Structure

Physi-Chem Properties

Molecular Weight:  260.18
Volume:  304.35
LogP:  3.801
LogD:  3.739
LogS:  -3.782
# Rotatable Bonds:  8
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.4
Synthetic Accessibility Score:  4.22
Fsp3:  0.529
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.577
MDCK Permeability:  2.6066365535371006e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.008
Human Intestinal Absorption (HIA):  0.143
20% Bioavailability (F20%):  0.996
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.545
Plasma Protein Binding (PPB):  100.7857437133789%
Volume Distribution (VD):  1.63
Pgp-substrate:  1.6146001815795898%

ADMET: Metabolism

CYP1A2-inhibitor:  0.41
CYP1A2-substrate:  0.512
CYP2C19-inhibitor:  0.909
CYP2C19-substrate:  0.675
CYP2C9-inhibitor:  0.888
CYP2C9-substrate:  0.977
CYP2D6-inhibitor:  0.067
CYP2D6-substrate:  0.496
CYP3A4-inhibitor:  0.901
CYP3A4-substrate:  0.175

ADMET: Excretion

Clearance (CL):  9.539
Half-life (T1/2):  0.85

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.254
Drug-inuced Liver Injury (DILI):  0.921
AMES Toxicity:  0.836
Rat Oral Acute Toxicity:  0.996
Maximum Recommended Daily Dose:  1.0
Skin Sensitization:  0.956
Carcinogencity:  0.35
Eye Corrosion:  0.957
Eye Irritation:  0.977
Respiratory Toxicity:  0.99

Download Data

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

  Natural Product: NPC153538

Natural Product ID:  NPC153538
Common Name*:   Dendroarboreol A
IUPAC Name:   (3S,8S,9Z)-heptadeca-9,16-dien-4,6-diyne-3,8-diol
Synonyms:  
Standard InCHIKey:  XVWSXBIPJCKJCU-RCQSYPNMSA-N
Standard InCHI:  InChI=1S/C17H24O2/c1-3-5-6-7-8-9-10-14-17(19)15-12-11-13-16(18)4-2/h3,10,14,16-19H,1,4-9H2,2H3/b14-10-/t16-,17-/m0/s1
SMILES:  CC[C@@H](C#CC#C[C@H](/C=CCCCCCC=C)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL459425
PubChem CID:   5469787
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001334] Fatty alcohols
          • [CHEMONTID:0002951] Long-chain fatty 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
NPO22011 Myrmekioderma styx Species n.a. n.a. n.a. n.a. n.a. PMID[1431947]
NPO22011 Myrmekioderma styx Species n.a. n.a. n.a. n.a. n.a. PMID[1453179]
NPO21711 Dendropanax arboreus Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[8792622]
NPO22185 Cocculus indicus Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22185 Cocculus indicus Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21369 Paullinia scarlatina Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21711 Dendropanax arboreus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12139 Cylindrotheca closterium Species Bacillariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19387 Hazardia squarrosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22185 Cocculus indicus Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21236 Annona crassiflora Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3495 Matsucoccus feytaudi Species Margarodidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22011 Myrmekioderma styx Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO22300 Soulamea amara Species Simaroubaceae 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
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. GI50 = 4600.0 nM PMID[498355]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. TGI = 14000.0 nM PMID[498355]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. LC50 = 25000.0 nM PMID[498355]

☑ 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 NPC153538 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
0.9783 High Similarity NPC72699
0.9574 High Similarity NPC93639
0.9574 High Similarity NPC151782
0.9565 High Similarity NPC248884
0.9565 High Similarity NPC31194
0.9565 High Similarity NPC85079
0.9556 High Similarity NPC124183
0.9556 High Similarity NPC35141
0.9167 High Similarity NPC59408
0.9167 High Similarity NPC71053
0.9149 High Similarity NPC125122
0.9149 High Similarity NPC471280
0.9149 High Similarity NPC471275
0.9149 High Similarity NPC471276
0.913 High Similarity NPC19834
0.913 High Similarity NPC55063
0.9111 High Similarity NPC101616
0.9 High Similarity NPC256209
0.9 High Similarity NPC110732
0.9 High Similarity NPC49059
0.898 High Similarity NPC142092
0.8958 High Similarity NPC249670
0.8958 High Similarity NPC473913
0.8958 High Similarity NPC471281
0.8958 High Similarity NPC474642
0.8958 High Similarity NPC291437
0.8958 High Similarity NPC199286
0.8958 High Similarity NPC477727
0.8958 High Similarity NPC328784
0.8913 High Similarity NPC269074
0.8776 High Similarity NPC76198
0.8776 High Similarity NPC197272
0.8776 High Similarity NPC55383
0.8776 High Similarity NPC471959
0.8776 High Similarity NPC477723
0.8776 High Similarity NPC256656
0.8776 High Similarity NPC475477
0.8776 High Similarity NPC170776
0.8776 High Similarity NPC224148
0.8776 High Similarity NPC9273
0.8776 High Similarity NPC329608
0.8776 High Similarity NPC89824
0.8776 High Similarity NPC294278
0.8776 High Similarity NPC165447
0.875 High Similarity NPC302310
0.8723 High Similarity NPC180575
0.8667 High Similarity NPC304151
0.8627 High Similarity NPC473532
0.8462 Intermediate Similarity NPC473910
0.8462 Intermediate Similarity NPC477726
0.8462 Intermediate Similarity NPC473721
0.8462 Intermediate Similarity NPC475353
0.8462 Intermediate Similarity NPC473725
0.8462 Intermediate Similarity NPC477725
0.8462 Intermediate Similarity NPC473896
0.8462 Intermediate Similarity NPC473735
0.84 Intermediate Similarity NPC129263
0.8333 Intermediate Similarity NPC157096
0.8302 Intermediate Similarity NPC161838
0.8302 Intermediate Similarity NPC471960
0.8302 Intermediate Similarity NPC470967
0.8302 Intermediate Similarity NPC475384
0.8302 Intermediate Similarity NPC470969
0.8302 Intermediate Similarity NPC477661
0.8302 Intermediate Similarity NPC473847
0.8302 Intermediate Similarity NPC470968
0.8302 Intermediate Similarity NPC470966
0.8298 Intermediate Similarity NPC108195
0.8269 Intermediate Similarity NPC48058
0.8148 Intermediate Similarity NPC212730
0.8148 Intermediate Similarity NPC265551
0.8148 Intermediate Similarity NPC193975
0.8148 Intermediate Similarity NPC470970
0.8125 Intermediate Similarity NPC276825
0.8113 Intermediate Similarity NPC474513
0.8113 Intermediate Similarity NPC471239
0.8113 Intermediate Similarity NPC470963
0.8113 Intermediate Similarity NPC474644
0.8113 Intermediate Similarity NPC146551
0.8113 Intermediate Similarity NPC152668
0.8077 Intermediate Similarity NPC34577
0.8077 Intermediate Similarity NPC61177
0.8039 Intermediate Similarity NPC474495
0.8039 Intermediate Similarity NPC473672
0.8 Intermediate Similarity NPC15934
0.7963 Intermediate Similarity NPC474643
0.7963 Intermediate Similarity NPC311648
0.7963 Intermediate Similarity NPC473865
0.7963 Intermediate Similarity NPC470964
0.7872 Intermediate Similarity NPC206906
0.7872 Intermediate Similarity NPC149668
0.7843 Intermediate Similarity NPC473768
0.7826 Intermediate Similarity NPC103236
0.7826 Intermediate Similarity NPC27444
0.7826 Intermediate Similarity NPC329762
0.7818 Intermediate Similarity NPC48968
0.7818 Intermediate Similarity NPC44542
0.7818 Intermediate Similarity NPC472445
0.7818 Intermediate Similarity NPC594
0.7759 Intermediate Similarity NPC29697
0.7736 Intermediate Similarity NPC477724
0.7736 Intermediate Similarity NPC26102
0.7736 Intermediate Similarity NPC187361
0.7736 Intermediate Similarity NPC474496
0.7736 Intermediate Similarity NPC284224
0.7719 Intermediate Similarity NPC471278
0.7708 Intermediate Similarity NPC116934
0.7692 Intermediate Similarity NPC29234
0.7586 Intermediate Similarity NPC271282
0.7586 Intermediate Similarity NPC325929
0.7586 Intermediate Similarity NPC66460
0.7586 Intermediate Similarity NPC475984
0.7547 Intermediate Similarity NPC35756
0.7544 Intermediate Similarity NPC473652
0.7544 Intermediate Similarity NPC222852
0.75 Intermediate Similarity NPC46248
0.75 Intermediate Similarity NPC249801
0.75 Intermediate Similarity NPC474460
0.7458 Intermediate Similarity NPC470965
0.7455 Intermediate Similarity NPC317899
0.7407 Intermediate Similarity NPC217188
0.74 Intermediate Similarity NPC160628
0.74 Intermediate Similarity NPC140501
0.7368 Intermediate Similarity NPC181872
0.7333 Intermediate Similarity NPC226592
0.7333 Intermediate Similarity NPC470320
0.7333 Intermediate Similarity NPC213767
0.7308 Intermediate Similarity NPC475153
0.7308 Intermediate Similarity NPC267110
0.7292 Intermediate Similarity NPC269823
0.7288 Intermediate Similarity NPC168407
0.7234 Intermediate Similarity NPC255042
0.7234 Intermediate Similarity NPC182840
0.7234 Intermediate Similarity NPC306850
0.7234 Intermediate Similarity NPC29091
0.7234 Intermediate Similarity NPC103213
0.7222 Intermediate Similarity NPC473705
0.72 Intermediate Similarity NPC138935
0.7193 Intermediate Similarity NPC121034
0.7174 Intermediate Similarity NPC216416
0.717 Intermediate Similarity NPC288381
0.717 Intermediate Similarity NPC473487
0.717 Intermediate Similarity NPC20934
0.717 Intermediate Similarity NPC475071
0.7143 Intermediate Similarity NPC256766
0.7143 Intermediate Similarity NPC213538
0.7143 Intermediate Similarity NPC227135
0.7143 Intermediate Similarity NPC329686
0.7119 Intermediate Similarity NPC327112
0.7111 Intermediate Similarity NPC58957
0.7069 Intermediate Similarity NPC226848
0.7059 Intermediate Similarity NPC474202
0.7059 Intermediate Similarity NPC76976
0.7059 Intermediate Similarity NPC474362
0.7021 Intermediate Similarity NPC34873
0.7021 Intermediate Similarity NPC40434
0.7018 Intermediate Similarity NPC324224
0.7018 Intermediate Similarity NPC472808
0.7 Intermediate Similarity NPC252978
0.7 Intermediate Similarity NPC477829
0.6964 Remote Similarity NPC300121
0.6964 Remote Similarity NPC189677
0.6957 Remote Similarity NPC79544
0.6949 Remote Similarity NPC473866
0.6949 Remote Similarity NPC475931
0.6949 Remote Similarity NPC122239
0.6897 Remote Similarity NPC471279
0.6897 Remote Similarity NPC474577
0.6897 Remote Similarity NPC471277
0.6889 Remote Similarity NPC250734
0.6889 Remote Similarity NPC81989
0.6885 Remote Similarity NPC55068
0.6852 Remote Similarity NPC182102
0.6852 Remote Similarity NPC26960
0.6842 Remote Similarity NPC251666
0.6842 Remote Similarity NPC232247
0.6809 Remote Similarity NPC174396
0.68 Remote Similarity NPC31121
0.678 Remote Similarity NPC155025
0.6727 Remote Similarity NPC200772
0.6727 Remote Similarity NPC244038
0.6724 Remote Similarity NPC48891
0.6721 Remote Similarity NPC26810
0.6721 Remote Similarity NPC113293
0.6719 Remote Similarity NPC473752
0.6667 Remote Similarity NPC136164
0.6667 Remote Similarity NPC318306
0.6667 Remote Similarity NPC322002
0.6667 Remote Similarity NPC308844
0.6667 Remote Similarity NPC255863
0.6667 Remote Similarity NPC474267
0.6667 Remote Similarity NPC269615
0.6667 Remote Similarity NPC245947
0.6667 Remote Similarity NPC322186
0.661 Remote Similarity NPC71755
0.6607 Remote Similarity NPC106531
0.6557 Remote Similarity NPC130807
0.6557 Remote Similarity NPC328311
0.6557 Remote Similarity NPC99487
0.6557 Remote Similarity NPC471081

  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 NPC153538 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
0.74 Intermediate Similarity NPD4265 Approved
0.7119 Intermediate Similarity NPD4246 Clinical (unspecified phase)
0.6885 Remote Similarity NPD3210 Clinical (unspecified phase)
0.65 Remote Similarity NPD585 Clinical (unspecified phase)
0.6452 Remote Similarity NPD368 Approved
0.6441 Remote Similarity NPD4219 Approved
0.6271 Remote Similarity NPD342 Phase 1
0.6212 Remote Similarity NPD4247 Clinical (unspecified phase)
0.6176 Remote Similarity NPD3212 Clinical (unspecified phase)
0.6111 Remote Similarity NPD39 Approved
0.6071 Remote Similarity NPD4220 Pre-registration
0.6 Remote Similarity NPD4732 Discontinued
0.6 Remote Similarity NPD4627 Clinical (unspecified phase)
0.6 Remote Similarity NPD3197 Phase 1
0.5844 Remote Similarity NPD5332 Approved
0.5844 Remote Similarity NPD5331 Approved
0.5833 Remote Similarity NPD8264 Approved
0.5818 Remote Similarity NPD4222 Approved
0.5789 Remote Similarity NPD3173 Approved
0.5741 Remote Similarity NPD5326 Phase 3
0.5714 Remote Similarity NPD6109 Phase 1
0.569 Remote Similarity NPD2268 Discontinued
0.5667 Remote Similarity NPD3172 Approved
0.56 Remote Similarity NPD5784 Clinical (unspecified phase)
0.56 Remote Similarity NPD4271 Approved
0.56 Remote Similarity NPD7322 Clinical (unspecified phase)
0.56 Remote Similarity NPD4268 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