.5965 Remote Similarity NPC84824
0.5965 Remote Similarity NPC46151
0.5965 Remote Similarity NPC474644
0.5965 Remote Similarity NPC67508
0.5962 Remote Similarity NPC22098
0.5962 Remote Similarity NPC195246
0.5962 Remote Similarity NPC276009
0.5962 Remote Similarity NPC157096
0.5957 Remote Similarity NPC229262
0.5957 Remote Similarity NPC139717
0.5957 Remote Similarity NPC45727
0.5957 Remote Similarity NPC297643
0.5957 Remote Similarity NPC48638
0.5938 Remote Similarity NPC472875
0.5938 Remote Similarity NPC269985
0.5938 Remote Similarity NPC73603
0.5938 Remote Similarity NPC96962
0.5938 Remote Similarity NPC69649
0.5938 Remote Similarity NPC82337
0.5938 Remote Similarity NPC68703
0.5932 Remote Similarity NPC329819
0.5926 Remote Similarity NPC288381
0.5926 Remote Similarity NPC20934
0.5918 Remote Similarity NPC269823
0.5918 Remote Similarity NPC144023
0.5918 Remote Similarity NPC469713
0.5909 Remote Similarity NPC49422
0.5909 Remote Similarity NPC34834
0.5909 Remote Similarity NPC107848
0.5909 Remote Similarity NPC92801
0.5909 Remote Similarity NPC9161
0.5909 Remote Similarity NPC213749
0.5902 Remote Similarity NPC282694
0.5902 Remote Similarity NPC79576
0.5902 Remote Similarity NPC194208
0.5893 Remote Similarity NPC26102
0.5893 Remote Similarity NPC477724
0.5893 Remote Similarity NPC187361
0.5893 Remote Similarity NPC474496
0.5893 Remote Similarity NPC165755
0.5893 Remote Similarity NPC217188

  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 NPC269862 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
0.75 Intermediate Similarity NPD342 Phase 1
0.6724 Remote Similarity NPD368 Approved
0.6429 Remote Similarity NPD4219 Approved
0.64 Remote Similarity NPD4265 Approved
0.6087 Remote Similarity NPD319 Phase 1
0.6038 Remote Similarity NPD9410 Clinical (unspecified phase)
0.5909 Remote Similarity NPD7143 Approved
0.5909 Remote Similarity NPD7144 Approved
0.5821 Remote Similarity NPD7152 Approved
0.5821 Remote Similarity NPD7151 Approved
0.5821 Remote Similarity NPD7150 Approved
0.5797 Remote Similarity NPD8264 Approved
0.5758 Remote Similarity NPD6923 Approved
0.5758 Remote Similarity NPD6922 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