Structure

Physi-Chem Properties

Molecular Weight:  156.15
Volume:  187.67
LogP:  3.252
LogD:  2.424
LogS:  -2.398
# Rotatable Bonds:  4
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.62
Synthetic Accessibility Score:  3.13
Fsp3:  0.8
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.314
MDCK Permeability:  1.878896728157997e-05
Pgp-inhibitor:  0.037
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.176
30% Bioavailability (F30%):  0.006

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.846
Plasma Protein Binding (PPB):  85.65001678466797%
Volume Distribution (VD):  1.126
Pgp-substrate:  18.68400764465332%

ADMET: Metabolism

CYP1A2-inhibitor:  0.261
CYP1A2-substrate:  0.466
CYP2C19-inhibitor:  0.16
CYP2C19-substrate:  0.886
CYP2C9-inhibitor:  0.062
CYP2C9-substrate:  0.491
CYP2D6-inhibitor:  0.027
CYP2D6-substrate:  0.147
CYP3A4-inhibitor:  0.052
CYP3A4-substrate:  0.218

ADMET: Excretion

Clearance (CL):  14.712
Half-life (T1/2):  0.529

ADMET: Toxicity

hERG Blockers:  0.022
Human Hepatotoxicity (H-HT):  0.438
Drug-inuced Liver Injury (DILI):  0.038
AMES Toxicity:  0.004
Rat Oral Acute Toxicity:  0.01
Maximum Recommended Daily Dose:  0.018
Skin Sensitization:  0.365
Carcinogencity:  0.205
Eye Corrosion:  0.635
Eye Irritation:  0.984
Respiratory Toxicity:  0.013

Download Data

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

  Natural Product: NPC188596

Natural Product ID:  NPC188596
Common Name*:   3,7-Dimethyloct-6-En-3-Ol
IUPAC Name:   3,7-dimethyloct-6-en-3-ol
Synonyms:  
Standard InCHIKey:  JRTBBCBDKSRRCY-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C10H20O/c1-5-10(4,11)8-6-7-9(2)3/h7,11H,5-6,8H2,1-4H3
SMILES:  CCC(CCC=C(C)C)(O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3183324
PubChem CID:   86749
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0001127] Acyclic monoterpenoids

*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
NPO7510 Ixora chinensis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7510 Ixora chinensis Species Rubiaceae 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. 12299.8 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 30637.9 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 68589.6 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 48557.7 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 54941 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 NPC188596 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
0.878 High Similarity NPC88079
0.878 High Similarity NPC108494
0.878 High Similarity NPC209279
0.878 High Similarity NPC180871
0.878 High Similarity NPC68889
0.878 High Similarity NPC194586
0.878 High Similarity NPC51758
0.878 High Similarity NPC67761
0.8261 Intermediate Similarity NPC329773
0.8182 Intermediate Similarity NPC165651
0.8182 Intermediate Similarity NPC210560
0.8182 Intermediate Similarity NPC24824
0.8085 Intermediate Similarity NPC214584
0.8085 Intermediate Similarity NPC26906
0.7917 Intermediate Similarity NPC157781
0.7917 Intermediate Similarity NPC177112
0.7917 Intermediate Similarity NPC179169
0.7917 Intermediate Similarity NPC35519
0.7917 Intermediate Similarity NPC181255
0.7917 Intermediate Similarity NPC306195
0.7917 Intermediate Similarity NPC68014
0.7917 Intermediate Similarity NPC71506
0.7857 Intermediate Similarity NPC56917
0.75 Intermediate Similarity NPC474460
0.7333 Intermediate Similarity NPC15162
0.7292 Intermediate Similarity NPC62755
0.72 Intermediate Similarity NPC208638
0.72 Intermediate Similarity NPC35756
0.72 Intermediate Similarity NPC40417
0.72 Intermediate Similarity NPC294358
0.717 Intermediate Similarity NPC278550
0.7115 Intermediate Similarity NPC281590
0.7115 Intermediate Similarity NPC218525
0.7115 Intermediate Similarity NPC227135
0.7115 Intermediate Similarity NPC251666
0.7115 Intermediate Similarity NPC232247
0.7083 Intermediate Similarity NPC100445
0.7037 Intermediate Similarity NPC181872
0.7 Intermediate Similarity NPC244038
0.6981 Remote Similarity NPC48891
0.6981 Remote Similarity NPC274396
0.6977 Remote Similarity NPC34873
0.6977 Remote Similarity NPC40434
0.6957 Remote Similarity NPC269862
0.6923 Remote Similarity NPC474127
0.6909 Remote Similarity NPC475931
0.6909 Remote Similarity NPC469321
0.6909 Remote Similarity NPC5698
0.6905 Remote Similarity NPC92224
0.6905 Remote Similarity NPC282119
0.6852 Remote Similarity NPC52012
0.6818 Remote Similarity NPC182840
0.6818 Remote Similarity NPC255042
0.6818 Remote Similarity NPC29091
0.6818 Remote Similarity NPC103213
0.68 Remote Similarity NPC26960
0.68 Remote Similarity NPC288381
0.68 Remote Similarity NPC20934
0.68 Remote Similarity NPC182102
0.6792 Remote Similarity NPC148163
0.6792 Remote Similarity NPC298299
0.6792 Remote Similarity NPC329686
0.6792 Remote Similarity NPC130209
0.6792 Remote Similarity NPC148216
0.6786 Remote Similarity NPC252809
0.6786 Remote Similarity NPC240506
0.6786 Remote Similarity NPC135648
0.6786 Remote Similarity NPC323153
0.6786 Remote Similarity NPC66020
0.675 Remote Similarity NPC206088
0.6744 Remote Similarity NPC34764
0.6744 Remote Similarity NPC76145
0.6744 Remote Similarity NPC190810
0.6744 Remote Similarity NPC185839
0.6731 Remote Similarity NPC192962
0.6731 Remote Similarity NPC165755
0.6727 Remote Similarity NPC155025
0.6727 Remote Similarity NPC226848
0.6667 Remote Similarity NPC474495
0.6667 Remote Similarity NPC475251
0.6667 Remote Similarity NPC473672
0.6667 Remote Similarity NPC48162
0.6667 Remote Similarity NPC140501
0.6667 Remote Similarity NPC79576
0.6667 Remote Similarity NPC207007
0.6667 Remote Similarity NPC321867
0.6667 Remote Similarity NPC282694
0.6667 Remote Similarity NPC87439
0.6667 Remote Similarity NPC194208
0.6667 Remote Similarity NPC63111
0.6667 Remote Similarity NPC210346
0.6667 Remote Similarity NPC68679
0.6607 Remote Similarity NPC122239
0.6607 Remote Similarity NPC278202
0.66 Remote Similarity NPC91765
0.66 Remote Similarity NPC15912
0.66 Remote Similarity NPC234597
0.6596 Remote Similarity NPC116934
0.6596 Remote Similarity NPC252978
0.6591 Remote Similarity NPC229262
0.6591 Remote Similarity NPC180840
0.6591 Remote Similarity NPC139717
0.6591 Remote Similarity NPC297643
0.6585 Remote Similarity NPC213749
0.6552 Remote Similarity NPC174956
0.6552 Remote Similarity NPC81615
0.6552 Remote Similarity NPC474480
0.6531 Remote Similarity NPC276009
0.6531 Remote Similarity NPC8610
0.6531 Remote Similarity NPC262558
0.6531 Remote Similarity NPC22098
0.6531 Remote Similarity NPC195246
0.6522 Remote Similarity NPC269823
0.6512 Remote Similarity NPC38497
0.6491 Remote Similarity NPC469694
0.6491 Remote Similarity NPC471081
0.6491 Remote Similarity NPC99487
0.6481 Remote Similarity NPC223604
0.6481 Remote Similarity NPC297280
0.6481 Remote Similarity NPC67367
0.6471 Remote Similarity NPC32351
0.6471 Remote Similarity NPC27264
0.6471 Remote Similarity NPC289388
0.6471 Remote Similarity NPC131623
0.6471 Remote Similarity NPC225974
0.6458 Remote Similarity NPC108195
0.6444 Remote Similarity NPC15934
0.6441 Remote Similarity NPC300593
0.6429 Remote Similarity NPC475830
0.6415 Remote Similarity NPC217188
0.6415 Remote Similarity NPC474496
0.64 Remote Similarity NPC91962
0.6383 Remote Similarity NPC256766
0.6383 Remote Similarity NPC213538
0.6379 Remote Similarity NPC274704
0.6379 Remote Similarity NPC64971
0.6379 Remote Similarity NPC225342
0.6379 Remote Similarity NPC64985
0.6364 Remote Similarity NPC141699
0.6364 Remote Similarity NPC39068
0.6364 Remote Similarity NPC179024
0.6346 Remote Similarity NPC178586
0.6346 Remote Similarity NPC27438
0.6346 Remote Similarity NPC148056
0.6346 Remote Similarity NPC244452
0.6341 Remote Similarity NPC3649
0.6341 Remote Similarity NPC66577
0.6341 Remote Similarity NPC471327
0.6341 Remote Similarity NPC100879
0.6333 Remote Similarity NPC261782
0.6333 Remote Similarity NPC469326
0.6333 Remote Similarity NPC471200
0.6333 Remote Similarity NPC205618
0.6333 Remote Similarity NPC308844
0.6327 Remote Similarity NPC76976
0.6327 Remote Similarity NPC276825
0.6327 Remote Similarity NPC160628
0.6304 Remote Similarity NPC183670
0.6275 Remote Similarity NPC267110
0.6275 Remote Similarity NPC302310
0.6271 Remote Similarity NPC279200
0.6271 Remote Similarity NPC190049
0.6271 Remote Similarity NPC473759
0.6271 Remote Similarity NPC474155
0.6271 Remote Similarity NPC473508
0.6271 Remote Similarity NPC322457
0.625 Remote Similarity NPC216921
0.625 Remote Similarity NPC106819
0.625 Remote Similarity NPC165808
0.625 Remote Similarity NPC123965
0.625 Remote Similarity NPC138113
0.625 Remote Similarity NPC115959
0.625 Remote Similarity NPC301972
0.623 Remote Similarity NPC279434
0.623 Remote Similarity NPC267027
0.623 Remote Similarity NPC197089
0.623 Remote Similarity NPC250977
0.6226 Remote Similarity NPC216407
0.6226 Remote Similarity NPC170167
0.6226 Remote Similarity NPC151919
0.6222 Remote Similarity NPC48638
0.6222 Remote Similarity NPC45727
0.6222 Remote Similarity NPC266298
0.6222 Remote Similarity NPC155880
0.6222 Remote Similarity NPC239039
0.6222 Remote Similarity NPC92863
0.6207 Remote Similarity NPC176621
0.617 Remote Similarity NPC144023
0.617 Remote Similarity NPC120926
0.617 Remote Similarity NPC218918
0.6167 Remote Similarity NPC309300
0.6167 Remote Similarity NPC225415
0.6167 Remote Similarity NPC290367
0.6154 Remote Similarity NPC163984
0.6154 Remote Similarity NPC58970
0.6154 Remote Similarity NPC176819
0.614 Remote Similarity NPC10017
0.614 Remote Similarity NPC329819
0.6129 Remote Similarity NPC278895
0.6129 Remote Similarity NPC73603

  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 NPC188596 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
0.6792 Remote Similarity NPD342 Phase 1
0.6744 Remote Similarity NPD319 Phase 1
0.6667 Remote Similarity NPD4265 Approved
0.6667 Remote Similarity NPD368 Approved
0.6444 Remote Similarity NPD5783 Phase 3
0.6327 Remote Similarity NPD39 Approved
0.623 Remote Similarity NPD7331 Phase 2
0.6071 Remote Similarity NPD4219 Approved
0.6 Remote Similarity NPD4222 Approved
0.5962 Remote Similarity NPD3173 Approved
0.5918 Remote Similarity NPD5326 Phase 3
0.5758 Remote Similarity NPD4243 Approved
0.5714 Remote Similarity NPD539 Approved
0.5692 Remote Similarity NPD6923 Approved
0.5692 Remote Similarity NPD6922 Approved
0.5672 Remote Similarity NPD4732 Discontinued
0.566 Remote Similarity NPD4220 Pre-registration
0.5625 Remote Similarity NPD1153 Clinical (unspecified phase)
0.5606 Remote Similarity NPD7143 Approved
0.5606 Remote Similarity NPD7144 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